#introductions
2016-11-23
Sean Davis (08:14:52): > @Sean Davis has joined the channel
Sean Davis (08:14:53): > set the channel description: For members to introduce themselves as they join slack
Sean Davis (08:20:06): > About me: > - At the National Cancer Institute > - Bioconductor user since 2003 > - Pediatric oncologist > - Translational and basic genomics research areas, broadly > - Cloud technologies and cloud-scale genomics are recent interests > - Runner, 2 kids and a cat
Levi Waldron (08:21:48): > @Levi Waldron has joined the channel
Peter Hickey (08:21:48): > @Peter Hickey has joined the channel
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Jack Zhu (08:21:48): > @Jack Zhu has joined the channel
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Benjamin Haibe-Kains (08:21:49): > @Benjamin Haibe-Kains has joined the channel
Aedin Culhane (08:21:49): > @Aedin Culhane has joined the channel
Vince Carey (08:21:49): > @Vince Carey has joined the channel
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Lucas Schiffer (08:21:49): > @Lucas Schiffer has joined the channel
Kasper D. Hansen (08:21:49): > @Kasper D. Hansen has joined the channel
Marcel Ramos Pérez (10:57:12): > A few quick points about me:
> * At the WaldronLab and Bioconductor > * MultiAssayExperiment package maintainer > * working on data for the curatedTCGAdata package > * interested in data representation (CN package in the works) > * tech enthusiast
Benjamin Haibe-Kains (17:43:49): > About me: > - At the Princess Margaret Cancer Centre > - Bioconductor user since 2004 > - Computer Scientist who is not really one anymore > - Translational research, omics biomarker discovery, pharmacogenomics > - Reproducible research > - Lazy runner, 2 kids > - Interest in renewable energy > - Still try apprehend the fact that Trump has been elected to rule US
2016-11-28
Nitesh Turaga (13:47:43): > @Nitesh Turaga has joined the channel
2016-12-13
Levi Waldron (16:45:02): > About me: > * assistant professor at the CUNY School of Public Health in NYC > * I teach introductory biostat and regression methods for our MPH program in epic/bios > * Bioconductor user only since about 2007 > * education was in physics and wood science > * involved in MultiAssayExperiment, curatedMetagenomicData, ovarian cancer subtype validation, validation of prediction models, and a few other things > * cyclist, coffee drinker > * still in denial about Trump
Nitesh Turaga (21:31:51): > About me: > - New addition to the Bioconductor Core team at Roswell Park. > - Previously a Software Engineer at the Galaxy Project at Johns Hopkins. > - Still figuring Buffalo, NY out. > - I like to travel, and Crossfit.
2016-12-15
Phil Chapman (08:55:42): > About me: > - At the University of Manchester in the UK working in the Drug Discovery Unit at the Cancer Research UK Manchester Institute > - Previously at AstraZeneca > - Bioconductor user since 2012 > - Originally a molecular biologist before moving into bioinformatics > - Interested in applying published pharmacogenomic methods to data we have generated on our preclinical compounds, also RNAseq, methylation, lots of things really - whatever it takes to move our projects forward towards the clinic and find/validate new drug discovery targets > - Like working with normalised/tidy data i.e. SQL db’s, tidyverse etc > - Kind of relieved Trump got elected as everyones stopped laughing at us about Brexit
Sean Davis (11:25:28): > @Phil Chapman, have you played with BigQuery much? It is really amazing technology and is really ripe for data integration with pharmacogenomics data. If you need an account and happen to be working on anything cancer-related, let me know.
Phil Chapman (11:40:08): > Thanks@Sean Davisthat sounds really interesting, i’ve heard@Vince Careytalk about it but not tried it myself. Have been mainly using@Benjamin Haibe-Kains’s PharmacoGx recently as it stores drug response data as well as genomic data and solves a number of issues such as cell line naming conventions.
Marcel Ramos Pérez (11:42:12): > @Phil Chapmanthat reminds me to work on the port frompSettoMultiAssayExperiment..
2017-04-26
Lori Shepherd (11:37:21): > @Lori Shepherd has joined the channel
2017-05-03
Artem Sokolov (10:33:47): > @Artem Sokolov has joined the channel
2017-05-19
Ludwig Geistlinger (15:29:49): > @Ludwig Geistlinger has joined the channel
Ludwig Geistlinger (15:30:07): > About me:
Ludwig Geistlinger (15:33:22): > - recently joined the lab of Levi Waldron at the CUNY School of Public Health in NYC
Ludwig Geistlinger (15:34:54): > - gene expression data analysis with a focus on gene sets, pathways, and networks
Ludwig Geistlinger (15:36:03): > - these days moving more towards multi-assay analysis
Ludwig Geistlinger (15:36:37): > - some other interests include sports, nature, and literature
Ludwig Geistlinger (15:38:18): > - to keep the flame burning: still amused that Trump refused to shake hands with Chancellor Merkel
2017-05-20
John Readey (13:59:53): > @John Readey has joined the channel
John Readey (14:00:13): > About me:
John Readey (14:00:47): > - have been working at The HDF Group for last two years
John Readey (14:01:25): > - interested in data services, cloud computing
John Readey (14:01:53): > - previously worked at Amazon/AWS
John Readey (14:02:35): > - other interests: sailing, chess
Sean Davis (14:03:10): > Great that you could join us,@John Readey.
2017-05-23
Aedin Culhane (12:21:40): > Sorry I missed this channel… About me
Aedin Culhane (12:21:58): > - Working in Bioconductor since early 2000s
Aedin Culhane (12:22:26): > Working in Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health
Aedin Culhane (12:23:30): > - Previously in Ireland (UCC, UCD), UK (Univ Manchester, Pfizer, BBSRC in Harpenden), France (briefly.. worked with ade4 guys in Lyon)
Aedin Culhane (12:23:55): > - Interested in Data integration, dimension reduction methods, gene sets, single sample gsea methods, biclustering
Aedin Culhane (12:24:31): > - PanCancer analysis, TCGA, tumor microenvironment, neuro-immune, immune role in disease
2017-06-01
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2017-06-05
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2017-07-26
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2017-07-28
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2017-07-31
Lorena Pantano (12:35:35): > @Lorena Pantano has joined the channel
Lorena Pantano (12:39:18): > Hi all, I am Lorena Pantano, working on the bioinformatic core at Harvard School of Public Health. We use a lot bioc, interesting in rnaseq, singlecell,data integration … I have two packages in BioC already.
Peter Hickey (13:24:15): > welcome, Lorena!
2017-08-07
Nitesh Turaga (16:07:25): > Nice blog post@Peter Hickey
2017-10-06
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2017-10-27
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Guangchuang Yu (05:37:43): > I am Guangchuang YU. Recently got my PhD degree and now work as a postdoc in school of public health, the University of Hong Kong. I have contributed several pkgs and my favorite one is ggtree:blush:
Sean Davis (06:37:38): > Great to have you join us,@Guangchuang Yu.
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2017-11-28
Stephanie Hicks (14:19:44): > @Stephanie Hicks has joined the channel
Simina Boca (14:25:12): > @Simina Boca has joined the channel
Simina Boca (14:25:39): > Hi all!:wave:
Simina Boca (14:26:07): > I’m an Assistant Professor in Biomed Informatics, Oncology, and Biostat at Georgetown
Simina Boca (14:26:23): > I have a few Bioc packages and would love to be more involved!
2017-11-29
Matthew McCall (09:35:13): > @Matthew McCall has joined the channel
Matthew McCall (09:41:25): > Hello all. I’m an Assistant Professor in Biostatistics and Computational Biology at University of Rochester. I have several BioC packages and more in the works. I’m currently working a lot with network-like data for which it would be useful to store information about pairs (possibly groups) of features rather than single individual features. Not sure if something like this already exists in BioC.
Ludwig Geistlinger (09:47:34): > Hi Matthew, thegraphpackage implements general representations for networks. On the other hand, theInteractionSetpackage is a more specific package for genomic interaction data. In case, you are missing functionality for your data, this would be interesting to discuss on bioc devel.
Sean Davis (09:48:58): > Hi,@Matthew McCall. Good to see you again.
Matthew McCall (09:54:27): > Hi Sean! I recalled hearing about this slack at the last BioC but was too busy to follow up at the time.@Stephanie Hicksgets credit for providing me the link to join.
Matthew McCall (09:57:29): > Hi Ludwig, we should probably move this conversation out of#introductionsbut I do use the graph package for some stuff. The limitation there is (to my knowledge) the inability to link the relational data to the marginal data (e.g. feature counts in a SummarizedExperiment). I wasn’t aware of the InteractionSet package. That looks closer to what I’m interested in, but I’ll need to dig more to see whether it would work. - Attachment: Attachment > Hi Matthew, the graph package implements general representations for networks. On the other hand, the InteractionSet package is a more specific package for genomic interaction data. In case, you are missing functionality for your data, this would be interesting to discuss on bioc devel.
Levi Waldron (09:59:05): > Hi@Matthew McCall! There’s been some related discussion in the#tree-like-sechannel here. Our application has been more specifically focused on microbiome data, but I have wondered whether the data class we’re discussing should be more general. Would be interested in your input.@natedolsonhas posted a draft class of an extension of DataFrame to represent phylogenetic trees, which are a network. The motivation for extending DataFrame is that it could then be used as rowData in a SummarizedExperiment.
Matthew McCall (10:05:28): > Hi@Levi Waldron. Yes, that’s exactly what I was thinking — that this info could be a special type of rowData if formatted correctly. I just joined the#tree-like-sechannel, and I’ll take a look at the DataFrame extension for phylo trees. Thanks!
Simina Boca (14:04:26): > Piggy-backing onto what@Matthew McCallsaid, if we have questions similar to his questions (e.g. “I would like this feature, but if it doesn’t exist I would be happy to help out”) what is the recommended decision tree of posting it here vs bioc-devel or elsewhere?
Lucas Schiffer (14:10:57): > @Simina BocaI don’t know that there is a consensus just yet but I see bioc-devel as more for something like “I am having a problem with X, can someone help me”. Then Slack is more about envisioning new things and cooking up ideas like#tree-like-se:wink:
Simina Boca (14:12:08): > Got it! Cool, thanks!
Simina Boca (14:14:03): > Many of my applied projects involve metabolomics, so if there’s a lot of interest in that, I would be happy to at least brainstorm some ideas around usability and some workflows in that space (I know at least@Kasper D. Hansenwork on some metabolomics too)
Levi Waldron (14:42:24) (in thread): > The Slack channel does seem to be more interactive around this kind of cooking up of ideas. That said, I think it doesn’t hurt to post that kind of question on bioc-devel as well, since I believe it has a larger membership.
Levi Waldron (14:44:39) (in thread): > I don’t have a specific interest around metabolomics, but as one of the authors of MultiAssayExperiment (http://bioconductor.org/packages/MultiAssayExperiment/), I’m interested in seeing that how different kinds of data are represented and making sure they’re compatible with MultiAssayExperiment! - Attachment (Bioconductor): MultiAssayExperiment > Multi-assay ’omics experiments on a set of samples are increasingly commonplace in biomedical research. MultiAssayExperiment implements data structures and methods for representing, manipulating, and integrating multi-assay experiments via efficient construction, subsetting, and extraction operations. These methods are implemented matching Bioconductor user experience by straightforward extending concept and design of single-assay classes such as SummarizedExperiment or ExpressionSet.
Simina Boca (15:51:47) (in thread): > Cool! Let’s keep in touch! You’re also funded through ITCR right? I just became an ITCR investigator in June.
2017-12-06
Levi Waldron (05:05:54) (in thread): > Yes I am! Sorry I didn’t see your reply until now:open_mouth:
Simina Boca (11:39:40) (in thread): > No worries! Threads can be easy to miss.
2017-12-08
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Federico Marini (12:45:57): > Hi everyone:wave:I’m a soon-to-start Postdoctoral Fellow, working mainly in Translational Bioinformatics at the University Medical Center in Mainz, Germany. > Nice to have an even stronger taste of community over here:smile:
Lucas Schiffer (14:16:20): > Cool! Nice to meet you@Federico Marini
2017-12-12
Levi Waldron (09:59:58): > Welcome,@Federico Marini!
2018-05-03
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2018-09-24
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Kim-Anh Lê Cao (21:51:26): > hi all from Australia. I develop the mixOmics package for omics data integration. Our methods focus on bulk omics, microbiome and lately single cell RNA-seq. We are in the process of migrating mixOmics now to bioC, about time:slightly_smiling_face:. Spoiler alert: I’ll have many dum questions along the way.
2018-09-28
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2018-12-18
Lluís Revilla (07:29:10): > I’m the developer ofhttps://doi.org/doi:10.18129/B9.bioc.BioCor, if you want to know more about it let me know - Attachment (Bioconductor): BioCor > Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships…
2018-12-19
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Leo Lahti (04:40:55): > Hello Bioc. I just found my way in this Slack. Author of 4 bioc packages over the last 10 years, including the latest one, microbiome R package (http://microbiome.github.io/microbiome/). I met some of you at the European BIoc Meeting in Munich this year. More info on our research athttps://openresearchlabs.github.io/- currently my primary interests include combinations of machine learning & ecological models and multi-omics data integration in the context of microbiome research. - Attachment (openresearchlabs.github.io): Open Research Labs - Home > Open Research Labs, University of Turku, Finland.
2018-12-28
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Workast (05:46:34): > @Fabiola Curioncreated a space in Workast for this channel.Click here to collaborate
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2019-03-05
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2019-03-31
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2019-04-03
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2019-04-04
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2019-04-10
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Sridhar N (12:08:35): > Hey all!
2019-04-15
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2019-04-17
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Craig (22:48:49): > Hey folks:wave:
2019-04-18
Dario Strbenac (01:46:01): > Hello.
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2019-04-19
Domenick Braccia (09:25:19): > @Craighi!
2019-04-21
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2019-04-23
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2019-04-25
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Jake Taylor-King (06:35:02): > Hi all, I was hoping for some advice. I’m a bioinformatician typically working on RNA-Seq with patient data. > > However, a new project has come up working with DNA-Seq on a novel plant variety. We need someone who can construct a library for the genome from scratch, vaguely estimate genes of interest through homology between species, and thereafter choose genes for KO experiments (with some end phenotype in mind). They would also be working with experienced plant biologists. > > We’re in the process of writing a job advert. If anyone has 3 minutes, could you let me know the kind of packages/programmes I would be expecting someone to have experience in?
Jake Taylor-King (06:38:35): > Thanks in advance! Best, Jake
Vince Carey (14:46:43): > @Jake Taylor-Kinghave you considered posting your question tosupport.bioconductor.com? There is a much broader readership. The slack might well be highly biased towards applications to human genome.
Vince Carey (14:58:58): > On the other hand if you are talking about constructing Bioconductor packages (you mention “library for the genome” which can have various interpretations) it might be worthwhile to have a look at all the packages athttp://bioconductor.org/packages/release/BiocViews.html#___Arabidopsis_thaliana– this addresses a variety of annotation approaches relevant for a plant. The landscape of packages ranging from BSgenome* through TxDb* to hom* should be understood by anyone tackling the tasks you mention in a Bioc-oriented way.
2019-04-26
Jake Taylor-King (06:26:55): > Hi@Vince Carey- thanks for the message, much appreciated.:slightly_smiling_face:
2019-04-30
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2019-05-01
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2019-05-05
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2019-05-06
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2019-05-08
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2019-05-13
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Corina Lesseur (10:51:36): > Hi all, I use Bioconductor packages frequently, Happy to join this community.
Levi Waldron (23:00:03) (in thread): > Welcome@Corina Lesseur, glad to have you here!
2019-05-14
Corina Lesseur (09:43:01) (in thread): > Thanks Levi! I have been to one of your New York City R/Bioconductor Meetups, I think these are great. Best,
Corina Lesseur (09:43:05) (in thread): > Corina
Levi Waldron (10:22:10) (in thread): > Oh cool, thanks@Corina Lesseur!
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2019-05-15
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2019-05-17
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2019-05-18
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2019-05-20
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Assa (05:27:26): > Hi, happy to be here
2019-05-21
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2019-05-22
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2019-05-23
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2019-05-24
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Nicholas Knoblauch (13:25:49): > Hi everybody, I’m Nick Knoblauch, a PhD student in the Genetics Genomics and Systems Biology program at the University of Chicago and a part-time consultant for the HDF group (the nonprofit behindHDF5). I’m a long timeHDF5andRuser in my own research (statistical molecular genetics) but I’d be curious to know more about the broaderR/HDF5ecosystem in the life sciences (e.g what do people like/not like?)
Tim Triche (15:44:24): > people would like HDF5 and restfulSE / HSDS a lot if they knew more about it, I think@Nicholas Knoblauch:slightly_smiling_face:
Tim Triche (15:45:22): > if you work with John Readey, please pass along my apologies for taking so damned long to get the TARGET multiAssayExperiments into a Restful form for HSDS. He has been very helpful and I am remiss for falling behind
Nicholas Knoblauch (16:30:13): > @Tim TricheI agree! I think@John Readeyis around the channel from time to time. One thing I’m particularly interested in helping out with around here is HSDS, so if there’s anything I can do to help let me know!
Tim Triche (16:31:21): > no good deed goes unpunished… will be corresponding with you next week I think:slightly_smiling_face:
2019-05-27
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Vince Carey (20:11:09): > @Nicholas Knoblauchthere is a brief discussion of HSDS in relation to Bioconductor athttps://f1000research.com/articles/8-21/v1 - Attachment (f1000research.com): F1000Research Article: restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor. > Read the latest article version by Shweta Gopaulakrishnan, Samuela Pollack, BJ Stubbs, Hervé Pagès, John Readey, Sean Davis, Levi Waldron, Martin Morgan, Vincent Carey, at F1000Research.
Vince Carey (20:13:20): > @Tim Tricheonce your HDF5 for TARGET is in an S3 bucket there should be no problem getting it indexed in HSDS. Let me know the situation.
2019-05-28
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Tim Triche (06:51:38): > I know – the deal with TARGET pAML is mostly that it has expanded so rapidly (@Vince Carey)
Tim Triche (06:54:44): > @Vince Carey: you and John and now@Nicholas Knoblauchhave been absurdly patient and I thank you for that. This week actually will be the end of the game, though; we’re resubmitting to Leukemia, Blood, and eventually (garbled glam pub) so it’s all I’m really doing these days. Also, thanks for the work on restfulSE – I noticed that an enormous number of large-scale studies are in there now! The TARGET pAML data is a huge MAE which will only get bigger with the WGS+WES (yes, both) data and DNA/RNA allelic imbalance results. I guess those are the only results that won’t be going in this week.
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2019-05-31
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2019-06-04
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2019-06-05
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2019-06-08
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2019-06-20
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Sanjeev Sariya (12:29:42): > Hello all!
Sanjeev Sariya (12:29:58): > Looking forward to attend the conference.
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2019-06-21
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2019-06-23
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Matt Brauer (23:00:42): > Hi all. I’m Matt Brauer, currently VP of Data Science for Maze Therapeutics, a recently launched biotech focusing on genetic modifiers and functional genomics. A year ago I was at Genentech, which is where I met and worked with Robert Gentleman. I’ll be at BioC starting Monday, and will look forward to meeting other members who are there.
Matt Brauer (23:03:20): > Also, I’m looking to start up and initially host a semi-regular R programmer’s meetup in SSF. I’ll announce details as they emerge.
Luis P Iniguez (23:04:16): > @Luis P Iniguez has joined the channel
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2019-06-24
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Robert Castelo (15:27:54): > Hi@Matt Braueryou might be interested in looking at our paper on the identification of a candidate genetic modifier for hereditary pulmonary arterial hypertensionhttps://jmg.bmj.com/content/56/7/481I’m also at BioC, do not hesitate to contact me if you want to chat about this work.
Matt Brauer (15:32:49): > @Robert CasteloThanks, will check it out and look you up!
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2019-06-25
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2019-06-26
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2019-06-27
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2019-06-28
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2019-07-02
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2019-07-03
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2019-07-04
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2019-07-15
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2019-07-16
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2019-07-17
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2019-07-29
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2019-07-31
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2019-08-01
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2019-08-02
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2019-08-03
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2019-08-04
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2019-08-05
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2019-08-14
kipper fletez-brant (11:49:08): > Hi all, I am a computational biologist at 23andMe Therapeutics. I’ve been using Bioc for years, and have a few packages contributed. Much of my work right now is related to functional genomics. EDIT: I am also an alum of@Kasper D. Hansenlab
2019-08-15
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Constantin Ahlmann-Eltze (11:19:23): > Hi, I am a new PhD student in Wolfgang Huber’s group at EMBL. I have been using BioConductor for a while now and also recently submitted my first package called proDA:slightly_smiling_face:
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Boris Hejblum (19:02:40): > Hi, I’m an Assistant Professor of Biostatistics at the University of Bordeaux (France), and I intend to soon submit my first package to Bioconductor (dearseq).
2019-08-16
Mikhael Manurung (09:10:07): > Greetings everyone! I’m a PhD student at Leiden University Medical Center, the Netherlands. I have only been working with R/BioC for a year. However, it has been such a transforming experience and I am delighted to found such a welcoming community:slightly_smiling_face:.
Mikhael Manurung (09:11:03) (in thread): > Are you the one who made the vici package?
Boris Hejblum (09:11:29) (in thread): > Hi Mikhael
Boris Hejblum (09:11:36) (in thread): > Yes, I am.
2019-08-17
Mikhael Manurung (12:21:29) (in thread): > Thanks for making the package! I have tried to ask a statistician in my department to do something about background-subtracting practice when working with intracellular-cytokine staining data (some also set negative values to zero!), but no one really cared about it.
Boris Hejblum (20:17:29) (in thread): > Thanks, I’m glad you liked it ! A paper should be coming out soon. Any feedback on VICI is welcomed I added a few features last week
2019-08-18
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2019-08-19
Mikhael Manurung (05:22:40) (in thread): > I look forward to the paper! If you don’t mind, could you elaborate on why you use gls instead of lme for the intra-arm fit? If we use lme then I can use subject ID as random effect to take into account the repeated measures, right?
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2019-08-20
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2019-08-23
Boris Hejblum (06:06:55) (in thread): > This is a good question ! nlme::gls is what lets us fit the bivariate model we propose (with distinct variances for background and signal). Adding a random effect to such a model could lead to numerical convergence issues when the number of individuals is not large enough (and in our phase I/II trials we often have only a couple dozen of patients). An additional reason no to is to facilitate interpretation of the results, in particular for our immunologist collaborators.
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2019-08-24
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2019-08-25
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2019-08-26
Mikhael Manurung (10:34:08) (in thread): > That would be an issue indeed. However, what if we add information on the within-group correlation structure such as withcorrelation = corCompSymm(, form = ~1|ID)? In this way, we would avoid going into mixed models and decorrelate the residuals. What do you think?
Boris Hejblum (10:49:25) (in thread): > Well I think this formula fits a different variance for each individual, which would requires that you have enough measured time-points. In our case we typically have only two which is not nearly enough to get stable estimates.
Mikhael Manurung (11:04:14) (in thread): > Thanks for the prompt response. If one has enough time points, would the approach I describe previously be the better one? > > By the way, could you point me to a reference about sample size/time point requirement to get stable estimates? Thanks again for sharing your insights.
Boris Hejblum (11:11:20) (in thread): > It’s hard to talk of “the better” approach. Your proposed model would have more flexibility because it has more parameters, but the larger question would be whether this flexibility would be useful to answer your scientific question of interest. In the case of a large inter-individual variability it would probably be nice to to incorporate that in the model, as you propose to do. > > Now concerning sample-size/time points requirements I’m not sure there is a precise answer. The minimum to be able to compute a variance is two points, so you definitely need more than that to get a reliable estimate…
2019-08-28
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2019-08-30
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2019-09-11
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2019-09-18
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2019-09-19
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2019-09-25
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2019-10-01
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2019-10-02
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2019-10-03
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2019-10-05
John Hutchinson (12:08:38): > Hi, I’m the Associate Director of the Harvard Chan Bioinformatics Core. I haven’t submitted any packages but am a daily user of BioC and interested in it’s continuing development.
2019-10-07
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2019-10-10
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2019-10-14
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2019-11-08
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2019-11-09
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2019-11-11
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2019-11-12
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2019-11-13
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2019-11-14
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2019-11-15
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2019-11-18
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2019-11-19
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2019-11-20
Russ Bainer (19:36:46): > Hi Everyone, I’m a longtime BioC user and have contributed one small package (gCrisprTools), but just getting to know the slack community. I’m currently a Data Scientist at Maze Therapeutics.
2019-11-21
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2019-11-27
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2019-11-29
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2019-12-03
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2019-12-04
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2019-12-05
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Chris Fields (13:22:00): > Hi all, I’m Director of the High Performance Computing in Biology group at U. Illinois. I’ve been using BioC for a bit now, partly due to working w/@Jenny Drnevichat UIUC:slightly_smiling_face:
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2019-12-06
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2019-12-07
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2019-12-09
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2019-12-10
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2019-12-11
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Andrea Rau (09:20:32): > Hi all! I’m a long-time BioC user + developer (HTSFilter and coseq) and first-time Slack user:wink:, working as a researcher at the French National Institute for Agricultural Research in France in animal/plant genomics. I got motivated to check out the Slack channel after a great experience at#eurobioc2019(thanks@Laurent Gattofor organizing and@Federico Marinifor getting me set-up on Slack!). Looking forward to following discussions and getting involved in the community.
2019-12-12
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2019-12-13
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Teun van den Brand (14:35:27): > Hi everyone, I’m a medium-time (+-2 years) BioC user and aspiring contributor. I work as a computational PhD student on chromatin biology/gene regulation at the Netherlands Cancer Institute, coincidentally located at the eponymous country. I too wanted to probe the Slack channel due to the great#eurobioc2019conference. If the past is any guarantee of the future and since I’m new to slack, I’ll likely lurk around here and follow some discussions with ditto interest.
2019-12-15
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2019-12-16
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2019-12-17
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2019-12-18
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2019-12-19
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Paul Harrison (20:22:58): > Hi everyone. I’m with the Bioinformatics Platform at Monash University. I’ve contributed one package to Bioconductor, topconfects, which allows for differential expression analysis based on confidence bounds. Currently working a package for creation/calibration/component-extraction of matrices with precision weights. I also run a series of introductory R workshops at my university.
2019-12-20
Ino de Bruijn (16:23:33) (in thread): > :wave:Teun:slightly_smiling_face:
2019-12-22
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Jovana Maksimovic (23:03:59): > Hi! I am a bioinformatician in Alicia Oshlack’s Lab at the Peter MacCallum Cancer Centre (formerly at the Murdoch Children’s Research Institute). I am a long time Bioconductor user and lurker and have contributed one Bioconductor package, missMethyl, which contains various functions for methylation array analysis.
2019-12-23
Stephanie Hicks (06:37:22): > Welcome@Jovana Maksimovic! Great to see you on here!:smile:Lots of great channels to check out. Let me know if you have any Qs about them
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2019-12-24
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2019-12-25
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2019-12-30
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2019-12-31
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2020-01-05
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2020-01-08
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2020-01-09
Chris Vanderaa (10:48:39): > Hello ! I’m a PhD student at Laurent Gatto’s lab (in Brussels). I’m new to Bioconductor but already convinced by its power namely thanks to the#osca-book. I hope I’ll be able to contribute to the project by developing packages for MS-based single cell proteomics !:grin:
2020-01-10
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2020-01-11
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2020-01-12
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Ellis Patrick (18:38:58): > Hi:slightly_smiling_face:I’m a statistician from the University of Sydney. I’m a long time Bioconductor user but have made no contributions. I was motivated by@Helena L. Crowell’s inspiring presentation at the Australian Bioinformatics and Computational Biology conference to get involved in the community and try to find opportunities to contribute. I’m currently dipping my fingers more and more into analysis for spatial cytometry technologies.
Jovana Maksimovic (18:53:18) (in thread): > Thanks. It’s such a great resource. I can’t believe it took me so long to join:slightly_smiling_face:
2020-01-13
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2020-01-14
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2020-01-15
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2020-01-17
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2020-01-19
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2020-01-27
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2020-02-04
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2020-02-05
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2020-02-06
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2020-02-08
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2020-02-10
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2020-02-11
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2020-02-14
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2020-02-15
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2020-02-17
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2020-02-18
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bharati mathur (08:42:50): > Hi I am a Bioinformatics researcher, I would like to learn about bioconductor
Lluís Revilla (11:40:22) (in thread): > Welcome! Any doubt we can help with?
2020-02-19
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2020-02-21
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2020-02-24
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2020-02-25
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2020-02-26
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2020-02-27
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2020-03-01
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2020-03-09
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2020-03-11
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2020-03-12
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2020-03-13
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2020-03-17
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Giuseppe D’Agostino (07:26:27): > Hi all, I’m Giuseppe, a postcoctoral researcher in Sarah Langley’s lab at LKC Medical School in Singapore. I did my wet lab PhD in Milan befriending my then colleague@Pierre-Luc Germainand then moved on to computational biology. I dabble in analysis and some methods development for single cell RNA-seq, in the context of neurodegenerative and neurodevelopmental disorders. Glad to be here!
2020-03-20
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2020-03-23
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Edgar (10:21:16): > Hello everybody, I’m Edgar, a postdoctoral researched at Icahn School of Medicine in NYC. I’m a biologist. PhD in bioinformatics. I work primarily with transcriptomics in cancer and infectious diseases. Nice meeting you all.
Sean Davis (10:31:26): > Welcome,@Edgar
Sridhar N (10:53:31) (in thread): > OK
Peter Allen (11:33:47): > Hi all! I’m a doctoral student at the University of Alabama Birmingham working in the field of epigenomics in autoimmune diseases. Hope to learn something new here!
2020-03-24
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2020-03-25
brian capaldo (13:02:43): > @brian capaldo has joined the channel
brian capaldo (13:11:31): > Hello all, I am a bioinformatics scientist at the NCI working in prostate cancer. I’ve been doing this for about a decade and currently do a lot of single cell
Sridhar N (13:17:03) (in thread): > OK
Stephanie Hicks (14:54:07): > Welcome@brian capaldo!
brian capaldo (14:54:21): > thanks
Lauren Fitch (15:03:55) (in thread): > r/bioinformatics is leaking
brian capaldo (15:04:15) (in thread): > :shushing_face:
brian capaldo (15:04:29) (in thread): > we will take over all the slacks
Sridhar N (15:05:11) (in thread): > lol
Sridhar N (15:05:37) (in thread): > you guys don’t like our hospitality
brian capaldo (15:06:09) (in thread): > i just came here to scATAC and chew gum, and I’m all outta gum
Sridhar N (15:07:01) (in thread): > :neutral_face:
Sridhar N (15:49:56) (in thread): > @Kevin Bligheyou are not invited:stuck_out_tongue:
Sridhar N (16:37:24) (in thread): > haha I am right behind you
2020-03-26
Tamas Kiss (05:23:49): > @Tamas Kiss has joined the channel
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Paula Restrepo (09:32:46): > Hi all! I’m a bioinformatician at Mount Sinai in NYC, I’m pretty early career (in one those weird gap year things between undergrad and phd), and I work with a lot of cancer transcriptomics and lately some more RRBS stuff.
Sridhar N (10:27:56) (in thread): > That’s it@Paula Restrepois here to
Sridhar N (10:28:00) (in thread): > Im out
Paula Restrepo (10:28:05) (in thread): > hey!
Paula Restrepo (10:28:37) (in thread): > alternatively, does this mean the takeover is complete?
brian capaldo (10:29:01) (in thread): > only when fejes joins a slack dedicated to R
Paula Restrepo (10:29:18) (in thread): > lmao true
Sridhar N (10:29:55) (in thread): > blasphemy
Paula Restrepo (10:33:39) (in thread): > no, this is just a lot of joking around
Paula Restrepo (10:34:09) (in thread): > the slack workspace from the bioinfo subreddit is much higher quality than the subreddit itself though if you’re interested in joining it
Sean Davis (10:42:04) (in thread): > Hi, Brian. Welcome to where the real work happens!
Sean Davis (10:42:33) (in thread): > What group are you with at NCI,@brian capaldo?
brian capaldo (10:42:40) (in thread): > LGCP
brian capaldo (10:43:03) (in thread): > we met briefly after Levi Waldron’s talk a year or so ago, I used to be with Stephen Turner at UVA
Sean Davis (10:43:29) (in thread): > Apologies!
brian capaldo (10:43:35) (in thread): > no worries
brian capaldo (10:43:46) (in thread): > it was like five minutes
Vivek Das (14:09:44): > @Vivek Das has joined the channel
2020-03-27
Carmina Barberena Jonas (16:40:37): > @Carmina Barberena Jonas has joined the channel
2020-03-28
Julieta O’Flaherty (11:44:08): > @Julieta O’Flaherty has joined the channel
Julieta O’Flaherty (12:17:35) (in thread): > Hi guys, my name is Julieta, a PhD student and I am new to bioinformatics and R, trying to get to know more people working with R (and get help too!!) are there any slack channels or communities I can join?
2020-03-29
Pavitra Roychoudhury (19:45:56): > @Pavitra Roychoudhury has joined the channel
2020-03-30
Minoo (07:32:13): > @Minoo has joined the channel
Yagoub Ali Ibrahim Adam (08:47:19): > @Yagoub Ali Ibrahim Adam has joined the channel
Yagoub Ali Ibrahim Adam (08:54:19): > Hello all
Yagoub Ali Ibrahim Adam (08:56:52): > Hello all, I am a postdoctoral scholar at the Covenant Unversity, Nigeria. I earned my doctorate degree in Bioinformatics at the University of São Paulo, Brazil.
Susan Holmes (09:48:07): > @Susan Holmes has joined the channel
Benilton S Carvalho (13:37:10): > @Benilton S Carvalho has joined the channel
Julieta O’Flaherty (16:28:28) (in thread): > Thanks so much!!
2020-03-31
Raphaël Bonnet (07:39:47): > @Raphaël Bonnet has joined the channel
Raphaël Bonnet (07:46:38): > Hi everyone, my name’s Raphael I’m doing a PhD in Bioinformatics on single cell sequencing at the University of Nice, Fr. Nice to meet you all. I hope I’ll get more efficient in my package maintaining-routine/contributions with what I’ll learn here.
Matthew Carlucci (11:51:04): > @Matthew Carlucci has joined the channel
2020-04-02
Duy Pham (04:17:02): > @Duy Pham has joined the channel
Talha (07:31:38) (in thread): > Wow!! Icahn School - a privilege to meet you sir!
2020-04-06
Anna Lorenc (06:40:16): > @Anna Lorenc has joined the channel
Anna Lorenc (14:04:34): > Hello everyone, about me: > -biologist turned bioinformatician long time ago > -Bioconductor user for >12 years, contributed to the package maskBAD (remember when we were measuring gene expression on microarrays? We wanted to compare across species without a priori knowledge about sequence differences within probe binding regions) > -scientific interest: (various in the past, also a stint in a core bioinformatic support group) type 1 diabetes immunology, technologies in focus now : scRNAseq, TCR sequencing, flow cytometry > -Kings’s College London
Stephanie Hicks (14:28:23): > Welcome@Anna Lorenc!
Yuzhu Duan (20:24:48): > @Yuzhu Duan has joined the channel
2020-04-07
Anna Lorenc (04:02:16) (in thread): > Thank you@Stephanie Hicks!
2020-04-09
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2020-04-10
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2020-04-11
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2020-04-13
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2020-04-15
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2020-04-16
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2020-04-22
Kelly Eckenrode (09:24:17): > @Kelly Eckenrode has joined the channel
Kelly Eckenrode (12:35:01): > Hi everyone! > > I am a molecular biologist (PhD, at City University of New York) who is learning bioinformatics in my postdoc (with@Levi Waldronat School of Public Health at City University of New York). > > My research interests include bacterial biofilms (specifically how bacterial communities form. This could be pathogenic types or commensal human microbiomes) and developing packages for single cell multimodal datasets. > > I am a new Bioconductor user and enthusiastic about digging in.
Leonardo Collado Torres (14:19:30): > @Leonardo Collado Torres has joined the channel
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Lucy (15:29:22): > @Lucy has joined the channel
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Christopher Eeles (19:17:09): > Greetings all, > > I am a software developer in the Benjamin Haibe-Kains laboratory at Princess Marget Cancer Research Center and a colleague of@Petr Smirnov. I am the package maintainer for our existing R packages (seehttps://bhklab.ca/) and am actively involved in planning, design and coding of new features and packages from our lab for Bioconductor. > > Very excited to contribute to the community!
2020-04-23
Devika Agarwal (05:55:18): > @Devika Agarwal has joined the channel
Devika Agarwal (05:57:24): > Hi everyonem
Devika Agarwal (05:59:28): > I am a postdoc working on single cell genomics at the University of Oxford. My research interests include working on neurodegenerative models, state related changes (thirst , hunger), memory and learning changes in fly brains with single cell data.
Charlotte Rich-Griffin (06:00:05): > @Charlotte Rich-Griffin has joined the channel
2020-04-24
Anthony (20:06:54): > @Anthony has joined the channel
Preethy (21:26:36): > @Preethy has joined the channel
2020-04-27
Jonathan Hicks (13:48:26): > @Jonathan Hicks has joined the channel
2020-04-28
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Levi Waldron (09:01:01) (in thread): > Welcome@Edgar! I’m usually in NYC too (at CUNY SPH), but on sabbatical in Italy this year.
Levi Waldron (09:01:46) (in thread): > Welcome@Peter Allen!
Edgar (09:18:23) (in thread): > Thank you for the kind replies, that’s cool Levi!, are you a postdoc or a grad-student?.
Peter Allen (10:04:03) (in thread): > Thank you!
Anamaria Elek (12:56:54): > @Anamaria Elek has joined the channel
2020-04-29
Anthony Sonrel (03:45:24): > @Anthony Sonrel has joined the channel
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2020-04-30
Chase Clark (13:06:48): > Hello, I’m grad student in Chicago and have written a couple of R packages (chasemc.github.io/electricShine) (https://chasemc.github.io/IDBac/). > In the not-too-distant future I’ll be transitioning from mostly metabolomics to metagenomics/metatranscriptomics/genomics and would love suggestions of reading material for transitioning to python from R but also blogs/etc on current Bioc tools for those fields.
Nicholas Knoblauch (13:23:09): > If you’ve already written R packages this may be a bit basic, but I usually point python programmers towardshttps://tidynomicon.tech/ - Attachment (tidynomicon.tech): The Tidynomicon > The Tidynomicon
Chase Clark (14:31:26) (in thread): > Thanks, I’m actually looking for the opposite direction, python for someone who primarily programs in R
Nicholas Knoblauch (14:54:06) (in thread): > oops. As someone who does transcriptomics/genomics and uses R as my main scripting language I’ve found that unlike R, a lot of the bioinformatics tools written in python are meant to be run from the command line (the genomics community has a pretty intense flat text fetish) , and don’t actually require much python knowledge. That being said, snakemake is a pretty excellent workflow management tool that requires almost no python knowledge to start using (and is also very R friendly)
2020-05-01
michaelkleymn (09:02:05): > @michaelkleymn has joined the channel
2020-05-03
Nitin Sharma (11:11:22): > Hello everyone, Nitin here. > > I have a PhD in structural bioinformatics from the National University of Singapore. I have done postdocs in Cambridge and then CRUK-MI, where I worked in the analysis of RNA-Seq data mainly, with some exposure to Methylation data and Single-Cell RNA-seq analysis. I am currently working as a postdoc at the Institute of Cancer Research, Oslo to understand the drug resistance and cancer evolution in the gastrointestinal stromal tumour (GIST) using RNA-Seq, microarray and whole-exome analysis and Single-cell analysis. > > I will be more active in single cell domain from now on and have created a channel#singlecell-queriesfor more general queries regarding single-cell analysis.
Jack Zhao (19:59:35): > @Jack Zhao has joined the channel
2020-05-04
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Sanchit Saini (16:18:28): > Hi everyone! > I’m doing my post graduation in Computer Science and I’m new to bioinformatics:smile:. > This summer I’ll be contributing to rtracklayer can’t wait to get started too excited about this.
Michael Lawrence (16:31:06): > Welcome, Sanchit! Sanchit is sponsored by the GSOC to add UCSC track hub and bigBed support to rtracklayer, as well as port the table browser to use UCSC’s new web service, which will be a lot cleaner than posting web forms. Really looking forward to working with him.
2020-05-05
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2020-05-08
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2020-05-11
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Eli Miller (12:03:13): > Hey all, > I am a informatics developer working on open-source contributions to the R community. Right now I’m mainly focused on writing packages that assist in the reporting of clinical trial safety data. A lot of my focus is on promoting the use of R in life-sciences, creating validation workflows, and contributing to projects in the community where I can. > I’m excited to see what you’re all working on!
Joshua Sodicoff (12:44:53): > @Joshua Sodicoff has joined the channel
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2020-05-12
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2020-05-15
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2020-05-17
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2020-05-18
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2020-05-19
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2020-05-20
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2020-05-22
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2020-05-25
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2020-05-26
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2020-05-27
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2020-05-28
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2020-05-29
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Shuyu Zheng (09:59:29): > Hi everyone, > I’m a Ph.D. student in University of Helsinki. I’m working on drug combination screen data and maintaining the R packagesynergyfinder. I just started a project in the single cell domain. - Attachment (Bioconductor): synergyfinder > Efficient implementations for all the popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of the synergy scores as either a two-dimensional or a three-dimensional interaction surface over the dose matrix.
brian capaldo (10:46:54): > My entire grad school focused on synergy and now I find out about this package????
Shuyu Zheng (11:37:02) (in thread): > It seems that we should have built it earlier.:smile:Anyway, welcome to try and comment it.
2020-05-31
stefano mangiola (03:47:20): > @stefano mangiola has joined the channel
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Jonathan Goeke (23:44:27): > Hi all, I’m Jonathan, a computational biologist and group leader at the Genome Institute of Singapore, interested in long read sequencing and transcriptomics in general. I look forward to attending the virtual conference this year!
Stephanie Hicks (23:50:29): > Welcome@Jonathan Goeke!
Shian Su (23:58:09): > Yay more long read sequencing representation!
2020-06-01
Jonathan Goeke (01:26:18) (in thread): > Thanks@Stephanie Hicks!
Marcus Lindberg (03:59:41): > @Marcus Lindberg has joined the channel
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2020-06-02
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2020-06-03
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2020-06-04
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2020-06-06
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2020-06-07
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Adewale Ogunleye (06:19:40): > Hello world, I’m Wale, a Nigerian, grad student at Moscow institute of Physics and technology, Russia. I like RNAs, and I can’t explain why
Tanzeel Tagalsir (06:25:15): > @Tanzeel Tagalsir has joined the channel
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2020-06-08
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Shankar Shakya (09:59:35): > Shankar Shakya, associate bioinformatics scientist at Ball Horticultural company. Interests: Population genetics, Data analysis and R. Any plant breeders, pathologist, evolutionary biologist in the group
2020-06-09
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2020-06-10
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2020-06-11
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2020-06-12
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2020-06-14
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2020-06-15
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2020-06-16
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2020-06-17
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Ruben Dries (16:07:27): > Hi all, I’m currently a postdoc at DFCI/Harvard in GC Yuan’s lab and I will soon (August 1st) open the doors of my own lab at BUMC. I’m specifically interested in understanding developmental and cancer dynamics. Therefore I like to combine R data analysis with experimental approaches and state-of-the-art of functional genomics, like TT-seq, polyA-seq, HiChIP, … . In addition, I also have a particular interest in single-cell and spatial transcriptomic analysis and visualization. I look forward to contribute to the Bioc Community in the future!
Jason (18:49:35): > @Jason has joined the channel
2020-06-18
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2020-06-19
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Atul Deshpande (17:32:15): > Hi all, I am a postdoc at Johns Hopkins in the Fertig Lab. I am interested in understanding intercellular interactions within the TME, hopefully through spatial omics data. As a red-green colorblind person, and given that visualizations are a big part of research communication in this field, I am also extremely interested in helping the drive to make default visualizations colorblind friendly. To illustrate my point, in the Ishihara test here, normal vision people see the number 74, and I (and a lot of colorblind people) see the number 21. With this kind of disparity in pattern recognition when relying on solely colors, it is not only important to me to have access to colorblind friendly palettes while doing my own analyses, but also to promote colorblind friendly practices in the community so that more and more research is accessible to colorblind people. I look forward to brainstorm on this as well as contribute to other bioc community initiatives in the future. - File (PNG): Ishihara_9.png
Simina Boca (18:38:39): > At least 5% of the population is color-blind. When I was in grad school (also at Hopkins!) there were at least 2 people in the genomics group who were colorblind, which meant they couldn’t tell apart the “standard” red/green heatmaps.
Dan Bunis (18:47:46) (in thread): > I don’t even see the 21! I guess we have a different form of red-green colorblindness.
Atul Deshpande (18:48:27) (in thread): > I keep switching between 21 and 81 depending on my mood.:slightly_smiling_face:
2020-06-20
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Jim Hunter (08:28:30): > Hi, I’m Jim Hunter, an Adjunct Professor in Ricardo Diaz’ Retrovirology Lab at the Paulista School of Medicine, part of the Federal University of São Paulo in Brazil. My focus is on mutational patterns in HIV and how that affects treatments and a potential cure. Of course, this year, like everyone else, I’m spending more time on COVID-19 disease dynamics since we clearly don’t have a grip on this in Brazil.
2020-06-22
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2020-06-23
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2020-06-24
Serena Gerboni (03:27:26): > Hi, my name is Serena Gerboni, I am an italian Msc graduate in Big Data Analytics with statistics background. I’ve got no academic knowledge in bio-sciences but I am interested in applied statistics, looking for a domain where I could contribute with some analysis and possibly look for projects to start a portfolio/career. I’ve noticed that Bioconductor conference will soon be starting in July. Do you think that the participating as attendee would be suitable/useful for me? thank you! Serena
Dario Strbenac (03:30:06): > It will be suitable and useful for you.
Serena Gerboni (03:45:52): > thank you for the advice@Dario Strbenac
Kevin Rue-Albrecht (05:40:50): > @Serena GerboniAside from the excellent talks every year, I recommend birds-of-a-feather and workshop sessions to network and brainstorm ideas for new methods and packages useful to the community
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2020-06-25
Serena Gerboni (09:37:29): > Hi all, still about Bioc conference: as time is US Eastern, does anybody know if access for paying subscriptors is also to recorderd sessions, in case one needs to catch up from other time zones? thanks!
2020-06-26
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wisam (08:30:46): > Hi, my name is Wisam and I am working as a research assistant for analyzing microbiome data at Turku University, Finland.
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2020-06-27
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2020-06-28
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2020-06-30
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2020-07-02
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2020-07-04
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2020-07-05
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2020-07-06
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2020-07-07
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Simone Tiberi (09:32:39) (in thread): > I also don’t see any pattern:smile:
2020-07-08
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2020-07-09
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estepi (07:06:14): > Hi! My name is Estefi. I’m from Argentina, but now I am based i Barcelona. I am the manteiner of a Bioc package (ASpli) since 2016
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Giuliano Netto Flores Cruz (14:30:58): > Hi, everyone! My name is Giuliano. I am a bioinformatician currently living in Florianópolis, south of Brazil. I have mostly worked with microbiome data, but also with gene expression. Excited to be here and looking forward to the#bioc2020conference!
2020-07-10
Giuliano Netto Flores Cruz (00:29:23) (in thread): > Oi,@Kevin Blighe! Que legal!! Espero que tenha gostado! A comunidade de bioinformática e ciência de dados está crescendo na cidade. Muito obrigado!!
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Veronica Jimenez Jacinto (20:25:42): > Hi! I am Veronica. I’m a bioinformatician, and I live in Cuernavaca, Mexico. I am working in Universidad Nacional Autonoma de México (UNAM) and I am working in Analysis of Differential Expression in genes.
2020-07-11
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unnati97 (13:17:41): > Hi Everyone! I am Unnati and I am from India.I recently graduated with computer science degree.I am interested in data science.Currently looking for work.Always happy to connect and chat about interesting projects!
2020-07-13
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2020-07-14
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Nur-Taz Rahman (11:26:38): > Hello everyone! I am Nur, a Postdoc in Bioinformatics at Yale. I’m learning new methods, packages, ideas all the time!
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2020-07-15
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Izabela Mamede (19:22:44): > Hello, my name is Izabela and I am from Brazil, I am finishing my graduation in Biology this year, I am interested in alternative splicing and transcriptomic analysis in general.
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2020-07-16
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2020-07-17
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Roy Gulla (21:38:37): > Hello, my name is Roy - I am simply interested in the signal processing packages in BioConductor.
2020-07-18
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2020-07-19
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Kirill Tsyganov (19:30:26): > Hey people, thanks to@Aedin Culhanefor introducing me to this community - I had no idea such cool place existed. I’m from down under (Melbourne, Australia) with Russian root:smile:. I work at the Monash University, at the Monash Bioinformatics Platform. It’s too long to explain what the platform is about, but in the nutshell we are slightly bigger than just a “service providers”. Apart from working with researchers on solving biological problems with the data, we also do a hole lot of community engagement and outreach. > Myself - I essentially work with any kind of genomics data, anything that comes of sequencing machines. I’m trying to focus more on the “secondary” type of analysis, where raw data had been transform into some sort of tabular format that fits in R so that I can start answering biological questions. > > p.s I can be a little slow to respond (work load etc) please don’t hold against me, I’ll always answer given a little time. cheers !
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Hyun-Hwan Jeong (22:50:34): > Hi, I’m Hyun-Hwan Jeong. I am interested in developing bioconductor package and working onhttps://github.com/LiuzLab/CB2andhttps://github.com/LiuzLab/TraceQC. Nice to meet you all!
2020-07-20
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Dr Awala Fortune O. (02:51:22): > Hello everyone
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Bishoy Wadie (04:02:24): > Hello Everyone
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2020-07-21
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Dr Isha Goel (08:55:47): > Hey Everyone. > Myself Isha Goel, from India. I am a doctorate in Molecular Biology and have work experience in the field of Epigenetics and Cancer. > I wish to learn and switch to the Computational genomics aspect or in general utilizing Big Data Science in Biomedical Research. > Glad to be here, looking forward to attend the virtual conference with you all. > If you believe I can be of any help, please feel free to ping.#introductions
Dr Isha Goel (08:59:39) (in thread): > I see 74:grin:
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Krutika (10:51:44): > Hello! I’m looking forward to#bioc2020! Last year’s conference ( my first bioc conference ) was great and I really enjoyed the time I spent interacting with the bioc community! This year I’m presenting annoFuse ( my first R package ) at the poster session, I’d really appreciate if you come by and have a chat. Thanks!
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2020-07-22
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2020-07-23
Nur-Taz Rahman (10:17:17) (in thread): > Hi Krutika! What is the package annoFuse all about?
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2020-07-24
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Ruth Schmidt (10:45:03): > Hello everyone:wave:excited to meet you all virtually! My name isRuthand I’m a microbial ecologist and data scientist in the making. Currently, I am a postdoc between INRS (National Institute of Scientific Research) and the data analytic and dataviz company Plotly in Montreal, Canada. I’m developing Dash apps in R for omics data in microbiome research and this is my first time presenting at BioC. Looking forward to sharing how to build dash apps and showing some examples:hugging_face:I’m also looking for opportunities after my postdoc. Happy to connect and chat about projects & opportunities! - File (GIF): hello_bioc.gif
mirna (14:34:32) (in thread): > Hello Ruth, I was wondering if you know any metagenome binning package in R?
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Krutika (16:03:20) (in thread): > Hi Nur-Taz! We developed annoFuse because we saw a need for a fusion filtering and annotation framework that is not currently available as a tool/package. We provide users the ability to filter fusion by read support/read-throughs or if they are present in normal databases as well as annotate fusion calls as found in TCGA and gene partners as Oncogene/TSG/Kinase etc . In addition we provide summary plots and domain level plots for visualization and review.
Ruth Schmidt (19:18:06) (in thread): > hey mirna! haven’t used it myself but this one seems like something you might wanna check out:gbtools
2020-07-26
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2020-07-27
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2020-07-28
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Mirko Signorelli (11:35:42): > Hi everyone! My name isMirkoand I am a biostatistician who has been programming in R for a while now. I work as postdoc at the Leiden University Medical Center (in:flag-nl:) and my research deals with methods for the analysis of biomedical and omic data. This is my first Bioc conference and I am really enjoying it! I’m glad to have finally found out that there is such an active community behind Bioconductor:slightly_smiling_face:For full disclosure: so far I have uploadedmytwo R packagesto CRAN, but I am seriously considering uploading the next ones to Bioconductor! - Attachment (home): Mirko Signorelli, statistician and R programmer > Personal website of Mirko Signorelli, Postdoctoral researcher in Biostatistics at the Leiden University Medical Centre - Attachment (home): R packages - Mirko Signorelli > R packages and R code and data related to publications from Mirko Signorelli
Simina Boca (12:20:52): > Hi@Mirko Signorelli! I also do some work in DMD. Let me know if you want to chat about it!
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Nur M Shahir (13:06:53): > Hello! My name is Nur, I am a postdoctoral scholar at PSU! My research involves the microbiome and scRNA in lung disease
Matt Brauer (14:02:15): > Hello all. I’m Matt Brauer, head of Data Science at Maze Therapeutics. Maze is a startup biotech founded by such luminaries in the fields of functional genomics and genetics as Steve Elledge, Jonathan Weissman, Mark Daly, Sek Kathiresan and Aaron Gitler. We’re reducing a lot of their labs’ advances to practice, in the service of discovering meaningful medical advancements in difficult diseases. My group is looking for an accomplished computational biologist/bioinformatics scientist to join our team, and have a job posted on the job board. Please check it out!
Christian Mertes (16:14:52): > @Christian Mertes has joined the channel
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2020-07-29
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Mirko Signorelli (04:35:36) (in thread): > Definitely, I’m curious to hear your experiences with it! I am going to send you a pm:slightly_smiling_face:
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Ayush Aggarwal (09:09:40): > Hi everyone! I’m Ayush Aggarwal, a 4th year PhD student at CSIR-Institute of Genomics and Integrative Biology, Delhi, India. I am an experimental biologist with a huge interest in bioinformatics. I work in the field of skin pigmentation, currently interested in understanding the mechanism and the relevance behind melanocyte cell state transitions in normal and pathological conditions.
koki (10:21:55): > Hello, everyone. > I’m Koki Tsuyuzaki, the developer of Bioconductor packages metaSeq, MeSH.db, MeSH.AOR.db, MeSH.PCR.db,MeSH.XXX.eg.db, MeSHDbi,LRBase.XXX.eg.db, LRBaseDbi, scTensor, and scTGIF. > I’m going to talk about my packages at BioC Asia 2020, so please check it out.https://biocasia2020.bioconductor.org - Attachment (biocasia2020.bioconductor.org): BioC Asia 2020 > Oct 17 - 18
Nick Owen (12:54:29): > @Nick Owen has joined the channel
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Najeeb (13:11:09): > Najeeb from Qatar.
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Iara Souza (14:23:27): > Hello everyone! I’m Iara Souza, from Brazil. I’m a PhD candidate in Bioinformatics. I’m here because I use lots of Bioconductor packages in my analysis routine. My research interests are gene expression and evolutionary analysis.
lu wang (17:42:35): > @lu wang has joined the channel
Nick Owen (17:59:45): > Hi everyone. I am a postdoc a UCL, London, who’s jumped ship from wet lab research to dry lab, focusing on RNAseq, WGS and epigenetics of patients with inherited eye diseases. Kicking myself I didnt see the bioc2020 info sooner as would have registered!
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Simina Boca (18:33:59) (in thread): > You’ll be able to see the recordings in a couple of weeks though!
Simina Boca (18:34:32) (in thread): > Also if you look at the website and the#bioc2020hashtag, there’s already a lot of public info (slides and workshop material being shared etc)
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2020-07-30
Ayush Aggarwal (01:39:26) (in thread): > Hi, that’s great! I’m also in the process of jumping the ship:smiley:
Ayush Aggarwal (01:41:14) (in thread): > Hey! It’s a great poster and an amaing work. Thanks for explaining.:smiley:
CristinaChe (07:31:18): > Hello everybody! I am Cristina and I work as computational biologist in Milano, Italy, analyzing omics data from brain organoids as a model to study alterations of neurodevelopmental trajectories. I am also passionate about exploring datasets related to social and health issues. Happy to be following Bioc2020 these days!
sani (09:41:00): > @sani has joined the channel
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sani (09:47:36): > Hi everyone! nice to e-meet you.
Riyue Sunny Bao (09:52:25): > Hello everyone!! I am Riyue Bao (Sunny) from Pittsburgh, I am co-directing a team of bioinformatics scientists in the UPMC Hillman Cancer Center. My group supports the translational research at the Cancer Center and we also collaborate with UPMC Children’s Hospital and U Pitt. I also have my own lab focusing on tumor resistance mechanisms in immunotherapy in Dept of Medicine. We are interested in developing new methods to integrate multi-omics data, imaging data, and clinical data to find new targets that can be used to guide clinical trial design and development. - also we are actively recruiting talents to join us!! DM me, find me on twitter @RiyueSunnyBao, or shoot me an emailbaor@upmc.edu. Open for coffee chat!!!!:slightly_smiling_face:
Riyue Sunny Bao (09:55:53): > This is my first #BioC conference and it is my favorite conference this year!! I was not able to join previous conferences but happy this year the BioC organizers moved it to the virtual platform so I can finally join:hugging_face:kudo to all the organizers, committees, and sponsors to make this happen!!!!
Jonelle Villar (11:15:48): > @Jonelle Villar has joined the channel
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Riyue Sunny Bao (12:34:41): > hiiii folks I was inspired by the discussion from #BoF regarding the recog of bioinformatician career in academia vs industry. If you have time to check out the pollhttps://twitter.com/RiyueSunnyBao/status/1288875156849528834 - Attachment (twitter): Attachment > As #bioinformatician, do you feel your #contribution is #recognized in your current work environment? > > Inspired by comments from #BioC2020 #BoF session and very curious on how the poll looks like! > > @AcademicChatter #AcademicChatter #AcademicTweeter #research #careeradvice
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Andreas Gschwind (13:05:12): > Hi, I’m a computational biology postdoc at Stanford University. I mostly work on single-cell sequencing data, in particular Perturb-seq type screens for functional genomics elements. Previously I worked in human and population genetics, where I investigated expression and chromatin quantitative trait loci. Currently I’m interested in developing computational methods for novel experimental approaches and making them available to the community. My first R-package TAPseq (shameless plug, sorry ;)) was accepted to Bioconductor this cycle, so I would still consider myself a Bioconductor novice. I’m really enjoying the BioC2020 conference, thanks for organizing such a great meeting!
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2020-07-31
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Petr Smirnov (15:29:51) (in thread): > Hi Mirko! Just wanted to let you know, it is possible to migrate packages from CRAN to Bioconductor, if thats something you are interested in!
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2020-08-01
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2020-08-02
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Spiro Stilianoudakis (20:21:32): > Hello, my name is Spiro Stilianoudakis. I am a 4th year PhD student at VCU, working with@Mikhail Dozmorov
Spiro Stilianoudakis (20:22:38): > I just submitted my first Bioconductor package to be reviewed! It is called preciseTAD
2020-08-03
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2020-08-04
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rohitsatyam102 (15:16:27): > Hi Everyone. I am a Junior Research Fellow at CSIR-Institute of Genomics and Integrative Biology and I have worked on variety of sequencing data including ChipSeq, RNASeq, WGS, scRNASeq on HPC. I am a Bioinformatician in making with a Bachelors Degree in hand and almost an year of exposure in field of genomics. I primarily code in Bash and R ans sporadically in python for visualisation. I am seeking for doctoral studentship.
2020-08-05
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2020-08-06
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2020-08-07
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2020-08-10
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2020-08-14
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2020-08-16
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2020-08-17
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Daniel Baker (12:20:13): > Hi! I’m a CS PhD student at Hopkins, where I work on clustering, indexing, and search for sequences and single-cell data. I primarily write C++ but expose my projects to Python for usability, and I’m starting to use R/Rcpp.
2020-08-18
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2020-08-24
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Jose Alquicira (07:51:44): > Hello everyone! I’m José Alquicira. I’m a PhD student at the Garvan Institute of Medical Research in Sydney. I’ve primarily been working on single-cell analysis (scRNA-seq and CITE-seq), particularly on cell-type classification methods and population genetics.
2020-08-25
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2020-08-27
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2020-08-30
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Yagya Sharma (01:56:55): > Hello everyone, I am Java developer and a beginner in bioinformatics.
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2020-08-31
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2020-09-01
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2020-09-15
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2020-09-24
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2020-09-28
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2020-09-30
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2020-10-02
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2020-10-04
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Curtis (05:37:32): > Hello everyone. I am a graduate of SFSU. I earned a B.S. in Microbiology. I am proficient conducting a variety of assays aimed at optimization and concentrated in the immunological and just recently, dietary supplement industry. I have had experience using NIH-JGI during microbisl genomica and was impressed witht he applictaions of python to DNA/ Protein data. I am kooking forwad to focusing my attention on learning R?/ zpython porgramming lsanguage, sas I see visualization imperativr to funrtdsnfing hte fst.
2020-10-05
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2020-10-06
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Anjali Silva (16:27:08): > Hi All:wave:I’mAnjali, a postdoc fellow at University Health Network/University of Toronto, Canada:flag-ca:I work on developing statistical clustering software for analyzing biological data, mostly working with R. Thanks for letting me join! If I can be of any help, feel free to reach out. Take care.
2020-10-07
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ravindra raut (02:40:20): > Hello Fellows, I ravi, a Ph.D. student; working on transposon analysis of rice genome. I’m a newbie to R and Bioconductor, please suggest any R-package for analysis for a transposon in genome assemblies.
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2020-10-08
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2020-10-11
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2020-10-15
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2020-10-16
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2020-10-18
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2020-10-19
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2020-10-20
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2020-10-21
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2020-10-22
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Christa Toenhake (07:26:00): > Hi All! My name is Christa, I’m working on a tutorial that uses bioconductor for Bsc Biology course. I had expected to find a Education and Training channel here as well. Am I in the wrong group?:sweat_smile:
Dario Strbenac (07:30:04): > Yes. Press the + icon next to Channels in the left panel and you will be able to find an education and training channel.
Alan O’C (07:32:01): > #education-and-training
Federico Marini (07:37:47): > We can invite you there directly:wink:
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2020-10-23
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2020-10-26
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Jeffrey O’Brien (13:57:56): > Hi friends! I’m Jeffrey, an MD student at UConn. I’m working on variant detection in whole genome tumor-normal sequence data. I will likely be working with vcfR and VariantAnnotation in Bioconductor. If you have any suggestions for other packages that may be helpful for this analysis, let me know!
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2020-10-29
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2020-11-03
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2020-11-04
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2020-11-05
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2020-11-11
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2020-11-12
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2020-11-13
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2020-11-16
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Carmen Abaurre (06:10:33): > Hi everyone! I’m Carmen, a MSc in Bioinformatics student at Uppsala University. I’m working on my master’s thesis at Karolinska institutet at the moment. I will be studying the development of human oligodendroglia with scRNA-seq. I’m looking forward to learning more about Bioconductor tools and how to make the most out of them.
XinqiaoZhang (11:24:55): > @XinqiaoZhang has joined the channel
XinqiaoZhang (11:37:39): > Hi, friends! With long time wet bench experience, I’m studying bioinformatics for cancer treatment, currently focus on RNAseq analysis, both bulk and single cell.
2020-11-17
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2020-11-18
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eugenia.galeota (05:11:23): > @eugenia.galeota has joined the channel
eugenia.galeota (05:31:10): > Hi everybody
Valeria Ranzani (05:53:27): > Hi all!
2020-11-19
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David Dittmar (08:46:53): > Hello to all of you! I am a PhD student from the University Hospital in Regensburg (UKR) in Bavaria and currently focussing on scRNA-seq analysis of my first 10x data. I am glad to have found this workspace and scRNA-seq associated channels!:confetti_ball:Especially I am happy to have found the osca-book:raised_hands:
Stephanie Hicks (08:50:50): > welcome@David Dittmar:wave:
David Dittmar (08:53:01) (in thread): > thank you:slightly_smiling_face:
2020-11-20
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2020-11-21
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2020-11-22
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2020-11-23
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Dominique Paul (08:39:12): > Hi all!:wave:I’m a statistics master student at ETH Zurich, currently working a lot with (and very excited about) bioconductor packages and genomic data. Very cool that this slack group exists!
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2020-11-25
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2020-11-26
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2020-12-01
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2020-12-02
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2020-12-03
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2020-12-04
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Kary Oetjen (20:15:49): > Hi:wave:I’m a junior faculty at Washington University in St Louis working with the acute myeloid leukemia group. Single cell RNA sequencing with CITE-Seq and variant mutation are current interests
Sridhar N (20:32:26): > :tada:
Kary Oetjen (20:44:23) (in thread): > Thanks for pointing me to this, I should have joined sooner!!
2020-12-05
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2020-12-14
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2020-12-15
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2020-12-16
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2020-12-17
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2020-12-18
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António Domingues (17:56:42): > Hi, I am António. A biologist that become a data analysist. Sort of a jack of all trades master of none. Currently moving from a core facility to the private sector (pharma start-up). I recently became a BioC package maintainer after offering to fix a bug introduced by a R4.0 in one of my favorite packages. Yay open-source!:flag-pt::flag-england::de:
2020-12-19
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2020-12-20
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Giacomo Antonello (11:31:14): > Hi everyone! I am Giacomo, a PhD student at Eurac Research, Bolzano, Italy. I am involved in the analysis of multi-omics data in a cross sectional population study. I am new to software development and open source, but I would like to contribute with my, so far, little knowledge but big enthusiasm. One day I hope I can be an active member of this lovely community. > > See you “around”! > Giacomo
Lluís Revilla (18:12:41) (in thread): > Hi I’m also doing multi-omics analysis:hand::hand:. You might have already found it but in case you’ve not, check out this list of methods (and papers)https://github.com/mikelove/awesome-multi-omics
Wancen Mu (23:05:01): > @Wancen Mu has joined the channel
2020-12-21
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2020-12-22
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2020-12-23
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2020-12-24
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2020-12-26
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2020-12-30
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2021-01-01
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2021-01-05
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2021-01-07
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Julie Aubert (06:08:34): > Hello, my name is Julie Aubert. I am a statistician involved in development and application of stat. methods to adress pbs in microbial ecology.
Soumya Banerjee (06:46:58): > Hello everyone I am Soumya Banerjee. I do data science, computational biology and clinical informatics
2021-01-11
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2021-01-12
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2021-01-13
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Espen Riskedal (08:34:47): > Hi all, Espen here. I do EWAS and develop prediction models. Currently focused on Rheumatoid arthritis and COVID-19.
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2021-01-14
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2021-01-16
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2021-01-29
mariadermit (04:51:59): > Hi! I’m a postdoc at Barts Cancer Institute. My work interest is on RNA binding proteins using proteomics. I hope I can contribute with proteomics-related packages for Bioconductor!
mariadermit (05:56:41) (in thread): > Its a small world! where do you work now?
mariadermit (08:42:17) (in thread): > Very nice! Is your company biotech-related? Yes, I know Michael
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2021-01-31
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2021-02-01
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2021-02-13
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2021-02-19
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2021-02-22
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2021-02-23
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2021-02-24
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Kyle Alford (11:39:09): > Hi everyone! I’m Kyle, an undergraduate at Columbia University as well as an aspiring Computational Biologist with interests in Oncology and Biotech. I’m currently working on clustering & RNA-splicing using ML and I’m excited to learn more about Bioconductor/R!
2021-02-25
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2021-02-26
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Scott Lipnick (13:41:49): > Hi. Physicist/computational biologist/bioinformacian now working to create biotech/healthcare companies. Current projects at Flagship Pioneering are at the interface of single-cell RNAseq, EHR, and genomics.
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2021-03-01
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2021-03-02
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Alan Murphy (09:00:47): > Hey all, I’m a bioinformatician working in a neurogenomics lab in ICL. Currently working on the development of differing packages to interpret multi-omic, single-cell neurological datasets
Alan Murphy (10:46:10) (in thread): > Yep! Well, the UK Dementia Research Institute at Imperial to be specific. Thanks!
Gowtham (12:58:32): > @Gowtham has joined the channel
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2021-03-04
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2021-03-10
António Domingues (09:26:13) (in thread): > Hi@mariadermit! As a Mass-spec n00b currently looking at TMT data (also RNA binding proteins!) I look forward for those packages :)
Seema Sheth-Voss (09:40:56): > Hello, Thanks for having me. I am from TileDB Inc. TileDBArrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances.
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2021-03-11
Sanchit Saini (09:14:34): > Hey everyone, I’m working along with@Michael Lawrenceon the maintenance of packages(like rtracklayer, ggbio), So sometimes you can also expect replies from me on GitHub issue/PRs.
2021-03-12
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Aoi Senju (21:27:11): > Hey Bioconductor community! Any fellow scientist entrepreneurs here?
2021-04-08
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2021-04-29
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Ijeoma Chinwe Uzoma (13:13:04): > :wave:I’m here! What’d I miss?
2021-04-30
JAVAN OKENDO (02:57:11): > Hello good people….I am a new comer and I am currently looking for a bioinformatics job…any pointer will be appreciated
Lluís Revilla (03:12:40) (in thread): > Hi! Welcome to the slack:smile:You might find your job at#jobsorhttps://support.bioconductor.org/t/jobs/good luck!
JAVAN OKENDO (03:33:39) (in thread): > Thanks@Lluís RevillaI will have a look at the link
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2021-05-01
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Oluwaseyi Ashaka (05:09:58): > Hello everyone. I am just joining this platform to learn more about the bioconductor program. Please feel free to invite me in any discussion or platform that i can learn from.
2021-05-03
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2021-05-10
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Aakash Mantri (08:22:59): > Hello everyone, I am Aakash. I am a Graduate student based in Bonn, Germany. I am working on an ML-based pipeline to recommend personalized nutrition based on the microbiome. I am hoping to learn about different tools and hoping to contribute something as well.
Sean Davis (09:06:50) (in thread): > intros,@Levi Waldron@Nicola Segata@Kelly Eckenrode
Federico Marini (10:10:23) (in thread): > and while we are at it, I guess some people currently at/related to Pendulum can be interested:wink:(@Fanny Perraudeau? I think@Davide Rissomentioned this some time ago)
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Konrad J. Debski (13:33:15): > Hi I am Konrad an R developer:slightly_smiling_face:
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Amir Shams (16:43:19): > Hi@Sean Davisalways a fan
Sean Davis (16:51:33): > Great to see you here,@Amir Shams.
2021-07-23
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Rosalina Tincopa Marca (20:29:00): > Hi, I am Rosalina Tincopa Marca, I am a biologist from Peru . I decided to join bioconductor community because I want improve my programming skills on it, find a support group or mentor. I love dancing, singing, enjoy listening to music. I am learning how to play a Charango instrument:beret-parrot:
2021-08-04
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Matt McElheron (08:35:19): > Hey all, I am Matt McElheron, a young genetics and computational immunology PhD student from Ireland:face_with_cowboy_hat:I am interested in using machine learning and genetic/epigenetic data to identify patterns of biological ageing:dna::mag:I am excited to learn from everyone else and to connect with like-minded researchers on socials
Adit Wiryadana (08:36:55): > @Adit Wiryadana has joined the channel
Liisa Veerus (she/her) (08:38:32): > Hi all, I am Liisa, a postdoctoral fellow in Blaser Lab, working on the associations between microbiome, hormones, and health. Nice to meet you! Let’s connect on Twitterhttps://twitter.com/LiisaVeerus - Attachment (twitter.com): Dr Liisa Veerus (she/her) (@LiisaVeerus) | Twitter > The latest Tweets from Dr Liisa Veerus (she/her) (@LiisaVeerus). Postdoctoral fellow in @BlaserLab @RutgersCABM, working on microbiome • #scicomm & #sciart enthusiast :microbe::art: • All doodles are my own, please tag :female-scientist::skin-tone-3::flag-ee:. Oxford
Niraj Khemka (08:38:36): > @Niraj Khemka has joined the channel
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Rasha Shraim (08:44:04): > Hi, I’m a genomics data science PhD student in Ireland studying gene-environment interactions, excited for the next 3 days!:female-technologist:(on twitter@rashabun)
Sebastian Worms (08:44:31): > What’s happening in the next three days? Feel stuck under a rock ^^
Lori Shepherd (08:45:06) (in thread): > Its the Bioc2021 virtual conference
Lori Shepherd (08:45:24) (in thread): > https://bioc2021.bioconductor.org/
Tulasi Marrapu (08:47:13): > @Tulasi Marrapu has joined the channel
Assa (08:49:56): > Hi everyone, thrilled to be here as well, I’m a bioinformatician from Munich, Germnay. (@AssaYeroslaviz)
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Niraj Khemka (08:57:21): > Hi, I am Niraj from Dublin. twitter@rambhorese#introductions
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Stephanie Hicks (13:39:31): > Welcome everyone!:wave:
Sean Davis (13:53:25): > Joining@Stephanie Hicksin saying hello to new members. Introduce yourselves if it suits you. There are lots of channels to match specific interests as well.
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Julien Roux (02:12:07): > Hi all, I’m bioinformatician in the Core facility of the Department of Biomedicine at the University of Basel (https://biomedizin.unibas.ch/en/core-facilities/bioinformatics). I’m realising pretty late that joining the Bioc Slack channel might be a good idea:slightly_smiling_face: - Attachment (biomedizin.unibas.ch): Bioinformatics | Department of Biomedicine
2021-09-10
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Aris Budiman (11:31:49): > Hi everyone, I am Aris from Indonesia, twitter@Aris Budiman
Vince Carey (12:20:34): > :clap:
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2021-11-10
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Jill Lundell (10:47:47): > Hello, I am a genomic data science postdoc in Boston.
2021-11-11
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2021-11-20
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Zachary DeBruine (16:38:31): > Wow Bioconductor has a slack channel with awesome community discussion?! Way to go. Zach DeBruine here from the Van Andel Institute, Michigan. I work on high-performance Non-negative Matrix Factorization (RcppML R package) and atlas-scale single-cell experiment data wrangling (ah, shall we perhaps make this a Bioconductor package?).https://www.zachdebruine.com/ - Attachment (zachdebruine.com): Zach DeBruine > Postdoctoral Fellow in Bioinformatics
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2021-11-21
Vince Carey (15:55:21) (in thread): > Hi Zach – very nice post on NMF. What is the source of the aml data? Has it been published?
2021-11-23
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Zachary DeBruine (19:25:21) (in thread): > Hi Vince, the AML data is yet unpublished and part of a larger work in progress, along with new methods for data integration with NMF.
2021-11-24
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Helge Hecht (13:14:48): > Hi all! I’m developing mass spectrometry pipelines in R and python and would like to learn more about Bioconductor and eventually move our packages there or make them compliant. We currently publish things in bioconda, but interfacing with the Bioconductor ecosystem would be nice! > > I’d also be interested in getting involved in the review processes after publishing the first packages.
2021-11-29
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Castro Mbithi (02:40:08): > Hi, I am Castro, and I look forward to learning a lot from this group. I’m a developer atLD Talent, a project born out of Stanford University. It’s a tool that helps you find diverse vetted developers and helps you manage them in an efficient and transparent way.Free Trial Details: The platform gives you~5 free hoursto try them before hiring them forcontract or full-timeroles. To see how incredibly unique LD is, check out these video clips: > * [~1m] anoverviewof the platform and vetting > * [~30s][transparent work sessions](https://www.youtube.com/embed/iuEKqJbm9O8?start=832&end=865) > * [~1m][data on developers](https://www.youtube.com/embed/iuEKqJbm9O8?start=185&end=285), i.e. productivity and responsiveness > * [~3m][interviewing tips and time estimation](https://youtu.be/Ize-Gxaalgw?t=113) > * [~1m][budget control](https://www.youtube.com/embed/iuEKqJbm9O8?start=924&end=1007) > Diversity meets Capitalism: Our mission is to help teams become stronger by encouraging them to droplocation biases and constraintsthat unknowingly and implicitly exclude qualified, motivated, andefficientpeople of color from impactful roles they are perfect for. These knowledge workers are undervalued and overlooked by industry, creating an opportunity for a new type of global collaboration, given the rise ofremote distributed teamsin the new normal. > > We are always looking for BRUTALLY HONEST feedback :) - File (GIF): aldgif-2FPS.gif
2021-12-09
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2021-12-16
Krithika Bhuvanesh (18:54:54) (in thread): > Better late than never :D
2021-12-17
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Garth Kong (20:27:52): > Hi all, my name is Garth and I am a computational biologist at Oregon Health and Science University! I use bioinformatics to study epigenetic changes in blood cancer. I’m looking to submit my first R package through Bioconductor in the second cycle (Oct 2022), and I look forward to signing up for the New Developer Program! > > Here is a link to my personal website and my lab:slightly_smiling_face:https://gartician.github.io/https://www.maxsonlab.org/ - Attachment (gartician.github.io): Garth Kong Personal Website > Your friendly research institute bioinformatic analyst - Attachment (maxsonlab.org): The Maxson Laboratory > The Maxson Lab. Studying the genomics of leukemia at the OHSU Knight Cancer Institute.
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John Cheney (21:04:33): > Hi all! I work with@Garth Kongand our team (@Thai Nguyen,@Wesley Rosales,@Anjali Panikar) visualizing CITE-seq data in collaboration with the Maxson Lab @ OHSU. Pleased to be here with you all!
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2022-02-01
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Jeanette Johnson (20:15:05): > Hi everybody, I’m a grad student in Elana Fertig’s lab at Johns Hopkins, right now I’m working on our NMF package, and my thesis is on TCR sequence analysis! I’m happy to be here and excited to learn from u all:relaxed:also happy to see some people from the PNW! I’m PNW born and bred, the east coast is cool but I miss the rain and the evergreens:evergreen_tree:
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Kevin Rue-Albrecht (04:10:25) (in thread): > Looking forward to see you on the developer program! Thanks for the reminder to make the link to the new form public, seehttps://bioconductor.org/developers/new-developer-program/
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Garth Kong (14:26:16) (in thread): > Thanks for being on top of it@Kevin Rue-Albrecht, I’m going to fill it out once I get the chance!
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Ruslan Rust (08:42:37): > Hi all, I’m Ruslan, group leader at the University of Zurich. I am working on new cell therapies for stroke. Look forward to join the community!
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Theodore Vichos (04:00:53): > Hello everybody, I am excited to join this beautiful community!
Zachary DeBruine (11:04:44) (in thread): > Awesome, what plans do you have for the NMF package? (author of an NMF package to another author of an NMF package:slightly_smiling_face:)
2022-04-06
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Kristian Ullrich (16:55:26): > Hi, I am Kristian, a bioinformatician at the Max Planck Institute For Evolutionary Biology. I recently could contributed a package to Bioconductor and I am excited to join the community and this slack channel.
2022-05-18
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Anuj Sharma (14:23:28): > Thank you Dr. Davis@Sean Davisfor introducing this slack community to bigcare@purdue in his lecture.
2022-05-19
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Amos Schorr (17:25:13): > Hey everyone! I’m launching a program with a nonprofit,Norn Group, to provide mentorship, bioinformatics training, and jobs to researchers around the world who are interested in the biology of aging and don’t have access to enough resources and opportunities. Excited to get to know some of y’all.
Lori Shepherd (21:58:30) (in thread): > Welcome!
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2022-07-08
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2022-07-10
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2022-07-19
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2022-07-21
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2022-07-22
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Claire Rioualen (16:00:00): > Hello! I’m Claire, I am French and I have been doing a PhD in genomics in Cuernavaca, Mexico, for the past 4 years. > I’ll also be attending the BioC 2022 conference in Seattle next week! See you there?
Lori Shepherd (16:01:52) (in thread): > Welcome! See you in Seattle!
2022-07-26
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2022-07-27
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Ryan C. Thompson (10:47:45): > Hi everyone! I’m Ryan. I’ve been a long-time user and occasional contributor to Bioconductor, and I’m excited to attend Bioc 2022 virtually from NYC!
Rushika (10:48:41): > @Rushika has joined the channel
Olga (10:50:43): > @Olga has joined the channel
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Alexandre Gouy (15:04:31): > Hi everyone! I’m Alex, I’m a bioinformatician by training and I’ve been using and developing Bioconductor resources for several years now. I’m now working for Tercen, bringing some BioC single cell pipelines into a user friendly data analysis platform. Feel free to ping me for a coffee IRL at BioC2022 or for a virtual chat!
Garreck Lenz (15:56:51): > @Garreck Lenz has joined the channel
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SILVIA GIULIA GALFRE’ (13:47:21): > Hi, I’m Silvia. I’m working on scRNAseq and I developed a Bioconductor package (COTAN) during my PhD and now I still developing it. If you would like to see a completely different point of view on sc data, get in touch.:relaxed:I’m very happy to be virtually at BioC2022.
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Jennifer Holmes (16:13:47): > Hi everyone! I’m Jennifer - You can call me Jenn. I work for the CDC Foundation and I’m stationed at the Ohio Department of Health as a Bioinformatician. I’ve been using Bioconductor since I started my Masters back in 2015 and I ended up falling in love with R as I finished my program and started working in public health. I’m excited to be in the community and continue to improve my skills!:slightly_smiling_face:
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Umar Ahmad (17:33:12) (in thread): > You are welcome@Jennifer Holmes
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Chizi E (14:00:55): > Hello everyone and@Andres Wokaty!!! > My name is Chizi. I am here through Outreachy’s open source internship program. Hoping to learn about contributing to Bioconductor and open source in general. > Great job everyone! > > I am particularly interested in the project titled “Convert Sweave vignettes to R Markdown”…
Mariam Fayena (15:30:49): > Hello everyone my name is Mariam Fayena, i am an applicant of the Outreachy internship program. i would be learning and contributing to theConvert Sweave vignettes to R Markdown project. i hope to learn from you@Andres Wokaty
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2022-10-09
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Dike Victoria Chiemela (03:48:25): > Hello everyone, I am Dike Victoria, an applicant of the Outreachy internship program. > Looking forward to making my contribution.
Karsten Rinas (10:41:05): > @Karsten Rinas has joined the channel
Andres Wokaty (12:41:20): > Welcome Outreachy applicants, please be sure to join the#outreachychannel@Chizi E@Mariam Fayena@Dike Victoria Chiemela
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Ani Chibuike Damian (10:08:32): > Hi everyone, I’m Ani Chibuike Damian, an applicant of the Outreachy program in my contribution stage. Looking forward to learn and contribute to the “Convert sweave vignettes to R markdown project”. My mentor is@Andres Wokaty. Really nice to be here
chihurumnanya ikevude (10:23:43): > @chihurumnanya ikevude has joined the channel
Dike Victoria Chiemela (11:43:03) (in thread): > You are welcomed Chibuike.
Ani Chibuike Damian (11:49:22) (in thread): > Thank you Chemela. Great to be here
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Mercilena Benjamin (13:53:20): > :wave:Hello, team! I’m Mercilena, looking to learn the applications of next gen sequencing in oncology and translational research.
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Akwamfon Eventus (06:45:38): > Hi everyone, > Hello Mentor@Andres WokatyI’m Akwamfon Eventus (Him/He), an applicant for the Dec22 Outreachy Open Source Internship. > I am applying to contribute on this project. I wish to contribute to the “sweave2rmd” project. > Great to be here.
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Maria Fiorio (12:38:58): > Hi, I’m Maria. I’m applying for Outreachy and looking forward to contributing to Converting sweave vignettes to R markdown. I’m from Brazil, and I am glad to participate.
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2022-10-18
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Iman Linje (18:20:07): > Hello, I am Iman. An Outreachy Applicant, I will be contributing to Refactor the BSgenomeForge tools. Looking forward to working with everyone
2022-10-19
Atuhurira Kirabo Kakopo (05:48:15) (in thread): > Hi Iman, welcome to the community
Iman Linje (08:54:43) (in thread): > Thank you, Atuhurira
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2022-10-20
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Adeoye Beatrice (09:59:23): > Hello, I am Beatrice, an Outreachy Applicant, I am working on the Sweave2Rmd project. looking forward to various work collaborations. Thanks
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2022-10-21
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2022-11-30
rodrigo arcoverde (05:29:17): > Hi, I am Rodrigo, a Brazilian doing a PhD in Karolinska Institutet. I have recently contributed to Bioc with a package and have now applied for the Bioc carpentry instructor training course. If someone else applied for the same course (Feb 7-8 2023), please reach out:smile:
Maria Doyle (06:51:57) (in thread): > Welcome Rodrigo!:wave:Could you also post this in the#education-and-trainingchannel
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Zainab Ashimiyu-Abdusalam (04:43:41): > Hi, I am Zainab currently looking forward to further ny studies in Bioinformatics and Computational biology. I have a Pharmacology Therapeutics and Toxicology background. I am from Nigeria. I look forward to making meaningful contribution to the community. > > Can someone help me on how to get started to contributing. Thank you in advance.
Maria Doyle (05:47:03) (in thread): > Hi Zainab, welcome! I’m posting the link here to where@Kozo Nishidareplied to you with his slides with infohttps://community-bioc.slack.com/archives/CUKAPEE1Y/p1670840698438489in case helpful to anyone else - Attachment: Attachment > @Zainab Ashimiyu-Abdusalam Also, I recently made some slides about community contributions. Take a look. https://docs.google.com/presentation/d/1Wgs6y2ZMmbYGFk3WhEQ7Vc3NbvQxXjRFuyimidM1JxA/edit#slide=id.p
Zainab Ashimiyu-Abdusalam (06:08:43) (in thread): > That’s alright@Maria Doyle
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2022-12-19
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JP Courneya (00:21:57): > Hello Bioc Slack! Thanks for the invite. Looking forward to sharing and learning with you all. Kind regards. Oh and a little about me. I enjoy farting around on computers. Coding in R is great especially for Bioinformatics. Punk rock Skateboarding and family are life.:dove_of_peace::skateboard::guitar::computer::dna::heart:
David Henderson (14:00:03): > @David Henderson has joined the channel
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2022-12-20
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Jennifer Foltz (10:50:15): > Hello all! I am an Instructor at Washington University in St. Louis! Background as a wet-lab immunologist, and for the last 3+ years doing single-cell analysis:computer:on samples from immunotherapy clinical trials! Happy to be here:nerd_face:
Matti Ruuskanen (11:20:48): > Hello! I’m a postdoctoral researcher in@Leo Lahti’s group at University of Turku. Mainly working on gut and skin microbiomes, but I’m also interested in environmental microbiology. Method-wise, I’m dealing with multiomic data integration, machine learning, and spatial modeling. I’ve worked mostly with R since 2013, dabbled in python and now getting started with Julia. In my spare time I play music, sing in a choir and do various sports. Send me a message if you want to connect!
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2023-01-02
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2023-01-09
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2023-01-10
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2023-01-16
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2023-01-17
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Zedias Chikwambi (06:05:32): > Hi, am happy for the opportunity to learn new skills. I have a biotechnology background and have over the years transitioned into computational biology. Would love to develop packages to better the data analysis processes in these areas.
2023-01-18
Marie HIDJO (02:57:47): > Hi everyone My name is Marie hidjo and have been recently selected to be trained to be a carpentry instructor. It is great being here.
2023-01-20
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Aedin Culhane (12:23:53): > Welcome new members. Thanks for joining. There are lots of channels and resources, enjoy exploring.
2023-01-27
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2023-01-30
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mahamtariq58 (09:53:00): > Hi everyone! I am Maham Tariq and I have done computer engineering. I stumbled upon the Bioconductor project and found it interesting. Can anyone guide me on how to get started? Looking forward to making meaningful contributions and learning new skills
Maria Doyle (17:30:53) (in thread): > Welcome Maham! This may help you get startedhttps://carpentries-incubator.github.io/bioc-project/It’s being developed by@Kevin Rue-Albrechtand if you have any feedback would be great if you could let us know in that github repo
2023-01-31
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Doug Joubert (14:37:12): > Hi everyone, I am a new coordinator for our Bioinformatics program. I am a data-guy trying to learn bioinformatics so I am here to learn. I am really excited about thefollowingincubator lessons. I am slowing learn how to use bioconductor in R to help our users.
Maria Doyle (14:56:22) (in thread): > Welcome Doug! That’s great to hear:simple_smile:I saw you already started contributing to that lesson, thanks for that! We also have the#education-and-trainingchannel here please feel free to join it
2023-02-07
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2023-02-17
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Xiaolong Cheng (13:11:52): > Hi everyone, I’m a postdoc at Children’s National. I’m working on developing computational tools for understanding hight-throughput sequencing data (CRISPR screening and scRNA-seq). Look forward to making contribution to the community.
2023-02-18
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Jędrzej Świeżewski (05:34:18): > Hi all, > I’m the Head of AI at Appsilon. I’m personally involved in multiple projects related to the use of Machine Learning (mostly Computer Vision) for biological data. These include camera trap images, aerial imagery, microscopy imagery and more (you canread more here, or reach out to me directly). Glad to be here. - Attachment (appsilon.com): AI & Research - Appsilon | Enterprise R Shiny Dashboards > Appsilon delivers state-of-the-art machine learning and computer vision solutions for nonprofit organizations and enterprise clients.
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Zarmena Khan (13:16:12): > Hi everyone, my name is Zarmena and I’m a Key Account Manager for UK & Ireland here Oxford Nanopore Technologies! Supporting users of nanopore sequencing technology across the regions. Excited to be here as a part of the community! Please feel free to reach out with any questions
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Kayla Okereke (13:20:32): > Hello everyone, I’m Kayla from Nigeria and I just got accepted into the Outreachy Internship May batch. I’m glad to be here and hope to contribute to the project.
Emmanuel Taiwo devbird007 (13:39:31): > @Emmanuel Taiwo devbird007 has joined the channel
Emmanuel Taiwo devbird007 (13:48:52): > Goodday everyone, My name is Emmanuel and I am an Outreachy applicant for the May Cohort. I am interested in contributing to Bioconductor projects. My chosen project is: Convert Sweave Vignettes to RMarkdown.
khadijah (14:42:05): > H,i my name is Khadijah, an outreachy applicant May cohort. I am interested in contributing to bioconductor projects.
Anushka Sharma (15:04:42): > @Anushka Sharma has joined the channel
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Reece (16:06:07): > @Reece has joined the channel
Reece (16:14:46): > Hi everyone:slightly_smiling_face:My name is**** Reece an outreachy applicant for the May cohort ****. Interested in contributing and learning from the biconductor community particularly theConvert Sweave Vignettes to RMarkdown project
Madelyn Carlson (16:17:00) (in thread): > Welcome, Emmanuel! Great to meet you. Quick plug to join the Slack#outreachychannel if you haven’t done so already:tada:
Madelyn Carlson (16:17:29) (in thread): > Welcome, Kayla! Wonderful to meet you – > > Quick plug to join the Slack#outreachychannel if you haven’t done so already:tada:
Madelyn Carlson (16:18:14) (in thread): > Welcome, Khadijah! My name is Madelyn, great to meet you. Quick plug to join the Slack#outreachychannel if you haven’t done so already:tada:
Madelyn Carlson (16:18:50) (in thread): > Amazing ~ welcome, Reece! My name is Madelyn, great to meet you. Quick plug to join the Slack#outreachychannel if you haven’t done so already:tada:
Madelyn Carlson (16:22:10): > Welcome, Outreachy applicants!:tada:My name is Madelyn, pronouns she/her. We’re excited for this contribution period and to meet y’all. I’ve been working with Jen and Paul on the Sweave2Rmd project. If you have any questions about our contribution period, come take a look at the information pinned our#outreachychannel, which includes guidance on contribution tasks and information on upcoming office hours with members of our team. Talk more soon!
Reece (16:31:20) (in thread): > thank you@Madelyn Carlsoni have joined now
Madelyn Carlson (16:43:25) (in thread): > :tada:
Kayla Okereke (17:08:12) (in thread): > Thank you so much Madelyn.
Madelyn Carlson (17:08:25) (in thread): > absolutely!
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Maryam Gbemisola (22:31:23): > Hi, My name is Maryam Gbemisola. I just got accepted into the Outreachy internship. I am to contribute my best to the internship
Vivian Ginikachukwu Ikeh (23:12:39): > @Vivian Ginikachukwu Ikeh has joined the channel
Vivian Ginikachukwu Ikeh (23:27:00): > Hello, my name is Vivian Ikeh, pronouns she/her. > Just got accepted for the contribution stage, I am willing to learn and contribute to the project.
2023-03-07
KritikaVerma (00:06:23): > Hi > I am Kritika Verma. I am an Outreachy applicant for the May cohort. > I have already introduced myself and my initial application got approved. I look forward to learning and contributing with everyone. > Thank you
Violet Akpeh (00:56:44): > @Violet Akpeh has joined the channel
Maryam Gbemisola (00:59:49): > Welcome@Vivian Ginikachukwu Ikeh
Maryam Gbemisola (01:00:07): > Welcome@KritikaVerma
Maryam Gbemisola (01:00:26): > Welcome@Violet Akpeh
Violet Akpeh (01:18:25): > Hello everyone, My name is Violet. I am an outreachy applicant. I am really looking forward to contributing and learning.
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Sonali Kumari (02:42:16): > Hello everyone, My name is Sonali Kumari . I am from India (Delhi) , hope you all are doing well looking forward to make meaningful contributions and learning in the process.
Esther (02:48:31): > @Esther has joined the channel
Esther (02:53:03): > Hello Everyone > > My name is Esther Ewete.I am. Nigerian. > > So happy to be a part of this project,and I look forward to having a great experience.
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Patricia Brianna (03:10:22): > hello good people, I am Brianna(Brian in short), an outreachy applicant who is willing to learn, grow and make a difference
Ameerah Kabir (03:33:56): > I am Ameerah Kabir, from Nigeria, a contributing intern from Outreachy internship. I can’t wait to make an impact. Thank youu.
Maryam Gbemisola (04:12:26): > @Maryam Gbemisola has joined the channel
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Aayushi Singh (04:28:19): > Hi there, hope you all are doing great. I’m Aayushi, pronouns she/her from India an Outreachy Applicant. > I’m excited to be part of this journey and look forward to the challenges and opportunities that lie ahead.
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Maryam Gbemisola (04:35:58): > Welcome everyone
Diana Ofodu (04:36:31): > @Diana Ofodu has joined the channel
Maryam Gbemisola (04:47:47): > How do I get started? > How do I know the mentor?
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Petrah (05:50:20): > @Petrah has joined the channel
Busayo Ojo (06:13:09): > Hi@Maryam Gbemisolathere’s a specific chat for outreachy interns where you can ask your questions#outreachy
Vivian Ginikachukwu Ikeh (07:24:42) (in thread): > Thank you@Maryam Gbemisola
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Sweta Kumari (09:53:41): > Hello everyone this is Sweta Kumari, after going through Bioconductor project description i really find it very interesting particularly the Microbiome Study Curation, it matches with my interest. I really want to know about human microbiome so that we can protect ourself from future pandemic or health related disease. I am hoping to learn lots of things while doing this internship project.
Maryam Gbemisola (10:35:39) (in thread): > Thank you
Madelyn Carlson (10:39:31) (in thread): > Welcome Maryam, great to meet you! If you haven’t done so already, feel free to join#outreachySlack channel to learn more about the Sweave2Rmd project or the#bugsigdbto learn more about the Microbiome Study Curation project:tada:
Madelyn Carlson (10:40:00) (in thread): > Welcome Vivian, great to meet you! If you haven’t done so already, feel free to join#outreachySlack channel to learn more about the Sweave2Rmd project or the#bugsigdbto learn more about the Microbiome Study Curation project:tada:
Madelyn Carlson (10:40:38) (in thread): > Welcome Kritika, great to e-meet you! If you haven’t done so already, feel free to join#outreachySlack channel to learn more about the Sweave2Rmd project or the#bugsigdbto learn more about the Microbiome Study Curation project:tada:
Madelyn Carlson (10:41:21) (in thread): > Welcome Violet, great to e-meet you! If you haven’t done so already, feel free to join#outreachySlack channel to learn more about the Sweave2Rmd project or the#bugsigdbto learn more about the Microbiome Study Curation project:tada:
Ufuoma Ejite (10:41:32): > @Ufuoma Ejite has joined the channel
Madelyn Carlson (10:41:42) (in thread): > Welcome Esther, great to e-meet you! If you haven’t done so already, feel free to join#outreachySlack channel to learn more about the Sweave2Rmd project or the#bugsigdbto learn more about the Microbiome Study Curation project:tada:
Madelyn Carlson (10:42:18) (in thread): > Welcome Brian, great to e-meet you! If you haven’t done so already, feel free to join#outreachySlack channel to learn more about the Sweave2Rmd project or the#bugsigdbto learn more about the Microbiome Study Curation project:tada:
Madelyn Carlson (10:43:10) (in thread): > Welcome Ameerah! Give me a shout if you need any help finding the#bugsigdbchannel (re: our other thread)
Madelyn Carlson (10:43:39) (in thread): > Welcome Aayushi, great to e-meet you! If you haven’t done so already, feel free to join#outreachySlack channel to learn more about the Sweave2Rmd project or the#bugsigdbto learn more about the Microbiome Study Curation project:tada:
Madelyn Carlson (10:46:21) (in thread): > Welcome Maryam, great to e-meet you! Wonderful questions - there are 2 projects that you can learn more about: the Sweave2Rmd project (search the#outreachySlack channel for more) and the Microbiome Study Curation project (join the#bugsigdbfor more information/space to ask questions). On both channels, you can find links to our issues containing information and instructions on the project and contribution tasks. Reach out and tag me if you have any questions!
Esther (10:49:08) (in thread): > Thank you Madelyn. > > I already joined the#bugsigdbchannel. > > Please whats the next step after joining the project channel?
Maryam Gbemisola (10:49:43) (in thread): > Thank you@Madelyn Carlson
Madelyn Carlson (10:50:35) (in thread): > Amazing and welcome Sweta! Great to e-meet you. If you haven’t done so already, you can join the#bugsigdbSlack channel to learn more about the Microbiome Study Curation project. You can also use that channel to ask questions about the project and its contribution tasks. In case it’s useful, here is the link to theBugSigDB-Outreachy contribution guidanceissues pg (this can be found pinned in the#bugsigdbchannel as well) - Attachment: #1 Microbiome Study Curation - Outreachy Applicant Instructions > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > Contribution Task > > Review article on the human microbiome that is heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) and complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M. > > (Optional) Stretch Task: As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.
Madelyn Carlson (10:50:42) (in thread): > Please let me know if you have any questions!
Ufuoma Ejite (10:52:11): > Hello everyone!:blush:I feel good being here. I am Ufuoma Ejite. > I’m interested in contributing to the Microbiome Study Curation project.
Madelyn Carlson (10:52:19) (in thread): > Absolutely!
Madelyn Carlson (10:54:35) (in thread): > Welcome, we’re happy you’re here! Check out the#bugsigdbfor more information about the Microbiome Study Curation project
Evan Chinny (11:02:31): > @Evan Chinny has joined the channel
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Shravani Nag (12:01:03): > Hello everyone!Shravani this side.
Sweta Kumari (12:46:15) (in thread): > Thank you ma’am:blush:, i will let you know if i face problem.
Ibizugbe Merit (15:11:52): > @Ibizugbe Merit has joined the channel
Ibizugbe Merit (15:13:48): > Hi everyone,I’mMerit Ibizugbe,an outreachy applicant. I am glad to be here,open to contributing and learning from this space.
Rukky (15:30:00): > @Rukky has joined the channel
Rukky (15:41:45): > Hello everyone, I’m Rukevwe Ikanone an outreachy applicant from Nigeria. And I’m glad to be part of this project. I look forward to contributing and learning a lot from this Internship project.
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Emmanuel Taiwo devbird007 (21:31:37): > Hey guys, after the introduction make sure to join the#outreachyand#sweave2rmdchannels to get clued in on more info. and to get answers to your questions. I look forward to working alongside you.
anshika bhatt (23:29:11): > @anshika bhatt has joined the channel
2023-03-08
Unyime William (01:07:34): > @Unyime William has joined the channel
Unyime William (01:14:21): > Hi everyone, I’m Unyime.I’mhappy to be here. Looking forward to contributing and learning on this project.
MaryJones (01:23:59): > @MaryJones has joined the channel
MaryJones (01:31:27): > Hello Mary Jones here, an Outreachy intern and a novice working on Bioconductor project, please kindly guide me to the repository we are expected to work on for the first contribution, thank you
Ayantika Sen (01:34:27): > @Ayantika Sen has joined the channel
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Monalika Patnaik (02:32:18) (in thread): > Hey@MaryJones:wave:For first contribution we need to understand the basics of R and R Markdown..you can work on this issue as your first contribution task:blush:https://github.com/Bioconductor/sweave2rmd/issues/62 - Attachment: #62 Sweave2Rmd Knowledge Check > Welcome Outreachy applicants! > > Note: Multiple Outreachy applicants can work on this issue. > > Please choose this as your first contribution task to the Bioconductor Sweave2Rmd project as it will familiarize you with the R, R Markdown, GitHub processes, documentation, and the Sweave2Rmd conversion process (learn more about Bioconductor here). > > Sweave2Rmd Project > > Sweave2Rmd is a community project to convert Sweave vignettes to Rmd. Currently, there are approximately 900 vignettes .Rnw in software packages. These vignettes do not operate as effectively as .Rmd as they are older, combine latex with R, and compile to PDF whereas .Rmd vignettes compile to HTML, are BiocStyle compatible, and easier to read and maintain. Therefore, the aim of the Sweave2Rmd project is to convert these Sweave vignettes to .Rmd. > > Prep Work > > If you’re not familiar with R and R Markdown, please learn a little about them. The following links should be sufficient to get you started: R Primer - Programming basics or R Markdown. Then you may complete the following steps: > > • Install R > • Install RStudio > • In RStudio or through the terminal, install devtools and BiocManager:
> install.packages(c("devtools", "BiocManager")) > • Read through the Sweave2Rmd Contribute article, which explains step-by-step the process of converting a Sweave document to Rmd. The article will be important for completing this contribution task. > > Contribution Task > > After reading the Sweave2Rmd Contribute article, you may complete the 2023 Outreachy Sweave2Rmd Contribution Familiarity Quiz. The quiz contains questions about the process of converting a Sweave vignette to Rmd. It is an opportunity to both test your familiarity with the Contribute article and learn how to convert a vignette if you choose to complete the second (optional) contribution task. We expect the quiz to take up to 3 hours to complete. If you have any questions about the quiz, feel free to post on the Sweave2Rmd Outreachy Slack channel. To join the Slack channel, view https://slack.bioconductor.org/ then search for the channel #outreachy. > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/convert-sweave-vignettes-to-r-markdown/contributions/
Rukky (02:33:59) (in thread): > Thank you.
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Indraneel (04:16:39): > @Indraneel has joined the channel
Vivian Ginikachukwu Ikeh (04:45:36) (in thread): > Thank you@Madelyn CarlsonI really look forward to learning and contributing where I can and hope I make it to the internship stage.
Treasure Okafor (05:28:26): > @Treasure Okafor has joined the channel
Treasure Okafor (05:33:24): > Hello everyone, I’m Treasure. Delighted to be here and looking forward to working with you all
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Madelyn Carlson (09:19:49): > Outreachy applicants: > > As a reminder, we are hosting the Sweave2Rmd-Outreachy office hour at 11-11:45AM ET today (Zoom link). This will be time where we explain the project and answer questions about the contribution tasks. If you’re unable to make it, no worries - we have another office hour session next week on Thursday, March 16, 10-10:45AM ET (and sessions each week for the 2 weeks after) and I will try my best to remember to record the session today and post it on this channel. Talk soon!
Desire Oluwarotimi (10:29:55): > @Desire Oluwarotimi has joined the channel
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Shallie (11:00:49): > Hi guys!:wave:My name is Shallie, I’m an outreachy applicant and I’m very delighted to work with Bioconductor. Looking forward to Thursday’s meeting and to get to know everyone. Happy to be here:purple_heart:
Job David (11:10:05): > @Job David has joined the channel
Job David (11:13:44): > Hi everyone,I’mDavid,I’mhappy to be here. > And as well looking forward to contribute and learn on this project
Desire Oluwarotimi (11:16:00): > Hello everyone, I’m Desire, an Outreachy applicant and I’m looking forward to contributing positively to the community.
Fatima Zohra (11:42:42) (in thread): > Welcome Desire!
Fatima Zohra (11:43:04) (in thread): > Welcome to the project!
Aditi Singh (13:02:00): > @Aditi Singh has joined the channel
Aditi Singh (13:08:14): > Hello everybody! My name is Aditi, an Outreachy applicant and I’m enthusiastic about learning and contributing to Bioconductor!
Swazi (13:46:38): > @Swazi has joined the channel
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Patricia Brianna (15:12:44): > hello everyone, nice to be here
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OLADIRAN OLUWASHOLA (18:23:56): > Hello everyone, I’m Shola from Nigeria and I just got accepted into the Outreachy Internship May batch. After going through Bioconductor project description, I really want to know more about human microbiome so that we can protect ourselves from future health conditions. I know I’d learn lots of things while doing this internship project. Please how do I get started and know my mentor?
sophy (23:34:29): > @sophy has joined the channel
Busayo Ojo (23:38:54) (in thread): > Welcome Shola, for Outreachy related questions you’re to ask in this channel#outreachyand if you want to work on the microbiome project, you can join this channel#bugsigdbto get started and know your mentors.
sophy (23:50:19): > Hi everyone, my name is sophy, an outreachy applicant interested in the human microbiome projects.
Tsoure (23:57:11): > @Tsoure has joined the channel
2023-03-09
Tsoure (00:05:27): > Hi everyone! I am Tsoure, an Outreachy applicant. I look forward to learning and contributing to this community.
Busayo Ojo (00:44:29) (in thread): > Welcome!
Ukpai Bishop (02:20:46): > @Ukpai Bishop has joined the channel
Hannah Honda (03:03:04): > @Hannah Honda has joined the channel
Chioma Grace (03:59:17): > @Chioma Grace has joined the channel
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Fortune Nnamdi (04:25:23): > Hi everyone, I’m fortune and I’m glad to be here
K Nodia (04:28:38): > Hello Everyone , i m K Nodia Happy to join this community , and Hoping to contribute to my Best and learn from you all
Tsoure (05:04:19) (in thread): > Thank you Busayo!
Tsoure (05:05:04) (in thread): > Welcome Fortune!
Tsoure (05:05:23) (in thread): > Welcome K Nodia!
Fortune Nnamdi (05:08:41) (in thread): > You’re much welcomed.
Fortune Nnamdi (05:09:12) (in thread): > Thanks Tsoure:heavy_heart_exclamation_mark_ornament:
Fortune Nnamdi (05:09:38) (in thread): > Nice to e-meet you, Nodia
K Nodia (08:04:39) (in thread): > Thank you , and Happy to e-meet you:heart:
Bazgha Razi (08:29:34): > @Bazgha Razi has joined the channel
Ukpai Bishop (10:07:34) (in thread): > Hi, you are welcome Fortune
Ukpai Bishop (10:08:09) (in thread): > Hi, you are welcome@K Nodia
Ukpai Bishop (10:08:32) (in thread): > Hi shola you are welcome
Yogita Tufchi (10:15:08): > @Yogita Tufchi has joined the channel
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Aguobi Amara (22:52:18): > @Aguobi Amara has joined the channel
Aguobi Amara (22:57:07): > Hello everyone > My name is Aguobi Amara, pronouns she/Her. > I am an outreachy applicant for May cohort. > I am interested in contributing to bio conductor projects. Excited to be here
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Advit Mittal (23:52:56): > Hello mentors and fellow applicants, Advit Mittal this side, an Outreachy intern. I am interested in contributing to the project “microbiome study curation”, thus I would like to connect with people who are already working on it for further guidance and help. Looking forward to building connections!
2023-03-10
Busayo Samuel (she/her) (00:30:50): > @Busayo Samuel (she/her) has joined the channel
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jnsereko (00:38:38): > Hello, am Jess, an outreachy applicant, so excited to be here. I like the activeness athttps://support.bioconductor.org/
Dilara (03:43:42): > @Dilara has joined the channel
Busayo Samuel (she/her) (03:55:43): > Hello, I’m Busayo. I’m an Outreachy applicant, and I’m looking forward to contributing to this project!!!
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Dennis Ndubi (04:24:26): > Greetings mentors and fellow applicants, Dennis Ndubi here, an Outreachy intern. I am interested in contributing to the project “Optimize microbiome data science framework”, thus I would like to connect with people who are already working on it for further guidance and help. Looking forward to building a great network and community. Thank you.
Dennis Ndubi (04:25:30): > Greetings mentors and fellow applicants, Dennis Ndubi here, an Outreachy intern. I am interested in contributing to the project “Optimize microbiome data science framework”, thus I would like to connect with people who are already working on it for further guidance and help. Looking forward to building a great network and community. Thank you.@Tuomas Borman
K Nodia (04:30:59): > Welcome@Dennis Ndubifirstly join the#miaversechannel and the important thing is that you understand the miaverse and the data container that it is utilizing. To start, there are some exercises and OMA book that you can look at. Those exercises should be on outreachy website. After you have finished those, you can contribute to the packages (information on those is also available on website [hopefully])
Dennis Ndubi (04:34:35): > thank for the insightful information
Busayo Ojo (04:39:21) (in thread): > Hi Busayo welcome:hugging_face:
Busayo Samuel (she/her) (04:40:15) (in thread): > Thank you namesake:hugging_face:
Busayo Ojo (04:41:46) (in thread): > What project are you working on
Busayo Samuel (she/her) (04:43:57) (in thread): > SweaveToRmd… I’m currently going through the instructions on github on to contribute.
Busayo Ojo (04:57:32) (in thread): > Alright B > Welldone!
Chioma Nnadi (08:11:54): > @Chioma Nnadi has joined the channel
Chioma Nnadi (08:29:29): > As a potential Outreachy intern, my name is Chioma Nnadi. I am interested in contributing to the “Microbiome Study Curation” project, so I’d like to connect with those currently involved to get more advice and assistance. Also,@C. Mirzayi (please do not tag this account)and@Fatima ZohraIs it okay if I ask some questions? > I look forward to giving value, building a great network, and learning from the community.
Andres Wokaty (09:04:07) (in thread): > Hi@Chioma Nnadi, consider joining#bugsigdbthe project’s channel to ask questions:slightly_smiling_face:
Chioma Nnadi (09:04:41) (in thread): > Alright. Thank you so much@Andres Wokaty
Aguobi Amara (09:45:27) (in thread): > You are welcome@Chioma NnadiFeel free to ask questions
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2023-03-11
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ezinne (04:55:46): > @ezinne has joined the channel
ezinne (05:00:45): > Hello, i’m Ezinne an outreachy applicant, i am super excited to be here and i look forward to contributing to this project
Harrydas Ombati (05:02:00): > Hello everyone, I’m Harrydas, an Outreachy applicant from Kenya . I am happy to be a part of this community and would love to contribute on your projects with your help.
Jeffery Orazulike (07:16:07): > @Jeffery Orazulike has joined the channel
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MaryJones (09:27:17) (in thread): > @Monalika PatnaikHi, Ok , thanks just saw this now..:pray::+1:
Cindy Apiyo (10:53:14): > @Cindy Apiyo has joined the channel
Emmanuel Taiwo devbird007 (12:32:56): > Hello fellow Outreachy applicants, there are a couple of channels reserved for Outreachy Contributions so you’ll need to join to get updates and more information on how to contribute: > 1. #outreachyis the general outreachy channel > 2. #sweave2rmdis for the “Convert Sweave Vignettes to R Markdown” project. > 3. #bugsigdbis for the “Microbiome Study Curation” project. > 4. #miaverseis for the “Optimize microbiome data science framework” project > I hope this has been helpful. :-)
Andres Wokaty (13:29:23) (in thread): > Thanks for sharing this. The third channel is#miaversefor the “Optimize microbiome data science framework” project.
Emmanuel Taiwo devbird007 (14:24:16) (in thread): > Noted…I’ll edit my message to include it.
2023-03-12
Maryam Gbemisola (06:55:58) (in thread): > Yes@Emmanuel Taiwo devbird007.
Taofeekat Olorunkosebi (20:51:24): > @Taofeekat Olorunkosebi has joined the channel
2023-03-13
Suwaibat Suleiman (03:58:35): > @Suwaibat Suleiman has joined the channel
Emile-Daisy (04:50:53): > @Emile-Daisy has joined the channel
Emile-Daisy (05:39:10): > Hello I am Emile Daisy an Outreachy intern from Cameroon. I am so happy to be here hoping to learn a lot from you and make valuable contributions
Parul Chaddha (08:48:25): > @Parul Chaddha has joined the channel
Parul Chaddha (08:56:10): > Hello I am Parul an outreachy intern from India. Hoping to learn something new and contribute in this project.
Anushka Sharma (16:05:21): > Hello everyone I am Anushka sharma an outreachy applicant from India . I am happy to be a part of this community and looking forward to have a new learning experience. Also I would like to know how to begin with this project as I already requested for the account .kindly guide . > Thank you
Dennis Ndubi (16:27:35): > welcome@Anushka Sharma
Andres Wokaty (16:32:11) (in thread): > Hi, it’s not clear what project you’re working on. Checkhttps://community-bioc.slack.com/archives/C36B0HK7W/p1678555976874649to see what channel might be more appropriate ;) - Attachment: Attachment > Hello fellow Outreachy applicants, there are a couple of channels reserved for Outreachy Contributions so you’ll need to join to get updates and more information on how to contribute: > 1. #outreachy is the general outreachy channel > 2. #sweave2rmd is for the “<https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#convert-sweave-vignettes-to-r-markdown|Convert Sweave Vignettes to R Markdown>” project. > 3. #bugsigdb is for the “<https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|Microbiome Study Curation>” project. > 4. #miaverse is for the “<https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#optimize-microbiome-data-science-framework|Optimize microbiome data science framework>” project > I hope this has been helpful. :-)
Anushka Sharma (17:47:33) (in thread): > Thank you@Andres Wokaty
Taofeekat Olorunkosebi (20:18:43): > Hello everyone, > I’m Taofeekat Olorunkosebi (She/her) from Nigeria, I have a background in software development and I’d like to work on ‘Convert Sweave Vignettes to R Markdown’ project. I’m looking forward to networking with like minds and learn more from the community while making valuable contributions. > > Thank you.
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dherahrose (21:35:52): > Hi everyone my name is Rose, I am here to learn and connect with this amazing community.
2023-03-14
Ibizugbe Merit (01:47:11) (in thread): > You’rewelcome@dherahrose
Joanna Mocko (04:27:18): > @Joanna Mocko has joined the channel
Joanna Mocko (04:32:54): > Hi all, I’m Joanna and I’m Community Manager at Appsilon, happy to be here!
Mugdha Pendse (07:57:57): > @Mugdha Pendse has joined the channel
Elisheba Asiimwe Joanita (09:55:54): > @Elisheba Asiimwe Joanita has joined the channel
Elisheba Asiimwe Joanita (10:12:04): > Hello everyone,my name is Elisheba Asiimwe, an outreachy applicant from Uganda. I am happy to be here and connect with you all
Ibizugbe Merit (10:21:55) (in thread): > You’rewelcome@Elisheba Asiimwe Joanita
Juanjuan Song (11:02:10): > @Juanjuan Song has joined the channel
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2023-03-15
Patricia Brianna (04:23:07): > hello friends
Patricia Brianna (04:23:34): > @C. Mirzayi (please do not tag this account), how good is this curation
Patricia Brianna (04:23:45): > https://bugsigdb.org/Study_751 - Attachment (BugSigDB): Study 751
Patricia Brianna (04:24:01): > waiting for your response
Patricia Brianna (04:24:07): > thanks
Patricia Brianna (04:26:18): > @Fatima Zohra, kindly requesting for your say on thishttps://bugsigdb.org/Study_739 - Attachment (BugSigDB): Study 739
Patricia Brianna (04:26:31): > thanks a lot
Andres Wokaty (08:19:15) (in thread): > I recommend asking this on the#bugsigdb
Patricia Brianna (08:40:20) (in thread): > so sorry please,
Patricia Brianna (08:40:29) (in thread): > thanks for the reminder
Rishi Singh (08:42:49): > @Rishi Singh has joined the channel
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Joaquin Reyna (13:33:59): > Hi! My name is Joaquin and I am part of the nipalsMCIA team where we are trying to push our package to decompose multimodal data. The team is actually remote so we are all over the place but I’m personally in San Diego (CA), working on my PhD and several projects. Nice to meet you all and to join the Bioconductor Slack:slightly_smiling_face::r:.
Enis Afgan (13:44:32): > @Enis Afgan has joined the channel
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2023-03-16
pande.erawijantari (05:04:33): > @pande.erawijantari has joined the channel
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Queen Anthony (16:26:06): > Hello everyone, I’m Queen Anthony an outreachy applicant from Nigeria. I’m happy to be part of this community and I look forward to working with all of you and learning more
Ibizugbe Merit (16:59:43) (in thread): > You’rewelcome@Queen Anthony
Queen Anthony (17:01:50) (in thread): > Thank you so much
Beekaz (17:02:04): > @Beekaz has joined the channel
Ibizugbe Merit (17:06:26) (in thread): > You can go through@C. Mirzayi (please do not tag this account)pinned message to get started
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2023-03-29
Matteo Tiberti (10:05:17): > hi, I’m Matteo, staff scientist at the Danish Cancer Society. We are about to submit one (or two, if we make it!) package for evaluation for the inclusion in BioC, so I thought I’d say hello. From the BioC GitHub I understand there might be a specific channel for that? Thank you and happy computing everyone!:computer:
Lori Shepherd (10:08:17) (in thread): > BioC GitHub? If you mean package development and potential access I would recommend the#developers-forum,#bioc_git,#bioc-buildsand potentially#github-actionscheers
Matteo Tiberti (10:11:09) (in thread): > sorry - I mean, from the template text for the submission in the Contributions GitHub repohttps://github.com/Bioconductor/Contributions/issues/new- “please use the#package-submissionchannel of our Community Slack”. Thank you, I’ll try join those as well!
Lori Shepherd (10:11:55) (in thread): > ah yes. well glad to have you apart of the community:slightly_smiling_face:
Matteo Tiberti (10:20:53) (in thread): > thank you! Happy to be here:smile:
2023-03-30
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2023-03-31
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2023-05-04
Franck RICHARD (05:43:19): > Hello, > > I have participated in several collaborations in astrophysics and particle physics. I also offer an astronomy program on the web:winstars.net/enI had the opportunity to follow closely the activities of a neuroscience group in Madrid. This was the opportunity for me to discover Bioconductor. Today I would like to contribute, as far as possible, to this beautiful project….
Maria Doyle (06:00:51) (in thread): > Thats’s great to hear, welcome!
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2023-05-11
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Gamal Akabani (01:33:46): > Hello, my name is Gamal Akabani, and I am a novice on Bioconductor. I’m looking forward to working together in the area of spatial biology.
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Louis Le Nézet (03:28:09): > Hi everyone ! > My name is Louis Le Nézet and I’m working in genetic. I’ve never contribute before to Bioconductor but I motivated to do so. > I have one package that was on Cran, that could be of interest on Bioconductor (kinship2: pedigree functions). I’m also part of a group where we develop shiny modules that we would like to share as a bioconductor package. > What would be the best course of action ?
Lori Shepherd (07:30:02) (in thread): > There are a few difference from CRAN to Bioconductor –http://contributions.bioconductor.org/has a full run down but careful attention to the first few sections on “General BIoconductor Package Development” and “Important Bioconductor Package Development Features” –@Aedin Culhaneis there going to be another round of the mentorship program as that might also be a good experience if you already have the basics of packages set to go
Louis Le Nézet (08:29:58) (in thread): > I would be really interested in a mentorship program. > I have the some basics knowledge on packages but I would really appreciate some guidance.
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Shivang Bhanushali (08:18:20): > Hello ! My name is Shivang Bhanushali, I have started my PhD studies at the University of Turku, Finland. I am interested in exploring Bioconductor for understanding antimicrobial resistance in gut microbiome! Happy to connect with everyone!!:slightly_smiling_face:
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2023-07-11
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2023-07-12
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Vivek Sharma (16:11:59): > Hi,
Vivek Sharma (16:12:26): > My name is vivek and I have just started on using Bioconductor. Hope to learn from the group
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2023-07-13
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2023-07-17
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Physalia-courses (06:27:08): > Hi all, we arePhysalia, a platform that specializes in providing high-quality training in Genomics, Bioinformatics, statistics and related disciplines. These courses are conducted by renowned experts and cover a wide range of topics, and our aim is to empower researchers with the tools and techniques necessary to excel in their respective fields. Nice to meet you all:wave:
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2023-07-26
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2023-07-27
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2023-07-28
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2023-07-29
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Izabela Mamede (16:15:23): > Hello everyone! > My name is Izabela, I am a PhD Student at the Federal University of Minas Gerais (UFMG) in Brazil. My biggest interest is how alternative splicing plays a role in mammalian differential expression results. I will be in person at Boston presenting a package demo on the end of the last day of BioC2023. Happy to connect and come to talk with me in person!
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2023-07-31
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2023-08-01
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Esther Camacho (01:53:32): > Hi everyone! My name is Esther and I work as a bioinformatics technician at VHIR in Barcelona. I believe this conference will be a great opportunity to broaden my knowledge and to do net-working. Nice to meet you!
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Mohamed S.AboHoussien (11:35:35): > Hello everyone nice to meet you all > My name is Mohamed Said Ahmed AboHussien, and I am very interested in becoming involved in research in the Metagenomics field. I have aBSc.inGenetics Agriculture College Al-Azhar University > I have taken the following courses related to Metagenomics : > I studied > 1. QIIME 2 Cancer Microbiome Intervention Tutorial > 2. Fecal microbiota transplant (FMT) study > 3.“Moving Pictures” tutorial - Multiple Interface Edition > 4.“Atacama soil microbiome” tutorial > 5. Parkinson’s Mouse Tutorial > 6. Differential abundance analysis with Gneiss > For all of the above, I used the Qiime2 command line interface (Bash) > Galaxy pipelines and workflows like > 1. Metagenomics data analyses > 2. Metatranscriptomics analysis > 3. Amplicon 16srRNA data analysis > 4. Shotgun metagenomics > 5. Taxonomic profiling and Visualization for Meta-genomics data. > 6. Assembly of Metagenomics sequence data > > I participated in three internships related to the Bioinformatics > 1.Galaxy Training Network GTN Smörgåsbord 3 > 2. Hack Bio Internship > 3.H3ABioNet Internship > > I have the following related experience > • Metatranscriptomics analysis using microbiome RNA-seq data > • Amplicon 16srRNA data analysis and visualization > • 16S Microbial Analysis with Mothur (short) > • AMR Antibiotic resistance detection > • Pathogen detection from (direct Nanopore) sequencing data using Galaxy –Foodborne Edition > • Taxonomic profiling and Visualization for Meta-genomics data > • Assembly of Metagenomics sequence data > • SARS_cov2 variant analysis > • Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India > • Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data > • imported: Processed Indian, Sweden Datasets: Taxonomic classification and extraction of functional information
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2023-08-02
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Erinn Dady (08:28:12): > Hello everyone! My name is Erinn Dady, I am a graduate student at University of Illinois Urbana-Champaign, studying plant-insect interactions in tomato and maize. > > I am a former chef, so I love working with crops and farmers, excited to approach food from a new angle!
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2023-08-28
Mikaila Chetty (07:42:43): > Hi all! I’m Mikaila and work as a researcher/PhD candidate. I work on C. elegan model organism (everything from locomotion, behavior, oxidative stress, mitochondria assays, protein assays, transriptomics and molecular docking are all my kind of thing). My long term goals are to focus on Aging & Alzheimer’s in the biotech/pharma industry. I am looking forward to connecting with everyone. Also - all guidance and tips on the industry & career development are welcome :) > > Feel free to connect with me here: > • Twitter (https://twitter.com/mikaila_chetty_) > • LinkedIn (https://www.linkedin.com/in/mikailachetty/)
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2023-08-30
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2023-08-31
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2023-09-04
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2023-09-05
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2023-09-12
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2023-09-13
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2023-09-22
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Brad Hall (05:59:25): > Hey Bioconductor community:wave:My name is Brad and I’m a full stack software engineerthat’slooking to make contributions to open source genomics software such as Bioconductor. > > My website:bradhall.ioMy LinkedIn:https://linkedin.com/in/c-b-h
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2023-09-24
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2023-09-29
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2023-09-30
Victoria Nduka (12:16:48): > @Victoria Nduka has joined the channel
Victoria Nduka (12:19:31): > Hi everyone.I’mVictoria andI’ma graduate of Chemical Engineering and a UI/UX designer.I’mexcited to be a part of this community and I look forward to making meaningful contributions
2023-10-02
myles (12:26:43): > @myles has joined the channel
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Peace Sandy (12:37:21): > @Peace Sandy has joined the channel
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Chinwendu Enyinna (12:45:34): > @Chinwendu Enyinna has joined the channel
Chinwendu Enyinna (13:14:39): > Hello everyone, I’m Chinwendu, a software developer with a background in Applied Biochemistry. I was looking for an open-source project that intersected with life sciences, and I was excited to discover the Bioconductor repository on GitHub. This is an exciting opportunity for me, and I look forward to making significant contributions. > > Here are my socials. I’d love to connect with you
https://www.linkedin.com/in/enyinna-chinwendu-promise/
Faizah Salami (13:24:35): > @Faizah Salami has joined the channel
Faizah Salami (13:27:58): > Hi everyone. My name is Faizah Salami from Nigeria. I am Physiology graduate and a Software Quality Assurance Engineer. I am excited to contribute to the Microbiome Study Curation project, and I look forward to working with other applicants on the project.
Aleru Divine (13:30:34): > @Aleru Divine has joined the channel
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Onalo Deborah (13:49:40): > Hi everyone, hope you’re having a great day. I’m Deborah, a product designer, researcher and with a strong background in pharmaceutical science.I am super excited to be here and to contribute to the Microbiome Study Curation project as an outreachy intern as I had an interest in contributing to a life science open source project.I’m looking forward to making significant contributions to the project and working with mentors and other applicants.Let’s connect:https://www.instagram.com/designwithdebbs
Joan C. Chukwuemeka (14:34:30): > @Joan C. Chukwuemeka has joined the channel
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Sabastine Iroka (17:29:05): > Hello everyone, > I’m Sabastine Iroka, a content writer with a background in biochemistry. > I’m glad to contribute to the Microbiome Study Curation project as an outreachy intern. > > I can’t wait to connect and contribute with other interns and mentors.:fire:
Kehinde Adebisi (17:55:57): > @Kehinde Adebisi has joined the channel
Kehinde Adebisi (18:03:47): > Hi everyone! > I’m Kehinde Adebisi, an Outreachy Applicant, a Researcher and a Data Analyst. I’m excited to be here! > I look forward to learning from and contributing to the BugSigDB Project > > Happy to meet you all:hugging_face:
Earl-Millen Toh Akwe (18:26:07): > @Earl-Millen Toh Akwe has joined the channel
Earl-Millen Toh Akwe (18:37:57): > Hello everyone:hugging_face:My name is Earl-Millen, an outreachy applicant. > I am so excited to be here and to contribute to the BugSigDB project. > Looking forward to having a great time with you all while getting to know you better while making the project a big success.Thank you:hugging_face:
Mary Ikott (19:44:54): > @Mary Ikott has joined the channel
2023-10-03
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Kabirat Adeniyi (01:34:53): > Hello, I’m Kabirat Adeniyi, a data scientist and an outreach applicant with a background in microbiology. I’m glad to be part of the Bioconductor community and I look for forward to contributing to the Microbiome Study curation project .
Chinecherem Joy (02:34:21): > @Chinecherem Joy has joined the channel
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Thara Ehizogie (03:52:28): > Hello Everyone,My name is Thara and i am a content writer and biochemist.I am so happy to be here and i am looking forward to connecting with more people with shared interests. Most importantly,i look forward to learning and contributing to this project.Thank you so much for this opportunity
Paulina Boadiwaa Mensah (04:46:01): > @Paulina Boadiwaa Mensah has joined the channel
Paulina Boadiwaa Mensah (04:48:00): > Hello everyone! I’m Paulina, a data analyst and medical doctor. I’m thrilled to work together to add value to this Outreachy project!
Scholastica Urua (04:51:34): > @Scholastica Urua has joined the channel
Scholastica Urua (05:03:20): > Hello everyone! > > I’m Scholastica Urua, an Outreachy applicant. I’m a Pharmacist and a Data Analyst. I am excited to be here and really looking forward to contributing to the Microbiome Study Curation project as well as working with other applicants.
cynthia (05:04:02): > @cynthia has joined the channel
Kehinde Adebisi (05:22:38) (in thread): > Welcome Scholastica
Chioma Onyido (06:06:04): > @Chioma Onyido has joined the channel
Hans-Rudolf Hotz (07:04:49): > @Hans-Rudolf Hotz has left the channel
Chioma Onyido (09:23:30): > Hi all, I’m Chioma Blessing, an outreachy applicant. I’m an Academic researcher with a special interest in Cancer and Malaria research. Delving into literature review and health research has been a thrilling adventure throughout my career, and I was excited (and curious) when I came across the Microbiome project. > I eagerly anticipate contributing and connecting with mentors and fellow interns. > My linkedIn is:https://www.linkedin.com/in/chioma-onyido/
kan (09:42:32): > @kan has joined the channel
kan (09:51:35): > Hello all, i am so exited to finally be here. I am Ngum Kan for the outreachy December internship contribution phase. I am looking forward to learning and working together with everyone for the next few week.
Esther Afuape (09:58:11): > @Esther Afuape has joined the channel
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Nwajei Edgar (10:59:55): > Hello everyone, I’m Nwajei Edgar, an Outreachy applicant. I am a Frontend developer and a Technical writer with a background in Biochemistry. Exited to be here, and I look forward to working with others to contribute to this project. Thank you for the opportunity.
Temabo Omame (11:03:36): > @Temabo Omame has joined the channel
Temabo Omame (11:05:46): > Hello everyone!I’mTemabo, an Outreachy application. I am a UI/UX Designer.I’mlooking forward to collaborating and learning in the space!
Chloe (11:36:29): > @Chloe has joined the channel
Chloe (11:42:46): > Hello everyone. I am Chloe Nabachwa from Uganda and an outreachy applicate. I am a UI/UX designer though am so interesting in data analysis. Am really so glad to be here , I eager to learn new things and share what I know.
Ugoo-Okonkwo Stella Ozioma (12:04:33): > @Ugoo-Okonkwo Stella Ozioma has joined the channel
Cynthia (12:15:06): > @Cynthia has joined the channel
Cynthia (12:19:23): > Hello everyone! My name is Cynthia, an Outreachy Applicant. Excited to be here.
Chidimma Blessing Onuora (12:25:00): > @Chidimma Blessing Onuora has joined the channel
Chidimma Blessing Onuora (12:31:42): > Good evening everyone. I’m Chidimma. Happy to be here. I look forward to contributing to this project with my knowledge as a Biochemist and Tech enthusiast.
Ugoo-Okonkwo Stella Ozioma (12:37:06): > Helloeveryone, my name is Stella, am happy to be here
Ugoo-Okonkwo Stella Ozioma (12:40:03) (in thread): > Welcome Cynthia, I am also an applicant nice having you here
Cynthia (12:56:46) (in thread): > Thank you:hugging_face:Stella. It’s a pleasure
Ayowale Ojo (13:20:03): > @Ayowale Ojo has joined the channel
Aminat Odedeyi (13:52:54): > @Aminat Odedeyi has joined the channel
Aminat Odedeyi (14:00:59): > Hi everyone. I’m Aminat, an Outreachy Applicant and I’m very excited to be here. Looking forward to connecting, learning and contributing to the community.
Karen254. Kingecha (14:14:51): > @Karen254. Kingecha has joined the channel
Chidimma Blessing Onuora (14:46:07) (in thread): > Welcome
Isoken Ibizugbe (16:18:32): > @Isoken Ibizugbe has joined the channel
Isoken Ibizugbe (16:25:12): > Hello, everyone, my name is Isoken and Im an outreach applicant. I am excited to contribute to the microbiome study curation
Chioma Onyido (16:29:48) (in thread): > Hi Isoken,you’rewelcome!
Ayomide Solarin (17:14:05): > @Ayomide Solarin has joined the channel
Odigiri Great Alume (18:04:52): > @Odigiri Great Alume has joined the channel
Shakira Ndagire (18:50:10): > @Shakira Ndagire has joined the channel
Shakira Ndagire (18:52:59): > Hello all, I am Ndagire Shakira Seruwagi from Uganda. I am an Outreachy applicant and looking forward to contributing to the Bioconductor Microbiome Study Curation
Chidimma Blessing Onuora (21:09:03) (in thread): > Nice to have you here
Albert Han (21:10:47): > @Albert Han has joined the channel
Quinuel Ndip-Agbor (21:38:15): > @Quinuel Ndip-Agbor has joined the channel
Quinuel Ndip-Agbor (21:41:00): > Hello everyone, I am Quinuel Ndip-Agbor from Cameroon . I look forward to contributing to Bioconductor and learning in the process, thanks.
2023-10-04
Nwajei Edgar (02:23:29) (in thread): > Welcome Quinuel, nice to have you here:innocent::innocent:
Shakira Ndagire (02:33:37) (in thread): > It is great to be here
Odigiri Great Alume (02:40:07) (in thread): > Welcome Quinuel, it’s a pleasure having you here.
Odigiri Great Alume (02:40:28) (in thread): > Welcome Shakira.
Odigiri Great Alume (02:41:03) (in thread): > Nice to have you here Isoken
Odigiri Great Alume (02:41:33) (in thread): > Hi Aminat, you are welcome
Gavin Rhys Lloyd (03:18:12): > @Gavin Rhys Lloyd has left the channel
Eric Kyalo (03:53:22): > @Eric Kyalo has joined the channel
Maryam Gbemisola (03:57:13): > Welcome@Eric Kyalo
Wangui Thuo (04:01:44): > @Wangui Thuo has joined the channel
edilawit (04:06:53): > @edilawit has joined the channel
Chiagoziem David (04:10:22): > @Chiagoziem David has joined the channel
Wangui Thuo (04:12:10): > Hey everyone, > I’m Wangui Thuo, an Outreachy applicant, a researcher and a data scientist. > So excited to be here and can’t wait to interact and learn from you all, while contributing to the BugSigDB Project > > Happy to meet you all:relaxed:.
Omoyeme Sim-Okoduwa (05:32:29): > @Omoyeme Sim-Okoduwa has joined the channel
Omoyeme Sim-Okoduwa (05:36:39): > Hello everyone,I’mOmoyeme Sim-Okoduwa from Nigeria, looking forward to contributing, learning and connecting with you all
Maryam Gbemisola (05:38:14) (in thread): > Welcome
Maryam Gbemisola (05:39:37) (in thread): > Welcome Omoyeme
Wangui Thuo (05:41:08) (in thread): > Thank you Maryam:slightly_smiling_face:
Omoyeme Sim-Okoduwa (06:10:06) (in thread): > Hi Maryam,it’snice to meet you,I’mstill trying to get a hang of slack and the group
Shakira Ndagire (06:52:18) (in thread): > Thank you Odigiri
Iram Jamshed (07:13:23): > @Iram Jamshed has joined the channel
Maryam Gbemisola (07:25:35) (in thread): > Kindly let me know if you have any challenge and I will be happy to help
Maryam Gbemisola (07:25:59): > Welcome@Iram Jamshed
Ajoke Yusuf (07:26:13): > @Ajoke Yusuf has joined the channel
Ajoke Yusuf (07:28:33): > Hello everyone, I’m Ajoke Yusuf, an Outreachy applicant, an avid researcher, and a data analyst. I am excited to be here. I’m looking forward to learning and doing my best to the success of this project. I hope to make an impressive impact in this community
Kehinde Adebisi (07:28:57) (in thread): > You’re welcome Ajoke
Ajoke Yusuf (07:29:19) (in thread): > Welcome@Quinuel Ndip-Agbor. It’s amazing having your here
Ajoke Yusuf (07:29:34) (in thread): > Thank you@Kehinde Adebisi
Quinuel Ndip-Agbor (07:41:59) (in thread): > Thanks so much everyone for the warm welcome:blush:
Shakira Ndagire (07:45:51) (in thread): > Welcome@Ajoke Yusuf
Yigakpoa Ikpae (08:40:09): > @Yigakpoa Ikpae has joined the channel
Romane Libouban (08:40:43): > @Romane Libouban has joined the channel
Khalidat Ola-Dauda (08:50:35): > @Khalidat Ola-Dauda has joined the channel
Peace Sandy (08:53:16): > Welcome Outreachy Applicant ! > Kindly join the#bugsigdbchannel to get started and get more information on how to go about your task.
Olajumoke Adeoyo (09:05:06): > @Olajumoke Adeoyo has joined the channel
Khalidat Ola-Dauda (09:06:49): > Hello Bioconductor community, it’s great to be here!:smile:I’m Khalidat Ola-dauda, a pharmacist and a product manager excited about contributing to the Bioconductor Microbiome Study curation as an Outreachy applicant. > > Looking forward to interacting with other applicants and the team:blush:
Nwajei Edgar (09:13:55) (in thread): > Welcome friend
Nwajei Edgar (09:14:22) (in thread): > If you need any help, ask so others can assist you…:innocent::innocent:
Chioma Onyido (09:16:00) (in thread): > Welcome to the community, Khalidat.
Khalidat Ola-Dauda (09:17:06) (in thread): > Thank you!
Zaha (09:21:22): > @Zaha has joined the channel
Peace Sandy (09:40:37) (in thread): > Welcome:pray:
Heran Ephraim (10:02:35): > @Heran Ephraim has joined the channel
Onalo Deborah (10:14:02) (in thread): > Welcome Woman of honor. Excited to have you here:wave::wave:
Greatman Ugorji (10:18:30): > @Greatman Ugorji has joined the channel
Greatman Ugorji (10:23:06): > Hello everyone. I’m Greatman Ugorji. A technical writer and front-end developer. > Looking forward to contributing and networking with you all:blush:
Khadija (10:24:16): > @Khadija has joined the channel
Nwajei Edgar (10:27:48) (in thread): > Welcome Greatman, nice to have you here… > > You can start here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.
Nwajei Edgar (10:28:13) (in thread): > If you need any help, do well to ask so others can assist:innocent::innocent:
Chioma Onyido (10:29:21) (in thread): > Welcome to the community, Greatman!
Greatman Ugorji (10:32:31) (in thread): > Thank you,@Nwajei Edgarand@Chioma Onyido:blush:
Dimitri Meistermann (11:26:22): > @Dimitri Meistermann has joined the channel
Dimitri Meistermann (11:32:43): > Hello there! > I am Dimitri, Postdoc/computational biologist. > I am developing for a long time now several projects that are close to be R packages that would fit in Bioconductor. I seek help for finishing my first package submission and I wish to help who I will be able to help!
Nwajei Edgar (11:35:37) (in thread): > Welcome friend:innocent::innocent:
Nwajei Edgar (11:36:55) (in thread): > You can start here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.
Greatman Ugorji (11:37:19) (in thread): > Welcome mate@Dimitri Meistermann
Odigiri Great Alume (11:49:29): > With the help and coaching of@Chioma OnyidoI was able to make my first contribution. Thank you for your patience. Now I feel confident to lend a helping hand to anyone who is confused on how to start with their first contribution.:blush:Please don’t be shy to reach out.
Chioma Onyido (11:52:46) (in thread): > Glad I could help, Great.:sweat_smile:
Dimitri Meistermann (12:02:30) (in thread): > Thanks for the welcome:blush:
Iram Jamshed (12:14:24) (in thread): > Thank you so much!
Nwajei Edgar (12:24:12) (in thread): > Nice….. now we have to help others:hugging_face::hugging_face:
Tolulope Ogunleye (14:03:33): > @Tolulope Ogunleye has joined the channel
Onalo Deborah (14:20:14) (in thread): > Well done@Chioma OnyidoYou’re doing great
Chioma Onyido (14:22:37) (in thread): > Thank you Deborah,:hugging_face:Really love the atmosphere in this community,everybody’swilling to help.
Odigiri Great Alume (14:37:18): > @Iram JamshedOnce you have identified the condition of study ( You can do that by reading the title of the annotated pdf) and going through the PDF to get context), for instance, if Breast Cancer is your disease of interest, the next thing is to search for it using the link provided on the survey. A list of other articles will pop. Merely looking at the titles of the articles, you can tell which one is closest to the article in the annotated pdf. That’s the one you choose. Then Fill in the information required of you. > > I hope this helps.@Iram Jamshed
Nwajei Edgar (14:53:58) (in thread): > Collaborative environment . I love it
Iram Jamshed (14:54:50) (in thread): > Yeah, I understood. Actually the site was not responding at that time that’s why I was not able to see the results. Thanks for your response.
Odigiri Great Alume (15:15:31) (in thread): > Anytime bro
Onyewuchi Esther Chikamso (15:16:35): > @Onyewuchi Esther Chikamso has joined the channel
Onyewuchi Esther Chikamso (15:31:51): > Hello everyone! > I’m Kamso, an outreachy applicant from Nigeria. I am so excited to be here! I look forward to learning, collaborating and contributing to the project:innocent::innocent:
Odigiri Great Alume (15:39:49): > Please if you are done with your first contribution, I want to ask please. > Do we get to record our first contribution before moving to the second? If yes…. > And how do we record it?
> > Please I need help
Odigiri Great Alume (15:40:25) (in thread): > Welcome:hugging_face:to the team
Chioma Onyido (15:48:45) (in thread): > Do you mean on Outreachy? > > You can document in your outreachy contributions that you completed the first contribution and either include a link to the survey or the GitHub issue talking about the first contribution.
Robert Phillips (15:50:59): > @Robert Phillips has left the channel
Odigiri Great Alume (15:51:33) (in thread): > Yes please, on outreachy. > Whats a github issue please and also, do you mean the survey I completed? And how do I get the link.
Chioma Onyido (15:53:01) (in thread): > Here’s the link:https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey
Odigiri Great Alume (15:54:04) (in thread): > Going through it now dear. Thanks:blush:for now
Chioma Onyido (15:57:01) (in thread): > That is the link to the survey > > The link to record your Outreachy contribution is different:https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation/contributions/add/For clarity, See@Chloedetailed response here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436532427109?thread_ts=1696412338.491489&channel=C04RATV9VCY&message_ts=1696436532.427109 - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website! - Attachment: Attachment > @Karen254. Kingecha You can just use this URL to document your contribution on outreachy: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu. We will know which survey response is yours.
Odigiri Great Alume (15:57:07) (in thread): > I already completed the survey. What I mean is how to record it on outreachy
Odigiri Great Alume (15:57:24) (in thread): > I’m sorry I’m a bit confused:confused:
Chioma Onyido (16:05:43) (in thread): > Have you been able to add your contribution now?
Odigiri Great Alume (16:07:35) (in thread): > On it ma’am > Thank you
Odigiri Great Alume (16:37:54) (in thread): > I have recorded my first contribution. > Thank you so much.
Lluís Revilla (16:44:37) (in thread): > Welcome, I usually don’t have much time, but I may be able to help. What are those packages about? What are your questions/doubts?
Odigiri Great Alume (16:47:20): > I’m done with recording my first contribution.:sweat_drops::sweat_smile:So how do I start my second contribution please?:pray:
Chioma Onyido (16:59:37) (in thread): > Hi Great, happy about your progress.github.com/waldronlab/BugSigDBcuration/issuesGo through the list of articles, Introduce yourself and request to claim an article (make sure it’s not been claimed already:sweat_smile:).
Odigiri Great Alume (17:00:12) (in thread): > On it maam
Chioma Onyido (17:02:24) (in thread): > Subsequently, you could look throughBugSigDBchannel. Some of the questions have already been answered by the mentors.
Shashank RM (20:10:56): > @Shashank RM has joined the channel
2023-10-05
Umjovial (02:27:25): > @Umjovial has joined the channel
Onyewuchi Esther Chikamso (03:09:00) (in thread): > Thank you
Bonheur (07:24:26): > @Bonheur has joined the channel
Spyke Lionel (08:15:03): > @Spyke Lionel has joined the channel
Spyke Lionel (08:19:35): > Hi, I am Ndi Lionel. A preselected Outreachy intern. I am excited to be here and contribute to the Bioconductor community.
Jonathan Nutsugah (08:33:24): > @Jonathan Nutsugah has joined the channel
Kabirat Adeniyi (09:49:53): > please can anyone assist me on the page with the step by step guide on how to perform the first and second tasks?
Lluís Revilla (10:07:55) (in thread): > Which task are you referring to? If this is something about outreach, mabye this message will help you:https://community-bioc.slack.com/archives/C36B0HK7W/p1696453177309319?thread_ts=1696452440.802139&cid=C36B0HK7W - Attachment: Attachment > Hi Great, happy about your progress. > > github.com/waldronlab/BugSigDBcuration/issues > > Go through the list of articles, Introduce yourself and request to claim an article (make sure it’s not been claimed already :sweat_smile: ).
Kabirat Adeniyi (10:08:35) (in thread): > Thank you very much, my questions have been answered.
Andres Wokaty (10:40:02): > Welcome Outreachy applicants. Please join the#bugsigdbchannel for Microbiome Study Curation-specific discussions.
Aishat Adebayo (11:20:59): > @Aishat Adebayo has joined the channel
Aishat Adebayo (11:23:02): > Hello everyone, my name is Aisha from outreachy, a pure and applied Biology degree holder with Frontend development skills. I look forward to contributing to projects:blush:.
James Hennessy (11:25:03): > @James Hennessy has joined the channel
Chika Nwachukwu (11:54:57): > @Chika Nwachukwu has joined the channel
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Nana Fidausi Mohammed (14:13:38): > @Nana Fidausi Mohammed has joined the channel
Chika Nwachukwu (15:28:08): > Hello everyone, > My name is Chika Nwachukwu, I materials engineer and a data analyst. I am glad to be among your midst. I am very eager to contribute.
Odigiri Great Alume (16:40:14) (in thread): > Welcome here. Don’t hesitate to reach out if you need a guide. It’s a pleasure having you
Chika Nwachukwu (16:41:00) (in thread): > Thank you
Anirudh (18:21:51): > @Anirudh has joined the channel
2023-10-06
Dimitri Meistermann (01:33:10) (in thread): > My first submission, a package named “markergrid”, is close to be ready. I just have a slight conflict between biocheck and roxygen that creates a file named R/markergrid-package.R and man/markergrid-package.Rd. As I understand those are created to manage namespace and create a global manpage to the package. My problem is that biocheck require that 80% of manpages should have a runnable example, and as the package is very small I have only one manpage for my function, so only 50% of .Rd files have examples. But man/markergrid-package.Rd doesn’t contain any function so it doesn’t make sense to me to include runnable examples. > > I’m not sure that introductions thread is the right place to ask, so I can move my question elsewhere.
Dimitri Meistermann (01:33:30) (in thread): > And thank you for proposing your help:slightly_smiling_face:
Maryam Gbemisola (02:12:09) (in thread): > Welcome Chika
Ayesha Younas (03:10:42): > Hey everyone, > I’m Ayesha Younas, an outreach applicant who’s really excited to be a part of this Community! I have strong foundation in AI/ML but relatively new to open source. looking forward to collaborate and learn from you all.
Taiwo Adeyombo (03:17:28): > @Taiwo Adeyombo has joined the channel
Taiwo Adeyombo (03:27:01): > Hello everyone, I’m Taiwo Adeyombo, and I’m an outreachy applicant. I’m eager to collaborate on exciting projects, contribute my skills, and, most importantly, continue learning and growing within this wonderful community.
Lluís Revilla (03:46:37) (in thread): > Probably the best way is in slack are the channels#developers-forumor#developers-mentorship. But you could also use the bioc-devel mailing list, but for this short question I can answer here, and if you have more doubts you can ask somewhere else
Lluís Revilla (03:47:17) (in thread): > The namespace of the package is controlled by the file NAMESPACE. It is based on the#' @exporttags you use. > Yes, usually help pages for the package do not include examples. This can be explained to the reviewer and I’m sure they will understand. However, it is not normal for a package to have just a single function.
Odigiri Great Alume (04:04:20) (in thread): > Welcome to the Bioconductor
Odigiri Great Alume (04:04:21) (in thread): > Welcome Taiwo
Hodan Abdirisak (04:11:59): > @Hodan Abdirisak has joined the channel
Hodan Abdirisak (04:27:09): > A Warm Hello to the Bioconductor Community! > > My name is Hodan Abdirasak and I from Somalia. > I am honored to be part of this esteemed program as an Outreachy intern. I learned veterinary medicine in my first degree with years of experience, with a strong interest in research and passion with IT related programs. > The prospect of contributing to open source projects and collaborating with experts in the field is incredibly exciting to me. I am excited to connect with all of you, learn from your experiences, and engage in meaningful discussions > Thank you all for your warm welcome, and I look forward to embarking on this enriching journey together
Taiwo Adeyombo (05:09:10) (in thread): > Thank you:blush:
Chioma Obioha (06:20:13): > @Chioma Obioha has joined the channel
Chisom Obidike (06:40:27): > @Chisom Obidike has joined the channel
Hodan Abdirisak (07:59:12) (in thread): > I hope you will make significant contributions and go forward to your career development
Sara Mohammed (08:02:09): > @Sara Mohammed has joined the channel
Romane Libouban (11:00:36): > Hello everyone, my name is Romane Libouban. I’m working on integrating and updating tools and workflows forGalaxy.fr. I was at the european galaxy days and followed Maria’s presentation. It would be a pleasure to learn more about Bioconductor and the community.:blush:
Hodan Abdirisak (11:15:38) (in thread): > @Romane Liboubanwarm welcoming:pray::tada:
Hodan Abdirisak (11:41:17) (in thread): > @Romane Liboubanplease Join to#bugsigdbchannel to start the tasks
Andrew Ghazi (12:16:58): > @Andrew Ghazi has left the channel
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Odigiri Great Alume (15:57:28): > Good evening guys. > Please I need assistance with a question > > In the study I’m curating, the study design is “Prospective single-centred cohort study” > > Now, while trying to fill it in, I only found in the drop down options “prospective cohort study” > > Should I choose the option in the drop down or, type in the study design as stated by the article I’m curating?
Onyewuchi Esther Chikamso (15:59:35) (in thread): > I think you should choose “prospective cohort study” from the drop-down menu as it closely aligns with the stated study design.
Odigiri Great Alume (15:59:58) (in thread): > Thank you so much.
Sophie Sorenson (16:02:42): > @Sophie Sorenson has joined the channel
Onyewuchi Esther Chikamso (16:03:46) (in thread): > Please for the recording first contribution, what can I put as description?
Liliana Garmendia (16:04:48): > Hello everyone, > I’m Liliana, a biochemist from Chile transitioning into data science. I’m an outreachy applicant, excited to contribute and learn within this community. > Best regards, Liliana
Odigiri Great Alume (16:05:55) (in thread): > I carried out a mini curation by studying the annotated pdf provided and providing answers to complete the survey that followed
Onyewuchi Esther Chikamso (16:06:18) (in thread): > Thank you
Odigiri Great Alume (16:06:24) (in thread): > You can rewrite in your own terms
Odigiri Great Alume (16:06:32) (in thread): > You are welcome dear
Sophie Sorenson (16:21:39): > Hi everyone. I’m Sophie, a recent psych and math major with minors in computer science and biology and an interest in computational biology and machine learning. I’m an outreachy applicant, and have been looking at the various programs to figure out what I would be best at and hopefully contribute well and fully to this project. I’ve not worked on open source before, and I am definitely a bit intimidated and anxious about this opportunity
Chioma Onyido (17:49:36) (in thread): > Welcome@Sophie Sorenson:hugging_face:It was kind of overwhelming for me too at first but I’ve only been here for about 3 days and I find the community warm and the projects exciting. > > Kindly go through the pinned chats to get tips on how to start with your contributions. The mentors@Levi Waldron@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovicare here if you need help and yeah, some of your fellow interns too.:hugging_face:
Shriya Kamat Tarcar (17:52:52): > @Shriya Kamat Tarcar has joined the channel
Levi Waldron (18:41:42) (in thread): > Welcome@Sophie Sorenson, thank you for your interest in this project!And thank you@Chioma Onyidofor your help and kind words:blush:I hope this will soon feel like your projects too after you have contributed.
Odigiri Great Alume (18:45:24) (in thread): > Don’t worry, you will be fine. Everyone assists here
Levi Waldron (18:46:42) (in thread): > Welcome@Liliana Garmendia!We’revery glad to have you here.
2023-10-07
Hodan Abdirisak (00:30:14) (in thread): > Warm welcoming,@Sophie Sorensonyour contribution will be easy and smoothly follow this where you get instructions about how to make first contributionhttps://github.com/waldronlab/BugSigDBcuration/issues/94and you can ask help to us every time you need - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation.
Hodan Abdirisak (00:34:05) (in thread): > Welcome to the community@Liliana Garmendiafeel excite with friendly conversation
Adefolake Durosinmi (08:12:53): > @Adefolake Durosinmi has joined the channel
Adefolake Durosinmi (08:15:45): > Hi everyone, my name is Adefolake and my pronouns are She/her.I am a legal practitioner that recently transitioned into tech; Cybersecurity precisely.I am an Outreachy Applicant but not engaged in the open source prior to this.Looking forward to learning and guidance from everyone.I am really excited about it though.Thank you.
Joan C. Chukwuemeka (08:34:21): > Welcome@Adefolake Durosinmido join the#bugsigdbchannel specified for Outreachy applicants
Hodan Abdirisak (09:27:07) (in thread): > Welcome@Adefolake DurosinmiI hope you will be feel excited to join here, join#bugsigdb
Mildred Anashie (09:57:46) (in thread): > Hi@Adefolake DurosinmiYou are welcomeDon’thesitate to ask for help, if you need any
Precious Adedeji (11:15:53): > @Precious Adedeji has joined the channel
Precious Adedeji (11:18:51): > Hello everyone, My name is Precious Adedeji and my pronouns are She/her. I recently transitioned into tech and studied Cell biology and Genetics in school I am an outreachy applicant and I hope to contribute my best to thus project and looking forward to work with you all. Thank you.
Hodan Abdirisak (11:36:14) (in thread): > Welcome to the community@Precious Adedejikindly Join#bugsigdbto get start
Erika Villa (11:39:58): > @Erika Villa has joined the channel
Erika Villa (11:44:56): > Hello, my name is Erika Villa, it is a pleasure to belong to this community.
Hodan Abdirisak (11:49:20) (in thread): > welcome@Erika Villa
Mildred Anashie (15:24:46) (in thread): > Welcome@Erika Villa
Mildred Anashie (15:25:26) (in thread): > Welcome@Precious Adedeji
Sara Mohammed (16:00:02) (in thread): > Welcome@Precious AdedejiNice to meet you.
Ukaoha Chizoba (18:58:43): > @Ukaoha Chizoba has joined the channel
Clarissa Abidog (22:27:50): > @Clarissa Abidog has joined the channel
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2023-10-08
Odigiri Great Alume (02:17:09): > Good morning guys. > So I need clarification on something please:pleading_face:I’m working on “Lower Respiratory Tract microbiome composition and smokers behavior”
> > The study subjects were grouped into three: Never smokers (NS), Active Smokers (AS) and Former smokers (FS). > > The study employed the Prospective cohort study design. > > Please how do I place these subjects into GROUP 1 and GROUP 0 seeing that they are three groups (NF, AF, FS)?:thinking_face:
Odigiri Great Alume (02:19:08): - File (JPEG): Screenshot_20231007-005253.jpg
Chioma Onyido (02:37:41) (in thread): > Hi@Odigiri Great AlumeI think one thing is to check the groups that were contrasted during the differential abundance analysis of the microbial taxa.
Chioma Onyido (02:44:11) (in thread): > Group 0 is usually the control/ reference group, while Group 1 is the “case”, for example, if the study is about AD, Group 0 is the normal group, I.e those without AD, while Group 1 would be those with AD. > > But sometimes it could get tricky. > In your case, maybe differential abundance was reported for NS vs AS and FS vs AS. > In this case you might have to create separate experiments for both. A clue is to check the figures, focus more on the table/ figure where the differential abundant taxa was reported, that should give you an idea. > > I hope this helps.
Odigiri Great Alume (04:00:11) (in thread): > Thanks dear. I will look now
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Andres Wokaty (13:53:19) (in thread): > Hi, please ask questions like this on the#bugsigdbchannel. Mentors monitor that channel and there are more people who can help and benefit from these discussions on that channel whereas this is the general introductions channel for all of Bioconductor.
Odigiri Great Alume (14:49:52) (in thread): > Alright@Andres WokatyI will
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Osaruese Faluyi (19:03:04): > Hi everyone, My name is Osaruese and my pronouns are She/her. I am a Medical Laboratory Scientist and I have a keen interest in tech. I am an Outreachy Applicant but have not engaged in the open source prior to this. I’m super excited to be here, looking forward to learning and contributing to this project.
Nana (19:36:23): > @Nana has joined the channel
2023-10-09
Hodan Abdirisak (01:27:28): > @Osaruese Faluyiwelcome to the community kindly Join#bugsigdbchannel where outreachy applicants present, feel free to ask any question and help
Dimitri Meistermann (01:34:18) (in thread): > Thank you for your help and advices. Indeed I will split up the function in several one before submission.
Mildred Anashie (02:32:57) (in thread): > Welcome@Osaruese Faluyi
Zoran Lee (03:46:26): > @Zoran Lee has joined the channel
Maria Doyle (04:33:09) (in thread): > Great to see you here@Romane Libouban:wave:
nyong godwill (05:40:00): > @nyong godwill has joined the channel
Osaruese Faluyi (05:40:44) (in thread): > Thank you
Osaruese Faluyi (05:41:24) (in thread): > Okay, will do that now
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2023-10-10
claudia isabel reyes moreno (00:16:48): > @claudia isabel reyes moreno has joined the channel
claudia isabel reyes moreno (02:28:55): > Hello everyone, I am Claudia Reyes from Colombia Latin America. It’s a pleasure to be with you all. I am a Data and Machine learning Engineer, the first Latin American mentee of Kaggle. Nowadays I am a mentor and leader of the South America region of the Kaggle BIPOC program whose goal is to democratize Data Science and ML in the most vulnerable communities around the world. I am the director of the GDG Cloud Sabana and Women Tech Makers.
Oluchi Nwankwo (07:54:14): > @Oluchi Nwankwo has joined the channel
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JulietMadu (09:28:10): > Hello friends > My name is juliet, feel good to be here
Hodan Abdirisak (09:29:45) (in thread): > Welcome@JulietMadu
AKSHAYA (10:08:34): > @AKSHAYA has joined the channel
Adeniji Agbolade (10:31:28): > Hello everyone, my name is Adeniji Agbolade and I am a medical doctor with interest in health tech. I am excited to be here and i look forward to contributing to this project!
Mildred Anashie (10:49:23): > Welcome@Adeniji Agboladeplease join#bugsigdbchannel
Nana (10:52:07): > @Adeniji Agboladeyou are welcome, this will help:https://github.com/waldronlab/BugSigDBcuration/issues/94
Hodan Abdirisak (13:12:29) (in thread): > Welcome@Adeniji Agbolade
Björn Grüning (13:40:28): > @Björn Grüning has joined the channel
Bianca (14:12:10): > Hi everyone. My name is Bianca, I am a brazilian undergraduated student. I am here because the outreachy projects. I studied biomedical informatics at the university and I find the project could be very interesting.
Mildred Anashie (14:42:19): > Welcome@Biancaplease join#bugsigdbif youhaven’t
Mildred Anashie (14:42:49) (in thread): > Alsohttps://github.com/waldronlab/BugSigDBcuration/issues/94This could be helpful - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. You’re also welcome to introduce yourself on the Bioconductor Slack channel #outreachy. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channels #bugsigdb and #outreachy. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation.
Chima Gerald Ukwuoma (17:30:02): > @Chima Gerald Ukwuoma has joined the channel
Adeniji Agbolade (18:23:54) (in thread): > Thank you so much I will
Adeniji Agbolade (18:24:04) (in thread): > Thank you very much
Adeniji Agbolade (18:24:18) (in thread): > Thank you!
2023-10-11
Leong Benny (06:42:17): > @Leong Benny has joined the channel
Nokuthula (07:52:44): > @Nokuthula has joined the channel
Julian (08:36:49): > @Julian has joined the channel
Odigiri Great Alume (08:44:27) (in thread): > You are welcome on board @Bianca
Francisca_Eze (13:34:10): > @Francisca_Eze has joined the channel
2023-10-12
victory lelekumo (00:54:40): > Hello Everyone, my name is Victory, I’m a Nigerian and a Data Scientist, i am an Outreachy applicant and it’s a privilege to be a part of an amazing community as this. I look forward to an interesting experience, contributing to this project.
Nana (02:17:06): > @victory lelekumoyou welcome. Join#bugsigdbchannel and look out for pinned messages. It will guide you
Hodan Abdirisak (03:12:25) (in thread): > Welcome@Bianca
Hodan Abdirisak (03:13:19): > Welcome to the community@victory lelekumo
Mildred Anashie (03:21:50): > Welcome@victory lelekumo
Julian (04:06:02): > Hi Everyone, I am Julian, a researcher from Kenya. I am excited to be here
Shruti Pal (04:22:09): > @Shruti Pal has joined the channel
Nana (04:46:19) (in thread): > @Julianyou are welcome. Join#bugsigdbchannel and look out for pinned messages. It will guide you
Fortune Nnamdi (04:54:34) (in thread): > Welcome@JulianJust do as a@Nanasaid. But if you find it difficult to locate the pinned messages, just check at the top of the#bugsigdbpage - File (JPEG): IMG_5427
Julian (05:46:15) (in thread): > I will, thank you!
winnie (10:46:23): > Hello I am Winnie, an Outreachy intern from Kenya. Aspiring to make tangible contributions toward this project.
Mildred Anashie (11:18:18) (in thread): > Welcome@winnieDo join the#bugsigdbchannel to get started
Mildred Anashie (11:19:14) (in thread): > Also check out the pinned messages, kindly reach out if you need any help
Uchechukwu Favour Ojunta (11:20:09): > @Uchechukwu Favour Ojunta has joined the channel
Uchechukwu Favour Ojunta (11:21:38): > Hello Everyone > > I’m Uchechukwu from Lagos, Nigeria > I’m excited to be here and ready to make my contributions.
Joan C. Chukwuemeka (11:49:53): > Welcome:blush:@Uchechukwu Favour OjuntaDo join#bugsigdbchannel where discussions and other info regarding the Outreachy contributions are shared. Also check the pinned messages there
Uchechukwu Favour Ojunta (11:51:01): > Thank you so much@Joan C. Chukwuemeka
Hodan Abdirisak (14:09:45): > Welcome@Uchechukwu Favour Ojunta
winnie (16:20:01) (in thread): > Thank you so much@Mildred Anashie
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2023-10-13
Frank-Opigo Emmanuel (04:07:41): > @Frank-Opigo Emmanuel has joined the channel
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Nancy Wairimu Nyambura (09:46:38): > Hello Everyone.. am Nancy,glad to be here
Nana (10:00:02): > welcome Nancy. join#bugsigdb. read pinned massages it will help you
Hodan Abdirisak (10:22:06): > @Nancy Wairimu Nyamburawelcome to the community
2023-10-14
Manka Velda Manjong (05:15:19): > @Manka Velda Manjong has joined the channel
Manka Velda Manjong (05:26:54): > Hello everyone., I am Manka Velda, happy to be here
Hodan Abdirisak (05:51:22): > Welcome@Manka Velda Manjong
Mariam Taleeb (13:41:53): > @Mariam Taleeb has joined the channel
Mariam Taleeb (13:44:07): > Hello everyone. I am Mariam Taleeb. I am elated to be here, and ready to make quality contributions.
Mildred Anashie (14:10:27): > Welcome@Mariam Taleeb
Mildred Anashie (14:10:52): > Join the#bugsigdbchannel > > Check pinned messages also
Hodan Abdirisak (16:17:14): > Welcome@Mariam Taleeb
2023-10-15
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raphael miyoyo (20:13:37): > Hello Everyone! > My name is Raphael, an Outreachy applicant from Kenya. I am a software engineer with interests in data. So excited to be here, looking forward to working on the projects.
2023-10-17
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Chioma Onyido (02:57:35) (in thread): > Welcome@raphael miyoyoKindly join the bugsigdb channel and go through the pinned messages to get started.
raphael miyoyo (03:05:20) (in thread): > Thank you very much@Chioma OnyidoDoing that:slightly_smiling_face:
Mildred Anashie (03:07:10) (in thread): > Welcome@raphael miyoyo
raphael miyoyo (03:17:12) (in thread): > Thank you@Mildred Anashie
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Hodan Abdirisak (05:29:50) (in thread): > Welcome@raphael miyoyo
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Odigiri Great Alume (13:47:39) (in thread): > You are welcome bro
2023-10-20
Peace Sandy (07:17:24) (in thread): > Welcome
2023-10-21
Ukwueze Pascaline Nnenna (00:14:25): > @Ukwueze Pascaline Nnenna has joined the channel
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Doreen Wanyama (14:30:56): > Good day everyone ! My name is Doreen Wanyama an outreachy applicant. I just joined the Microbiome Study Curation project. I hope to bring positive impact to the community and also exchange great ideas with fellow community members. Thanks a lot.
2023-10-22
Nana (05:15:07): > @Doreen Wanyamayou are very much welcome. Join#bugsigdband read the pinned messages and do your first curation
Hodan Abdirisak (06:14:03): > Welcome again@Doreen Wanyama
2023-10-23
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Doreen Wanyama (12:33:26) (in thread): > Thank you@Nana
Doreen Wanyama (12:33:47) (in thread): > Thank you@Hodan Abdirisak
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Chiagoziem David (15:11:33): > Hello hello
2023-10-24
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2023-10-25
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Eszter Ari (09:21:56): > Hi, I am Eszter Ari, a bioinformatician evol biologist (researcher and uni teacher) from Hungary (working in Biological Research Centre, Szeged and Eötvös Loránd University, Budapesthttps://genet.elte.hu/bioinformatics)
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Jonathan Gottlieb (16:04:28): > Hi everyone! I’m Jonathan Gottlieb from New York. I’m relatively new to Data science and excited to join this community and volunteer/help however I can. I’m a nonprofit data analyst and most of my background is from completing R certificates in datacamp and descriptive statistic projects at work.
2023-11-26
Juan Henao (12:28:48): > Hi everyone! My name is Juan Henao, I work on Multi-omics data integration. Currently at the end of my PhD at Helmholtz Centre Munich and Technical University of Munich
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Manvi Yaduvanshi (09:00:21): > Hey everyone! This is Manvi Yaduvanshi from India. I’m new to open source and really want to contribute to Bioconductor, but it seems bit confusing in the beginning. Can anyone help me, letting me know where to start and what documentations should I read?
Lori Shepherd (09:14:51): > @Manvi YaduvanshiHello and Welcome! What is your background? Are you interested in a particular area of research or programming?
Manvi Yaduvanshi (09:26:40) (in thread): > Hey Lori! I do programming in JAVA and python along with frontend web-development and ML and is acquainted to GoLang and R as well. I read about contributing packages to Bioc but couldn’t figure out how would i know if the similar package has been built before. Was a bit confused of how would i know the requirements. I honestly can work on any internal project , I’ll learn side by side if not awared about the tech stack. I’m inclined towards programming and really wanted to know about any beginner projects inside Bioc where i can start contributing and familiarize myself with Bioc more. Can you please help?
Lori Shepherd (09:40:42) (in thread): > Many are out with the new year holiday so it may be a few days before other offer some additional suggestions. > > Information on developing packages can be found here:http://contributions.bioconductor.org/. There has been a recent interest in trying to link better with other programming languages so you might have some novel ideas that could really be useful. > > Some existing packages that try to link python like basilisk might be worth looking at as well as the packages that utilize them.https://www.bioconductor.org/packages/release/bioc/html/basilisk.html. And a dedicated#biocpythonchannel for talking about related ideas. > > We are in process of moving over a new website design and looking for feedback and improvements too if your interested in that area. There is a#biocwebsitechannel for it.http://new.bioconductor.org/this layout will become live January 3 athttps://bioconductor.org/but we want to continue to improve and enhance various elements. > > There is also a#cloud-working-groupthat is looking at cloud related solutions for bioconductor resources. > > those might be some places to start.
Manvi Yaduvanshi (09:56:16) (in thread): > Thankyou so much Lori! Couldn’t ask for more.I’ll surely check them out:blush:
Krithika Bhuvanesh (23:14:42) (in thread): > Welcome Manvi ! Do you have a particular data type of interest such as RNA-seq or anything else ? That may help you narrow down the list as well .
2024-01-02
Manvi Yaduvanshi (10:23:45) (in thread): > Hey!@Krithika Bhuvanesh, thanks for your response. Honestly , I do not have a prior experience in Genomic Data. But definitely would love to learn and contribute. Could you suggest me any data types , a beginner like me can start with?
Krithika Bhuvanesh (15:14:07) (in thread): > If you are looking to start learning about genomic data, i recommend a coursera on genomic data and technologies. There is one from Johns Hopkins. It’s a good introduction to the data type, and they also have some hands on workshops that use R and BioC packages.
2024-01-03
Manvi Yaduvanshi (06:45:16) (in thread): > Thanks! Sure, I’ll check it out.
2024-01-04
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Yanina Bellini Saibene (14:38:42): > Hi, Hola! Mi name is Yani from Argentina. I live surrounded by sunflowers in summer and wheat in winter.:sunflower:I’m the rOpenSci Community Manager and R-Ladies Project Lead. I’m also part of The Carpentries as an instructor, trainer, and a member of the BoD. I’m a member of the RConsortium ISC, and I co-founded and chaired LatinR, the R conference in Latin America. I was a researcher for 24 years in the agricultural sector. > > I love chocolate and soccer:soccer:(especially now that we are world champions:flag-ar::wink:). > Very glad to be here:slightly_smiling_face:
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Abdullah Al Nahid (15:47:06) (in thread): > Hi Yani! Nice to meet you! All love for football and team Argentina from Bangladesh:flag-bd:We love Messi, Di Maria, and everyone in that team and beyond!
2024-01-16
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Maria Doyle (06:40:20) (in thread): > Welcome Yani! Great to see you here:smile:
2024-01-21
Saga (14:40:44): > Hello everyone :)) I am sagana from India.I am new to open source. I recently created my first pull request in bioconductor as a start (check it out:https://github.com/Bioconductor/bioconductor.org/pull/258). Itwas a good experience, and I’m eager to continue contributing .I’m keen to explore new opportunities for collaboration and growth. I’m reaching out today to seek guidance on areas where my skills and passion can be of service.I’m open to contributing in various areas—be it coding, documentation, or any other aspect where I can leverage my skills.I look forward to connecting with all of you:handshake:If anyone could point me in the right direction or recommend essential documentations to read, I would greatly appreciate your assistance. Thank You! - Attachment: #258 Change Low Resolution Icon > changed the low resolution image icon that present in home page - (added new svg file- fixes #257)
> old
> after adding new icon
2024-01-22
Maria Doyle (16:24:32) (in thread): > Hi Sagana, > Welcome to the Bioconductor community and congrats on your first PR!:rocket:To learn more about contributing to Bioconductor packages you could start herehttps://contributions.bioconductor.org/. Your coding and documentation skills will come in handy. Feel free to DM me if you need guidance or have questions. - Attachment (contributions.bioconductor.org): Welcome | Bioconductor Packages: Development, Maintenance, and Peer Review > This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook.
2024-01-23
Saga (00:14:05) (in thread): > Hii Maria,Thank you so much for your response. I will surely check them out:raised_hands::blush:
2024-01-25
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Isi Irabor (11:13:57): > Hello everyone, I am Isi from Nigeria. I have contributed lightly on open source previously and I am excited to work on the bioconductor projects
Linda Uchenwoke (11:18:37): > @Linda Uchenwoke has joined the channel
Chioma Onyido (11:19:15) (in thread): > Welcome@Isi Irabor. Good to have you here! > Kindly join the bugsigdb channel to get updates for your contribution steps.
Isi Irabor (11:21:05) (in thread): > :+1:
Mildred Anashie (11:21:29): > Hello Everyone, My name is Anashie Mildred Andokie, I’m an outreachy applicantI look forward tocontributing to the Boiconductor community and connecting with everyone
Mildred Anashie (11:21:55) (in thread): > Welcome@Isi Irabor
Adedoja Isaac (11:38:11): > @Adedoja Isaac has joined the channel
Linda Uchenwoke (11:41:17): > Hello everyone, I’m Linda, an Outreachy applicant. I’m interested in contributing to Bioconductor projects and excited to learn more about the community. Looking forward to connecting with you all!
samuel alison (11:41:34): > @samuel alison has joined the channel
Mildred Anashie (11:41:57) (in thread): > Welcome@Linda Uchenwoke
Mildred Anashie (11:43:37) (in thread): > Kindly join the bugsigdbchannel
Melodee Okigbo (11:46:23): > @Melodee Okigbo has joined the channel
Andres Wokaty (11:50:50): > Welcome Outreachy applicants! Please join#bugsigdbfor Microbiome Study Curation-specific discussions. You’re also welcome to join#outreachyto ask general questions and discuss anything related to Outreachy. Good luck:slightly_smiling_face:
George Opondi (11:51:23): > @George Opondi has joined the channel
Melodee Okigbo (11:53:04): > Hi everyone, my name is Melodee and I’m Outreachy applicant. I’m super excited to contribute to this project and learn from you all!
Linda Uchenwoke (11:53:05) (in thread): > @Mildred AnashieAlready joined, Thank you!
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Mildred Anashie (12:39:50) (in thread): > You are welcome
Mildred Anashie (12:40:31) (in thread): > Welcome Melodee
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samuel alison (13:12:38): > Hi everyone:wave:, my name is Samuel. I’m super excited to contribute to this project and learning from you all.
Mildred Anashie (13:14:52): > Welcome@samuel alison
Mildred Anashie (13:15:46): > Join the#bugsigdbchannel
Rahila-me (13:18:30): > @Rahila-me has joined the channel
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Melodee Okigbo (13:25:13) (in thread): > Thank you:relaxed:
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Juliet Ogbu (14:03:19): > Hi everyone, my name is Juliet andI’man outreachy applicant.I’msuper thrilled to be here with you all to contribute to this project, learn from you and connect with all of you. Thank you!:blush:
Mildred Anashie (14:05:18) (in thread): > Welcome@Juliet OgbuPlease join the#bugsigdband check the pin messages to get started
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Oluwaseyifunmi Taiwo (14:26:59) (in thread): > Welcome@Isi Irabor
Oluwaseyifunmi Taiwo (14:27:29) (in thread): > Welcome Mildred
Oluwaseyifunmi Taiwo (14:27:51) (in thread): > Welcome Melodee:hugging_face:
Oluwaseyifunmi Taiwo (14:28:12) (in thread): > Welcome Juliet
Mildred Anashie (14:42:08) (in thread): > Thank you:pray:
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Adedoja Isaac (17:00:29): > Hey everyone! Isaac here, happy to be a part of the Outreachy contribution phase as a software dev. Can’t wait to collaborate, learn, and hopefully not break too many things along the way!:grin:Let’s rock this phase together!
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EBERE ADEKOGBE (20:03:33): > Hi everyone my name is Ebere, and i am an Outreachy applicant. Happy being here
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Angella Namuli (23:22:08): > Hello team:smile:, my name is Angella. Iam excited to be here. I can’t wait to be working with all of you
Manisha Nair (23:35:40): > Hello everyone, I’m Manisha, an Outreachy applicant. I’m excited to contribute and learn with all.
2024-03-05
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Nanlop Blessing Dafwat (00:55:52): > Hi everyone, I’m Nanlop from Nigeria, an Outreachy applicant. I’m excited to be here, looking forward to learning and contributing with you all.
Roderick Momin (00:57:20): > Hello, Roderick here, Outreacy applicant.
Juliet Ogbu (01:02:44) (in thread): > Thank you:blush:
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Samreen Aftab (01:35:16): > Hello everyone, I am Samreen, from India. I am an Outreachy applicant. I’m excited to learn new things and contribute to this project!
levis Ngigi (01:36:39): > Hi,everyone I am Levis Ngigi from Nairobi Kenya and I am excited to be part of the community.I am an Outreachy applicant and I am looking forward to making meaningful contributions. I have joined#bugsigdband I am working on my first contribution.Thank you.
Anshuman Moharana (01:39:03): > Hello Everyone, I’m Anshuman, an Outreachy Applicant. Very Excited to be here and looking forward to learning and contributing.
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Blessing Laweh (01:51:12): > Good timezones everyone, my name Blessing Laweh from Lagos Nigeria, and I am excited to be here. Can’t wait to learn new things from everyone, thank you.
Ananya Tomar (01:56:10): > Hey everyone! Ananya here , super excited and glad to be here, hoping to contribute and learn along the way!
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Chinedu Ihedioha (03:51:55): > Hi everyone, I am Chinedu, an Outreachy Applicant. Super excited to be here, looking forward to learn and contribute.
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Zaynab Aderonke Ogunnubi (03:58:55): > Hi, everyone. I’m Zaynab, I’m a researcher. I’m so thrilled to be a part of this contribution phase. Looking forward to learning, collaborating and contributing to this project.
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Emmanuel Doreen (04:19:18): > Hi everyone my name is Doreen i am an outreachy applicant, I’m a research assistant and looking forward to contribute to this project
abdulwasiu maryam (04:24:01): > Good day everyone, I am Maryam, an outreachy applicant, i am a microbiologist, i would be glad to contribute to this project
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Amanda Adoyi (05:14:13): > Aloha friends! My name is Amanda Adoyi and I am an Outreachy 2024 applicant and a research writer. Can’t wait to contribute to the project :)
Mildred Anashie (05:22:19) (in thread): > Welcome@Amanda AdoyiKindly join#bugsigdb
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Amanda Adoyi (05:34:07) (in thread): > @Mildred AnashieDone so! thank you:slightly_smiling_face:
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Barakat Akinsiku (06:16:39): > Hi everyone, my name is Barakat and I’m super excited to be here and looking forward to learn and contribute
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Muqtadirat Yussuff (06:29:26): > Hi everyone, I’m Muqtadirat, a bit new to this field and first time in the open source world. Hoping to make meaningful contributions and learning from everyone. Thank you
Mildred Anashie (06:29:53) (in thread): > Welcome Barakat > > Kindly join#bugsigdb
Mildred Anashie (06:30:25) (in thread): > Hi Muqtadirat > > Kindly join#bugsigdb
Barakat Akinsiku (06:35:26) (in thread): > Alright, thanks!
Muqtadirat Yussuff (06:36:44) (in thread): > Will do, thank you so much
Iman Ngwepe-Ntshibida (06:54:00): > @Iman Ngwepe-Ntshibida has joined the channel
Iman Ngwepe-Ntshibida (06:56:58): > Hey, I am Iman from South Africa. Thrilled to join you all.
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Emem Eduoku (07:24:57): > Hello everyone. My name is Emem and I’m an Outreachy applicant. I’m new to open source contribution but have some experience writing literature reviews. Looking forward to contributing to this project and being of help to the community
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Amarachi Lewachi (07:42:25): > Hi everyone. My name is Amarachi. I am an Outreachy 2024 applicant, cybersecurity professional and researcher with a degree in Microbiology. I have experience with writing research papers and reviews. I look forward to contributing towards this project.#outreachy
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Emem Eduoku (08:00:26): > So although I just joined and don’t know where to start from yet I found the response above. For those of us just joining you can follow the instructions here. - Attachment: Attachment > Welcome Outreachy applicants! Please join #bugsigdb for Microbiome Study Curation-specific discussions. You’re also welcome to join #outreachy to ask general questions and discuss anything related to Outreachy. Good luck :slightly_smiling_face:
Semilore Atolagbe (08:00:38): > Hello everyone. My name is Semilore and I’m a 2024 Outreachy applicant. I am new to open source contributions and have little experience in writing literature reviews. I do look forward to contributing on this project with you all.
Adenike Oladimeji-Kasumu (08:03:48): > @Adenike Oladimeji-Kasumu has joined the channel
Adenike Oladimeji-Kasumu (08:08:10): > Hello Everyone:hugging_face:I am Adenike, a 2024 Outreachy Applicant. I have a bachelor’s degree in Microbiology and on a career transition to Data Analysis. I look forward to making contributions on this project with you all.
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Chioma Onyido (08:11:13): > Hi,:wave:this message is for allOutreachy applicants,Welcome to Bioconductor, Please join the#bugsigdb**** channel**for steps on how to make contributions to the Microbiome Study Curation project, the community is quite active.Also your mentors are there to answer any questions you have.:slightly_smiling_face:Goodluck!
Suru Olaitan (08:15:37): > Hello everyone. My name is Olaitan Suru and I’m an Outreachy applicant. I look forward to contributing my bits here in literature reviews. It;;s great to be here
Onyeahialam Gracious (08:43:11): > @Onyeahialam Gracious has joined the channel
Onyeahialam Gracious (08:56:53): > Hello everyone, I am Gracious Onyeahialam and I’m excited to be in your midst to contribute to this Microbiome Study Curation project and assist others in the Bioconductor Community as we all learn together.
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PinRathod (09:01:08): > Hello everyone, I’m Pinalee an Outreachy applicant. I am excited and looking forward to contributing to this project. Thank you.
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Erembe Arobo (11:15:27): > Hello everyone. I’m Erembe, an Outreachy applicant. Nice meeting you all here.
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Joan C. Chukwuemeka (11:19:22) (in thread): > Welcome@Erembe AroboPlease join#bugsigdbchannel for outreachy related discussions.
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Anju Maurya (12:37:49): > Hey Everyone! > I am Anju Maurya. I am an Outreachy applicant . I am excited and looking forward to contribute the project “Microbiome Study Curation” . I am excited to learn and collaborate with the all learners.
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Blessing Anumba (12:56:29): > Hi everyone, It’s Blessing Anumba, I am happy to be here. Looking forward to working together on the Microbiome Study Curation Project.
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Precious Orakwe (13:49:36): > Hello team, good evening to everyone and to the mentors. my name is precious an outreachy applicant. i am excited to contribute to this project because i know i have a lot to learn and a lot to give back to this community, i plead for the teams assistance and the the mentors support and guidline
Lluís Revilla (14:04:06): > @Lluís Revilla has left the channel
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Busingye lillian (14:31:50): > Hello everyone, I am an Outreachy applicant , happy to be here and looking forward to contribute to this project and learning from you all.
Abiola Salako (14:51:57): > Well done, Everyone. > > My Co-applicants and our respected Mentors > > I’m Abiola Salako, an Outreachy applicant looking forward to contributing to the Bioconductor communities. I would like someone to put me through the next steps after this introduction. Thank you.
Regina Rukeme Agaren (14:57:57): > @Regina Rukeme Agaren has joined the channel
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Regina Rukeme Agaren (15:03:53): > Hello Everyone, > > I’m delighted to introduce myself as Regina, an Outreachy applicant, thrilled to be a part of this vibrant community. I am eager to contribute my skills and knowledge while also learning from the esteemed mentors here. Looking forward to a fruitful journey together.
Idiat Alli (15:43:12): > @Idiat Alli has joined the channel
Idiat Alli (15:51:54): > Hi Everyone and@Svetlana Ugarcina Perovic. My name is Idiat Alli. An outreachy applicant excited to make my contributions to this project. Looking forward to exciting moments with everyone.
Ikeh Darlington Ikeh (16:10:52): > @Ikeh Darlington Ikeh has joined the channel
Success Ologunsua (16:23:52): > @Success Ologunsua has joined the channel
Chiemelie Carita Ndibe (16:28:29): > @Chiemelie Carita Ndibe has joined the channel
Chiemelie Carita Ndibe (16:36:24): > Hello team, I am an Outreachy applicant and am excited to be here. I hope to learn and contribute. Thank you.
Chioma Agu (16:53:52): > @Chioma Agu has joined the channel
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Benedicta Imelda (17:41:29): > :wave:Hello, team! I am happy to be here
Benedicta Imelda (17:42:45): > My name is Benedicta Imelda from Outreachy and I am happy to give my contribution
Khadijah Kamorudeen (17:43:49): > Hello everyone, my name is Khadijah Kamorudeen and I’m happy to be here. Looking forward to making my contributions.
Collins Carshy (17:48:26): > @Collins Carshy has joined the channel
Collins Carshy (18:00:56): > Hello team, I am an Outreachy applicant and I’m so excited to learn, share, and contribute to Bioconductor community. Cheers!
Ibukun Hassan (18:01:15): > @Ibukun Hassan has joined the channel
Vivian O (18:44:02): > @Vivian O has joined the channel
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2024-03-06
Ishita Pathak (00:03:08): > @Ishita Pathak has joined the channel
Siva (01:24:15): > @Siva has joined the channel
Mildred Anashie (02:04:06) (in thread): > Welcome > > Please Join#bugsigdbto get started
Rukayat Salaudeen (02:47:58): > @Rukayat Salaudeen has joined the channel
Rukayat Salaudeen (02:54:14): > Hello everyone. > I’m Rukayat from Outreachy, I’m excited to be here and to make effective contributions. > Thank you
Michael Adekanye (02:56:46): > @Michael Adekanye has joined the channel
Kapil (02:57:11): > @Kapil has joined the channel
Michael Adekanye (02:58:15): > I am Michael Adekanye. I am happy to be here. Looking forward to contributing to Bioconductor project
Ufomba Justina (03:00:53): > @Ufomba Justina has joined the channel
Manideep (03:09:52): > @Manideep has joined the channel
Kapil (03:17:37): > Hello everyone, I am Kapil an Outreachy applicant and I am super looking forward to learn and contribute to Bioconductor community.
vanessa kamunya (03:24:35): > @vanessa kamunya has joined the channel
Bolarinwa Abosede Julianah (03:49:31): > Welcome everyone.. Nice to meet you all
Abiola Salako (03:55:17) (in thread): > Welcome@Kapil. Do well to join the#bugsigdbchannel
Abiola Salako (03:56:15): > Welcome@Kapildo well to join the#bugsigdbchannel
Abiola Salako (03:57:18): > Welcome@Khadijah Kamorudeen. Do well to join the#bugsigdb
Aleru Divine (04:02:24) (in thread): > Hi@Rukayat Salaudeen, welcome:hugging_face:Please join the#bugsigdbchannel.Also, you can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Aleru Divine (04:02:57) (in thread): > Hi@Michael Adekanye, welcome:hugging_face:Please join the#bugsigdbchannel.Also, you can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Michael Adekanye (04:33:09) (in thread): > Thank you@Aleru Divine
Aleru Divine (04:39:49) (in thread): > You’rewelcome Michael
Neelam Mahraj (04:42:05): > @Neelam Mahraj has joined the channel
Adegboye Rukayat (04:53:16): > @Adegboye Rukayat has joined the channel
Adegboye Rukayat (05:01:23): > Hello everyone, my name is Rukayat. I am an Outreachy applicant, and I look forward to learning, working, and making a phenomenal contribution to the Bioconductor Project.
Deborah Oyawale (05:05:23): > Good morning Everyone! > I am Deborah Oyawale, an Outreachy applicant. I am so excited to be here, because I know i’d be able to learn a lot and as well, looking forward to contributing to the project “Microbiome Study Curation” under the tutelage of our mentor on this project@Svetlana Ugarcina Perovic
Aleru Divine (05:12:15) (in thread): > Hi@Adegboye Rukayat, welcome:hugging_face:Please join the#bugsigdbchannel.Also, you can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699
Aleru Divine (05:12:39) (in thread): > Hi@Deborah Oyawale,welcome:hugging_face:Please join the#bugsigdbchannel.Also, you can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Dolapo Mosuro (05:23:15): > @Dolapo Mosuro has joined the channel
sahir (05:28:40): > @sahir has joined the channel
Abiola Salako (05:29:00): > Welcome@Adegboye Rukayat@Deborah OyawaleDo well to join the#bugsigdbchannel to know the next steps to take.
Dolapo Mosuro (05:38:56): > Hello, everyone, My name is Dolapo Mosuro. I am drawn to this project based on content creation and always one to go for an actual challenge and good cause. Does anyone know whether I will be able to make any impact here despite not having any educational background in the Sciences?
Aleru Divine (05:48:39) (in thread): > Hi@Dolapo Mosuro, welcome:hugging_face:Join the#bugsigdbchannel and you can also go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Michael Adekanye (05:57:38) (in thread): > @Aleru Divineso in the in the first contribution,it’s just filling in the form which includes name, GitHub and so on? After do that, It has to be recorded,right?
Nancywrites (06:02:34): > @Nancywrites has joined the channel
Aleru Divine (06:03:32) (in thread): > You’ll be taken to another page that contains the task for the first contribution@Michael AdekanyeIt has a link to an annotated article(you’re to read), questions and answer options to pick from. > > This will be your first curation and your first contribution.This is the oneyou’llrecord as contribution.
Michael Adekanye (06:04:25) (in thread): > Ok thank you.
Aleru Divine (06:05:59) (in thread): > @Michael AdekanyeAfter you submit (when you finish curation, copy the link and record as your first contribution.
Aleru Divine (06:09:38) (in thread): > @Michael AdekanyePlease join the#bugsigdbchannel.This is where contributors and the mentors communicate.You will find other helpful resources in the channel too.Do not hesitate to reach out to me and others if you encounter any difficulties.:heart::hugging_face:
Michael Adekanye (06:10:09) (in thread): > I’m there already. Thank you.
Aleru Divine (06:12:09) (in thread): > Alright Michael
Elsie Dickson (06:15:26): > @Elsie Dickson has joined the channel
Mojisayo Awolesi (06:21:23): > @Mojisayo Awolesi has joined the channel
Raihanat Adewuyi (07:09:46): > @Raihanat Adewuyi has joined the channel
Medina Adeniran (07:15:41): > @Medina Adeniran has joined the channel
Faith Omolara Adegoke (07:16:30): > @Faith Omolara Adegoke has joined the channel
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Paseda Modupe oluwaseun (07:21:07): > @Paseda Modupe oluwaseun has joined the channel
Omoleye Jimoh (07:23:43): > Hello everyone, my name is Omoleye. I look forward to contributing, learning and connecting.
Paseda Modupe oluwaseun (07:27:30): > Hello everyone, I’m Modupe paseda an Outreachy applicant. I am excited and looking forward to contributing to this project. Thank you
Aleru Divine (07:31:49): > Hi@Omoleye Jimohand@Paseda Modupe oluwaseun, welcome:hugging_face:Join the#bugsigdbchannel and you can also go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Paseda Modupe oluwaseun (07:34:05): > Thanks for receiving me here will join#bugsigdband go through it all to get started
Aleru Divine (07:36:17): > Alrighty:hugging_face:
Janine Makorre (07:42:26): > @Janine Makorre has joined the channel
Grace Paul (08:03:33): > @Grace Paul has joined the channel
Kaycee Pyaar (08:11:17): > @Kaycee Pyaar has joined the channel
Faith Omolara Adegoke (08:38:08): > Hi everyone. I am Faith Adegoke. I look forward to contributing to the Bioconductor project. Thank you.
Aleru Divine (08:39:06) (in thread): > Hi@Faith Omolara Adegoke, welcome:hugging_face:Join the#bugsigdbchannel and you can also go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Nana (08:39:27): > @Faith Omolara Adegokewelcome.please join#bugsigdb
Faith Omolara Adegoke (08:42:18) (in thread): > Okay. Thank you.
Ikechukwu Chibuike (08:56:40): > @Ikechukwu Chibuike has joined the channel
104_Khushnuma Sadaf_ECE-AI2 (08:59:46): > @104_Khushnuma Sadaf_ECE-AI2 has joined the channel
Esther Nelson (09:12:58): > @Esther Nelson has joined the channel
Esther Nelson (09:22:29): > Hi everyone, I am sure we are all amazing. I am Nelson Esther, a prospective Outreachy intern. I am a passionate Data Analyst and Writer and I am super excited to contribute to this project. Glad to connect with every one of you. Feel free to ask anything, let’s connect.
Aleru Divine (09:26:30) (in thread): > Hi@Esther Nelson, welcome:hugging_face:Join the#bugsigdbchannel and you can also go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Prakriti Maurya (09:30:51): > @Prakriti Maurya has joined the channel
Esther Nelson (09:37:56) (in thread): > Thank you so much, Divine.
Aleru Divine (09:39:33) (in thread): > You’rewelcome Esther
Raihanat Adewuyi (09:47:08): > Hi everyone I’m Raihanat Adewuyi. Looking forward to contributing to the Bio conductor project.. I am a Frontend developer fell free to ask me any Question. > Thanks
Aleru Divine (09:48:52) (in thread): > Hi@Raihanat Adewuyi, welcome!:hugging_face:You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Aleru Divine (09:49:06) (in thread): > Please join the#bugsigdbchannel
Raihanat Adewuyi (09:55:12) (in thread): > Thank you@Aleru Divine
Tooba Amjad (10:36:49): > @Tooba Amjad has joined the channel
Adejoke Ogunyinka (10:40:07): > @Adejoke Ogunyinka has joined the channel
Adejoke Ogunyinka (10:43:04): > Hi everyone, I’m Adejoke Ogunyinka. I look forward to contributing to the Outreachy Bioconductor project.
Aleru Divine (10:44:02) (in thread): > Hi@Adejoke Ogunyinka, welcome!:hugging_face:Please join the#bugsigdbchannel > > You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Elsie Dickson (10:45:25): > Hi everyone, my name is Elsie and I look forward to working with you on the Outreachy Bioconcuctor Project.
Aleru Divine (10:48:12) (in thread): > Hi@Elsie Dickson, welcome!:hugging_face:Please join the#bugsigdbchannel, there are resources there and it is where everyone communicates.You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699Ask me anything,I’mhere to help.:hugging_face: - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Esther Nelson (10:49:34) (in thread): > Welcome, Elsie
Esther Nelson (10:49:48) (in thread): > Welcome Adejoke, love to connect with you.
Adejoke Ogunyinka (10:50:09) (in thread): > Thank you,@Aleru Divine
Adejoke Ogunyinka (10:50:23) (in thread): > @Esther NelsonThank you. Same here
Preethi grace Manthena (11:05:58): > @Preethi grace Manthena has joined the channel
Oluwatoyosi Victoria Olanrewaju (11:37:13): > @Oluwatoyosi Victoria Olanrewaju has joined the channel
Oluwatoyosi Victoria Olanrewaju (11:46:10): > Hello everyone, I’m Oluwatoyosi and I am more than pleased to be here as part of the Outreachy program as a contributor. Looking forward to connecting and making meaningful contributions.
Esther Nelson (11:47:21) (in thread): > Hi@Oluwatoyosi Victoria Olanrewaju, welcome:hugging_face:. It’s great to have you. Here are a few steps to get to speed with the exciting developments on this project: > > Join the#bugsigdbchannel and you can also go through this to get started. > > Follow this,https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699, to begin your first contribution. > > One of our mentors@Chioma Onyidowrote an amazing blog on getting started and what’s to be expected from us during this stage,https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/. It’s gold if you ask me. > > These should be enough to get you started. Oh, and once you’ve made your first contribution, don’t forget to record it. Great to connect with you. (edited)
Okhuomon Ajayi (12:06:30): > @Okhuomon Ajayi has joined the channel
EBERE ADEKOGBE (12:07:43) (in thread): > welcome Raihanat
Afnan Asif (12:09:14): > @Afnan Asif has joined the channel
ayesha khan (12:11:36): > @ayesha khan has joined the channel
Temitayo Ogidan (12:12:23): > @Temitayo Ogidan has joined the channel
ayesha khan (12:15:18): > Hey there ! Looking forward to being a part of Outreachy Program as Contributor .
Suru Olaitan (12:15:46): > You’rewelcome!@ayesha khanGood to have you here
Suru Olaitan (12:16:28) (in thread): > Welcome:tada:Should you need help getting started with your first contributionDon’thesitate to reach out
Suru Olaitan (12:17:19) (in thread): > Here’swhat you need to know to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699
Suru Olaitan (12:17:20) (in thread): > Here’swhat you need to know to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Temitayo Ogidan (12:18:22): > I’mexcited to be here!:innocent:I’mTemi, andI’mlooking forward to making meaningful connections and contributions with you all!
Suru Olaitan (12:19:23) (in thread): > Hello@Temitayo OgidanYou’rewelcome > > It’s good to have here
Aleru Divine (12:20:00) (in thread): > Hi@Temitayo Ogidan, welcome!:hugging_face:Please join the#bugsigdbchannel, there are resources there and it is where everyone communicates.You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699Ask me anything, I’m here to help.:hugging_face: - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
EBERE ADEKOGBE (12:50:28): > Hi,@Svetlana Ugarcina Perovic,@Chioma Onyidohttps://github.com/waldronlab/BugSigDBcuration/issues/urlThis link leads to nowhere. The article is empty. Kindly help me look into it. Thank you
EBERE ADEKOGBE (12:51:06) (in thread): > You are welcome
Rahila-me (12:52:28): > @EBERE ADEKOGBEkindly post this on#bugsigdbfor swift action
eneje promise (13:09:11): > @eneje promise has joined the channel
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idiaru Angela (14:33:31): > @idiaru Angela has joined the channel
Oluwatoyosi Victoria Olanrewaju (14:45:37) (in thread): > Thank you so much@Esther NelsonI’ll get to it!
Devashri (15:11:38): > @Devashri has joined the channel
NWAKAEGO VINCENT (15:52:41): > @NWAKAEGO VINCENT has joined the channel
NWAKAEGO VINCENT (16:08:36): > Hello everyone, my name is Nwakaego Vincent and i am excited to be part of this community of great people. i’m thrilled to make my contributions on the bioconductor project. happy to connect with you all
Perpetual Meninwa (16:14:03): > @Perpetual Meninwa has joined the channel
Suru Olaitan (16:21:58) (in thread): > Welcome,@NWAKAEGO VINCENTGood to have you here:tada::tada:
Suru Olaitan (16:22:44) (in thread): > Do well to join the#bugsigdbchannel, that’s where all the communication happens > > Get ready to make your first contribution! > Here’s what you need to know to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699Should you encounter any difficulties, I am here to help!:sparkles: - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Osayuki Raymond Okhuarobo (16:23:00): > @Osayuki Raymond Okhuarobo has joined the channel
Perpetual Meninwa (16:37:16): > Hello Good evening everyone. My name is Perpetual Meninwa and I am super excited to be here
Hamidat Mohammed (18:12:30) (in thread): > Welcome@Perpetual MeninwaDo well to join the#bugsigdbchannel, that’s whereEverycommunication happens. To makeyour first contribution, click on this link to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Blessing Williams (18:27:42): > @Blessing Williams has joined the channel
Blessing Williams (18:31:30): > Hi everyone. My name is Blessing Akhigbe-Williams and I’m excited to be here.. I look forward to contributing to this project and collaborating with everyone.
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consolation obazee (22:00:55): > @consolation obazee has joined the channel
NWAKAEGO VINCENT (22:25:27) (in thread): > Thank you@Suru Olaitan
NWAKAEGO VINCENT (22:27:49) (in thread): > I am finding it hard to make my first contribution, i don’t know what article to read. could you pls run me through the steps@Suru Olaitan
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2024-03-07
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Aleru Divine (01:03:12) (in thread): > Hi@Blessing Williams, welcome!:hugging_face:Please join the#bugsigdbchannel, there are resources there and it is where everyone communicates.You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699Ask me anything, I’m here to help.:hugging_face: - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
ADAEZE SIMON (01:55:50): > @ADAEZE SIMON has joined the channel
Suru Olaitan (02:01:58) (in thread): > Hiii@NWAKAEGO VINCENTApologies that I am just responding
Suru Olaitan (02:03:30) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/94This link takes you to the documentation page where you see what you need to do for the first contribution - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/
Suru Olaitan (02:06:14) (in thread): > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcThis is also the link to the survey you need to take, ensure you read the article states before proceeding to attempt the quiz > > All the best! > > If you still need any help,Don’thesitate to ask - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey
Nitya Singhal (02:08:25): > @Nitya Singhal has joined the channel
Suru Olaitan (02:09:10) (in thread): > Although,I thinkyou’restill in the introduction channel > Kindly join the#bugsigdbchannelThat’swhere all discussion takes place
Nitya Singhal (02:09:13): > Hey everyone! I, Nitya Singhal, am an outreach applicant and techno-savvy engineer on this side. I am eager to contribute to the project. I’m new to the project, so I would be grateful for the assistance. Please let me know where I can connect with the mentors.
Aleru Divine (02:11:48) (in thread): > Hi@Nitya Singhal, welcome:hugging_face:Please join the#bugsigdbchannel,there are resources there and it is where everyone communicates, including the mentors and fellow contributors.You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699Ask me anything, I’m here to help.:hugging_face: - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Blessing Ene Anyebe (02:12:15) (in thread): > Hello@Nitya Singhalyou’re welcome to the community. Check this article to get astarted.https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well. You should also join this channel#bugsigdb - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta… - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/
vanessa kamunya (02:19:21): > Hello Everyone,I am Vanessa Kamunya and I am excited to contribute to this project!
Aleru Divine (02:21:34) (in thread): > Hi@vanessa kamunya, welcome:hugging_face:Please join the#bugsigdbchannel, there are resources there and it is where everyone communicates, including the mentors and fellow contributors.You can go through this to get started. https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699Ask me anything, I’m here to help.:hugging_face:
Blessing Williams (02:48:06) (in thread): > Thank you@Aleru Divine
Chimdimma Nwachukwu (02:54:59): > @Chimdimma Nwachukwu has joined the channel
Chimdimma Nwachukwu (02:57:47): > Hi everyone. My name is Chimdimma and I am super excited to contribute to the community. I just have one little tiny problem. I don’t know where to start from.:blush:I am entirely new to open source so where do I start from?
Rahila-me (03:14:54): > @Chimdimma Nwachukwuplease join#bugsigdband read the pinned messages. go and work on first curation
Chimdimma Nwachukwu (03:17:47): > Thank you Liza
Ifenna Muonagolum (03:56:36): > @Ifenna Muonagolum has joined the channel
dehbeie donatus (04:05:32): > @dehbeie donatus has joined the channel
dehbeie donatus (04:08:16): > Hi everyone, I am Dehbeie.Happy to be here, looking forward to making contributions.
Aleru Divine (04:35:59) (in thread): > @Raihanat Adewuyithe next thing would be to request for an issue to be assigned to you so you can start your second contribution, but there are no available issues yet. So just wait until the mentorsadd new issues.@Svetlana Ugarcina Perovic@Peace Sandy@C. Mirzayi (please do not tag this account)@Chioma Onyido@Esther AfuapeFor now, you can go through this in preparation for your second contributionhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709803433606669?thread_ts=1709802162.577809&channel=C04RATV9VCY&message_ts=1709803433.606669 - Attachment: Attachment > Hello @Blessing Ene Anyebe > This is a summarized steps I made up for the second curation; > > 1. First go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly. > > 2. Check out already curated papers > > (I found it very helpful to do 1 and 2 simultaneously. That way you’ll easily understand what the curation policy is talking about) > > 3. Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study through the curation interface of BugSigDB” > > 4. After being assigned a paper, go through the paper and highlight informations to be curated. > > In addition, I find searching (Ctrl + f) for specific information to be very helpful. Like specifically searching for the word ‘match’ or ‘antibiotic’ to identify matched-on or antibiotics exclusion criteria respectively.
Rahila-me (04:39:23): > @dehbeie donatuswelcome: please join#bugsigdband read the pinned messages. go and work on first curation
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dehbeie donatus (11:00:30) (in thread): > Thank you@Rahila-me
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2024-03-08
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Matthew Idungafa (00:15:24): > Hello everyone, I am Matthew Idungafa an outreachy intern and i’m interested in contributing to this project
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idiaru Angela (01:31:40) (in thread): > Hi Matthew. Please join#bugsigdb. You can check the pinned messages for information on how to start
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Ajayi Mercy (05:43:57): > Hello everyone, My name is Mercy I’m happy to be here. I look forward to contributing to the project, I would appreciate it if anyone could help with the tips to start the journey. Thank you
Svetlana Ugarcina Perovic (05:44:45) (in thread): > Please do join#bugsigdb
Druscilla Nakanwagi (05:48:16): > @Druscilla Nakanwagi has joined the channel
Druscilla Nakanwagi (05:50:21): > Hello everyone my name is Druscilla and I am happy to be a part of this project
Ajayi Mercy (05:57:38) (in thread): > Thank you.
idiaru Angela (06:03:59) (in thread): > Hi Druscilla. You’re welcome. Join#bugsigdbto get started if you haven’t and look through the pinned messages to get started > The community is always ready to help if you have any more questions
Druscilla Nakanwagi (06:05:08) (in thread): > Thank you
Adenike Oladimeji-Kasumu (06:49:07) (in thread): > You are welcome@Druscilla NakanwagiYou might find this helpfulhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709898178301659 - Attachment: Attachment > Welcome! If you just joined. > Here is a summary I compiled on how to make your contributions. > 1. Join the BugSigDB channel on the Slack platform and introduce yourself on the channel. > Now all the information flying around here might seem overwhelming at times, do not worry. Take a deep breath as everyone on the channel is willing to help. Our mentors including @Svetlana Ugarcina Perovic @Chioma Onyido @C. Mirzayi (please do not tag this account) are also working to support us. You’ve got this. > 2. https://github.com/waldronlab/BugSigDBcuration/issues/94 Check out this link for information to get started. Take your time to go through every link in the Prep work and watch all videos, All information will come in handy. > Go through the BugSigDB page https://bugsigdb.org/Main_Page > Now click on the link to the First Curation Form (https://bugsigdb.org/Main_Page.) > > On your Browser, open this link https://github.com/join to create a github account. Do not worry if you have never used GitHub before. Its not that hard. Just follow every step on the page. > > Review the article tagged Annotated Shrode article pdf. Download and read through. Do not worry if you do not understand all the information. Do well to focus on the highlighted parts of the documents. Every answer to the survey question will come from these highlighted parts. > > Now enter your Name (the one you used to register on Outreachy), your email address, your username on GitHub and your username on Slack the channel. Then Click on the next button. Go ahead to answer the survey questions. > Request for an account here. https://bugsigdb.org/Special:RequestAccount > If you have troubles Identifying the disease from https://www.ebi.ac.uk/efo/ website, be calm. Look for the closest disease to the one you are curating and use that. > You have already begun. No need to fret now! That was your First contribution. > After submitting your First contribution, it is time to record it. > Go to the Outreachy main page www.outreachy.org , make sure you are logged in. Click on Applicants, then click on current projects. Click on Click on the ‘Microbiome Study Curation’, Click on ‘Record Contributions and Apply to This Project’. > This is the link to fill for link to your contribution https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc. Include the date when you made your contribution and the date you submitted. Then add a description of your contribution (describe what the article is about, the topic, purpose, analysis, discussions, and findings.) and Record. > Now to the Second Contribution: > Note: Our mentor has advised that for this second contribution task, you are strongly encouraged you to aim for quality over quantity. > https://github.com/waldronlab/BugSigDBcuration/issues/94 > See the Second Contribution heading. > Click on ”Paper to Curate” and check through all available articles, especially the ones that are yet to have the ‘assigned’ tags on them. Click on your choice Article and request that it be assigned to you. A mentor will give you a feedback soon enough. > After it is assigned to you, download the PDF file of your article and red through. > Go to the BugSigDB main page https://bugsigdb.org/Main_Page, make sure you log in. Then select ‘Add a study’ from the top Bar. > Enter the Study Design, you can find which design your Article falls under here: Curation Policy - BugSigDB > Under Citation, Select Auto mode, Enter the PMID and the Doi. You will find the PMID here https://pubmed.ncbi.nlm.nih.gov/ when you copy and paste the tittle of your Article on the search bar. The Doi is available on your Article, Most times on the top part. Now, scroll down to From Data and select Complete. Then save page. > The information on your Article should automatically populate on the next page. > Click on ‘Add a new Experiment’ > > Fill in all the gaps from the information in your Article > > Make sure on each page, you select complete and save > > Now, click on ‘Add Signature’. The onboarding videos will help a lot especially https://www.youtube.com/watch?v=yfpnwxefLFc > > You can now select ‘complete’ and ‘save page’ > > I advise that you allow other curators to review your work then proceed to Record your contribution on the BugSigDB main page. The link for your curation will be the link for that study that you finished Curating. For the merged date, you will have that when a mentor has reviewed your work, then you can update your contribution. > > #Note# It is emphasized that you Choose Quality over Quantity in our Contribution.
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Binita Dhakal (11:10:28): > Hello Everyone! I am Binita Dhakal. I am currently a freshman in pursuing undergraduate degree in Computer Science. This week I had a lot of exams so was fully occupied. However, as I have spring break coming week, looking forward to contribute with my full potential!
idiaru Angela (11:12:55) (in thread): > Hi Binita. You’re welcome. Join#bugsigdbto get started if you haven’t and look through the pinned messages to get started > The community is always ready to help if you have any more questions
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Aishat Ijiyode (16:07:22): > Hello everyone, my name is Aishat. I’m an outreachy applicant, I am excited to contribute to this project and connect with you all
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2024-03-09
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EBERE ADEKOGBE (05:12:48) (in thread): > Welcome@Aishat Ijiyodeyou can join the#bugsigdbchannel for steps on what to do.. Am also available when you need help
Sahana K (05:39:55): > @Sahana K has joined the channel
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Mariam Hammed Gambina (07:58:33): > Hello, my name is Mariam. I am an Outreachy applicant and I’m very excited to be here to contribute to a project.
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Flourish Ralph (12:23:08) (in thread): > Hi, you can join the#bugsigdbchannel to start contributing.Check through the pinned messages to see the next steps to take.
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Hamza Haji (23:19:29): > Hello everyone.My name is Hamza.I am excited to start my journey in contributing to open source and open science at bioconductor.#outreachy2024
2024-03-10
ANUKRATI CHATURVEDI (01:57:06): > @ANUKRATI CHATURVEDI has joined the channel
Mariam Hammed Gambina (06:02:02) (in thread): > Thank you so much@Flourish Ralph. My first contribution is done already.
Chen Jackson (07:08:18): > @Chen Jackson has joined the channel
Flourish Ralph (09:56:19) (in thread): > That’sgreat:hugging_face:
Abiola Salako (11:16:09) (in thread): > You’re welcome@Hamza HajiDo well to join the#bugsigdbchannel. Check through the pinned messages to see the next steps to take.
Irene Ighalo (11:42:42): > @Irene Ighalo has joined the channel
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Arnav Puri (14:07:15): > Hello everyone. My name is Arnav Puri. I’m a pre-final year in Bachelors of Technology. I’m really looking forward to working with you all
Hamza Haji (14:12:35) (in thread): > Thank you@Abiola SalakoI will do so.
Abiola Salako (14:42:01): > You’re welcome@Arun Chavanyou’re welcome. Kindly join the#bugsigdbchannel. Check through the pinned messages to know the next step to take.
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2024-03-11
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Isha Kashyap (10:23:29): > Hello everyone, myself Isha from India. It is overwhelming as well as exciting to be here to work and grow in open source with the guidance and community help. I am relatively new, so I will be looking forward to talk to all of you. Thank you.
idiaru Angela (10:32:43) (in thread): > Hi@Isha Kashyapwelcome! Join#bugsigdbto get started and check the pinned messages for information about how to get started
Samreen Aftab (10:51:03) (in thread): > Welcome@Isha Kashyap:relaxed:
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Idiat Alli (16:54:31) (in thread): > You are welcome@Isha Kashyap
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2024-03-12
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Mkpouto Shedrack (09:30:14): > Hello everyone, MK here, Excited to collaborate with all of you. Any tips on next steps for me will be highly appreciated.
Aleru Divine (09:32:23) (in thread): > Hi@Mkpouto Shedrackwelcome:hugging_face:discussions happen in the#bugsigdbchannel > > You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic
Mildred Anashie (11:24:33) (in thread): > Yea@Mkpouto Shedrackplease join#bugsigdbYou are welcome:hugging_face:
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2024-03-14
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Mkpouto Shedrack (12:33:16) (in thread): > Thank you so much for your replies. They were very helpful.
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2024-03-15
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EBERE ADEKOGBE (09:58:25) (in thread): > You are welcome@Mkpouto Shedrack. Join the#bugsigdband go through the link@Svetlana Ugarcina Perovicsent
EBERE ADEKOGBE (10:00:09) (in thread): > Welcome@Isha Kashyap. Please join#bugsigdband go through the links to know where to start from.
EBERE ADEKOGBE (10:01:55) (in thread): > You are welcome@Arnav Puri. Looking forward to work with you. Join the#bugsigdbto know what step to take next
EBERE ADEKOGBE (10:02:41) (in thread): > You are welcome@Hamza Haji
EBERE ADEKOGBE (10:03:30) (in thread): > Follow the link@Abiola Salakosent it will help you know the next step to take
2024-03-17
fetlework gubena arage (05:46:24) (in thread): > welcome Mattew
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Daniel Mullen (14:53:05): > Hello everyone, I’m Daniel - I’m interested in developing a Bioconductor package and I had a few questions that I wasn’t able to find a definitive answer for online. Is there a good channel to use to ask them here (or see if they’ve already been answered? I think they might be pretty commonly asked)?
Kasper D. Hansen (15:03:08): > I think#developers-forumwould be a good place.
Daniel Mullen (15:04:32): > Thank you!
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Svetlana Ugarcina Perovic (03:55:08): > If you were an**** OUTREACHY applicant ****and contributed to any of the Bioconductor projects#BugSigDB#sweave2rmd#BSgenomeForge#miaverse, please help us in spreading the word about your amazing work. > > You can share your experience (anonymously) by filling in this short surveyhttps://forms.gle/brqH5M2uTYMKy23x7Thank you! - Attachment (Google Docs): Outreachy-Bioconductor survey > Dear Outreachy-Bioconductor contributor, > Thank you for participating in the Outreachy-Bioconductor program. In order to improve the experience for future contributors as well as to spread the word about your amazing contribution to the Bioconductor projects in the form of a conference talk and publication, we would appreciate you taking just a few minutes to complete an online survey about your experience. > > All survey responses are collected anonymously. If you have any questions, please contact us. > > Many thanks in advance and best wishes, > Bioconductor team > Email address: mailto:jennifer.wokaty@sph.cuny.edu|jennifer.wokaty@sph.cuny.edu
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2024-06-17
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JACOB A DE JESUS-CANDELARIO (12:24:43): > Hello! I hope everyone is well. I’m Jacob de Jesus, a rising senior undergraduate student from Puerto Rico. This summer I was introduce to contribute to the Bioconductor Community as a mentee from th NSURP 2024 Cohort. I am eager and happy to contribute and form part of this project.
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Svetlana Ugarcina Perovic (03:32:43) (in thread): > Welcome, Jacob! Please join us in#bugsigdb
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Joyce Qiu (12:07:24): > Hi, I’m Joyce. I am an Applied Mathematics and Statistics major with a minor in Computer Science about to graduate, and I will be going into a MPH program. I was introduced tobugsigdb.orgby Dr. Waldron. I am grateful for this opportunity to gain experience in the field and look forward to contributing to this project.
2024-07-02
Svetlana Ugarcina Perovic (02:21:23) (in thread): > Welcome,@Joyce Qiu! Please join#bugsigdb
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2024-07-14
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Sudipta Hazra (18:17:22): > Hi Everyone, > > I am Sudipta Hazra, a Research Master’s student working on Food Proteomics. I have a B.E. in Food Engineering and a PGD in Statistics, along with a year of experience in Statistical Data Analysis. > > I came across Bioconductor almost a year ago for my Proteomics project and have been using it extensively since then. I am looking for opportunities to participate and contribute to projects (preferably Proteomics) and learn about the development process in R and Bioconductor. I joined this group to stay updated about opportunities.
2024-07-15
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Maria Doyle (15:17:54) (in thread): > @Laurent Gatto, check out Sudipta’s intro above. He’s into proteomics and looking to contribute. Could be a great connection if you have any suitable projects.
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Sudipta Hazra (19:38:31) (in thread): > Hi Maria, Thank you. Yes I am interested to contribute. > > A little more about me, > > Currently, I am focused on developing protocol for downstream analysis of food proteomics data using R and Biocondutor. While doing this, I have often needed to customize the code of existing packages. One example is, when enriching primary gene names from Uniprot using accession numbers. I observed that there is a possibility of having multiple accession numbers corresponding to one entry. Also, in a few cases, because of the continuous modification of databases, accession numbers through API calls, return NA instead of modified information. > > Though my current research mostly focuses on inferring knowledge from the dataset using open-source tools, I am very much interested in the development side of it. > > I would love to contribute (part-time) and simultaneously enhance my skills in package and shiny app development. My aim is to make it easier for researchers to extract meaningful insights from their data using open source tools (R and Bioconductor) without getting scared about “coding”. > > Though the same goal can be achieved through a combination of multiple other non-coding-based tools, but it reduces reproducibility.
2024-07-18
Laurent Gatto (05:19:32) (in thread): > Hi@Sudipta Hazra- welcome to Bioconductor and proteomics. > * There’s a#proteomicschannel - very low traffic, and you are welcome to bring some life to it. > * Re contributions, theR for Mass Spectrometryeffort is active, and welcomes contributions. > * Re your conversion issues, yes, that’s the nature of the beast. You would think that gene-transcript-protein identifiers should be in sync, according to the central dna-rna-protein dogma, but they are not, at least between databases and name spaces. - Attachment (rformassspectrometry.org): Home > R software for the analysis and interpretation of high throughput mass spectrometry assays.
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Adeshile Oluwatosin (11:32:48): > Hello Everyone, > > I am Adeshile Oluwatosin. I have a BSC in Biochemistry, hoping to further my masters in bioinformatics. > > I am writing to volunteer in any ongoing projects particularly bugSIgDB projects.I joined this group to gain experience in this field bioconductor. Kindly navigate me through what to do to begin my journey.
idiaru Angela (11:43:21) (in thread): > Hi and welcome@Adeshile Oluwatosin
Adeshile Oluwatosin (11:46:13) (in thread): > Thank you
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2024-08-05
Andres Wokaty (10:55:54) (in thread): > Welcome@Adeshile Oluwatosin. I recommend joining the project channel#bugsigdband asking there:slightly_smiling_face:
Adeshile Oluwatosin (10:56:23) (in thread): > Okay, thank you > I already did that
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2024-09-13
Gobi Dasu (18:23:17): > Hi, I amGobi, and I look forward to learning a lot from this group. I’m a tech lead and PM withldtalentwork.com— a project born out of Stanford University. It’s a tool that helps you find diverse vetted developers and helps you manage them in an efficient and transparent way.Free Trial: It gives you ~5 free hours to try them before hiring them for contract or full-time roles. To see how incredibly unique LD is, check out this video:https://www.youtube.com/watch?v=EVAo8LPCZmA.Mission: To strengthen remote teams by helping them drop location constraints and include qualified but overlooked talent from the majority world:diversity meets capitalism.Here is our one pager:https://bit.ly/3ShMLJZ. We are always looking for brutally honest feedback:slightly_smiling_face: - Attachment (YouTube): LD Talent - Find Diverse Vetted Developers - See the Future of Work
2024-09-14
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Jasmine Baker (12:49:58): > Hi everyone! I am a staff scientist. I would love to learn more about the education and training aspects of bioconductor! I have a background in bioinformatics, variants and genomics.
Vince Carey (14:33:17): > hi@Jasmine Bakerhave a look atworkshop.bioconductor.organd#education-and-training… there’s work to be done on our tools for genetic variants (VariantAnnotation package) if you have time and energy …
Jasmine Baker (15:04:08) (in thread): > Awesome. I will take a look!
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Maria Doyle (16:56:07) (in thread): > Welcome, Jasmine!:blush:Just to add to what Vince said, you can also check out the education and training resources here:https://bioconductor.org/help/education-training/. We also have monthly meetings, and you’d be very welcome to join or drop in anytime! - Attachment (bioconductor.org): Bioconductor > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.
Jasmine Baker (16:58:05) (in thread): > Thank you for the link@Maria Doyle. I will definitely drop into the monthly meeting.
2024-09-25
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Tobi Ogunbowale (09:52:12): > Hello everyone, I amTobi Ogunbowale, and I’m excited to join this community. I hold a bachelor’s**** in Microbiologyand two masters, one inMedical Microbiologyand another inBiomedical Informatics. I currently work as aResearch Technicianin the University of Buffalo’s Department of Medicine’sOncology Unit, where I apply my organizational and bioinformatics skills to research onprostate cancer**. I am looking forward to learning from and contributing to this community.
2024-09-26
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Peace Anosike (18:56:41): > Hi.. Everyone, I’m Peace from Nigeria, aM.scstudent of aquaculture. I have no knowledge of Bioconductor, but I am willing to learn and contribute with my little knowledge in tech.
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2024-10-02
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Ruqayyah (03:38:36): > Hello Everyone, I am Ruqayyah. I am excited and grateful to be here. > I would really appreciate all form of help and direction the mentors would give. > I am opened and quick to learn and I believe with you all’s help, we would be able ro make a great contribution to the project.
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Agatha (03:48:46): > Hello everyone, I am Agatha from Nigeria. I am so grateful to be here. I hold an M.sc degree in Entomology and Environmental biology. I have no knowledge in bioconductor but I am willing to learn and contribute with the little knowledge I have in tech. > I look forward to a successful teamwork . Thank you
Agatha (03:54:01): > I was told about a task that was given out by one of the mentors, I am still trying to navigate and get familiar with this space. Please can someone help and direct me to the task? Thank you
Eniola Kolawole (03:55:01) (in thread): > Are you an outreachy applicant?
Aleru Divine (03:55:57): > Hi@Agatha, please just the#bugsigdbchannel.There’sa lot of information on how to get started on there.Welcome:hugging_face:
Mohamed Osman Omar (03:58:29): > @Mohamed Osman Omar has joined the channel
Mohamed Osman Omar (04:06:09): > Hi, My Name is Mohamed Osman Omar, I am one of controbutors, So Happy part of you
Svetlana Ugarcina Perovic (04:08:58) (in thread): > Hi Mohamed, please go to#bugsigdband feel free to introduce yourself there. Welcome aboard!
Arpita (04:15:57): > Hi everyone, I am Arpita and I am happy to contribute to the community.
Svetlana Ugarcina Perovic (04:17:32) (in thread): > Hi Arpita, please go to#bugsigdband feel free to introduce yourself there. Welcome aboard!
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Joy (04:53:31): > Helloeveryone, > > My name is Joy, and I’m an Outreachy applicant for the December 2024 to March 2025 round. I’m excited to contribute to the MolEvolvR project and to collaborate with such a talented and diverse group! > > I have experience with R programming, bioinformatics, literature review, and I am eager to learn and grow alongside this community. I’m especially looking forward to contributing to the project’s development and learning more about bioinformatics tools. > > Looking forward to working with you all and learning from this experience!:blush:
Svetlana Ugarcina Perovic (04:54:51) (in thread): > Hi Joy, please go to#bugsigdband feel free to introduce yourself there. Welcome aboard!
Chris Awoke (05:00:47) (in thread): > Hi,@Joy. You’re welcome. Kindly join the#bugsigdbchannel to get started. > > You’ll see the pinned message by@Svetlana Ugarcina PerovicOr here’s it:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539You can thereafter, check this one by@Aleru Divine:point_right:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:
Agatha (05:08:23) (in thread): > Yes
Agatha (05:11:00) (in thread): > Yes dear and I will appreciate all the necessary help I can get > > Thank you
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Matthew Idungafa (07:39:40) (in thread): > Thanks@idiaru Angela, i appreciate
Jasmine Baker (09:48:12) (in thread): > @Vince Careywould you mind elaborating what type of work needs to be done? I looked around, but I wasn’t sure.
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Ekunola Paul O. (11:24:52): > Hello everyone! > > I’m Ekunola Paul, excited to contribute to the Bioconductor MolEvolvR project. I have experience in coding:computer:, bioinformatics:dna:, and love collaborating:handshake:Looking forward to learning from and collaborating with this amazing community!:blush:
Adeshile Oluwatosin (11:25:57) (in thread): > Welcome@Ekunola Paul O.check out#molevolvr:blush:
Mildred Anashie (11:25:58) (in thread): > Hi@Ekunola Paul O.Welcome:hugging_face:
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Dorcas Samuel (11:35:46): > Hello everyone!I’mDorcas Samuel andI’man outreachy applicantI’mnew to Microbiome butI’mready to learn and contribute to this awesome project,I’llbe contributing to the Microbiome Study Curation. > Can someone guide me in what steps to take
Adeshile Oluwatosin (11:41:00) (in thread): > Welcome@Dorcas Samuel:hugging_face:
James Efienemokwu (11:54:51): > Hello everyone, my name Is James Efienemokwu I am a full stack developer and technical writer with a background in bioinformatics and biochemistry. It is a pleasure to be part of the Bioconductor community, I am very eager to learn and contribute to this awesome project, thank you.
Ekunola Paul O. (11:58:34) (in thread): > Thank you@Adeshile Oluwatosin@Mildred Anashie
Andres Wokaty (12:15:47) (in thread): > I recommend joining#bugsigdband checking the pinned messages for guidance:slightly_smiling_face:
Adeshile Oluwatosin (12:33:58) (in thread): > Welcome:hugging_face:
Dorcas Samuel (13:00:31) (in thread): > Thank you
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Janani Ravi (13:45:46) (in thread): > hi@Joy, welcome to Outreachy – please join#molevolvrand introduce yourself.
Janani Ravi (13:46:27) (in thread): > Welcome to outreachy,@Ekunola Paul O.! As Adeshile mentioned, please join us at#molevolvrand introduce yourself there.
Janani Ravi (13:48:29) (in thread): > Hi James, would you be contributing to#molevolvr? If so, please join us there & introduce yourself!
Ekunola Paul O. (14:08:46) (in thread): > Thank you@Janani Ravi, will do that
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Matthew Idungafa (15:58:07): > Hello everyone, I am Matthew Idungafa An Outreachy applicant with a background in Human Anatomy, > > I have experience in software development and research writing. > Looking forward to have an amazing experience here
Mildred Anashie (15:59:04) (in thread): > Welcome@Matthew IdungafaPlease join#bugsigdbto join the conversation and get started if you will be contributing to Microbiome study curation
Chris Awoke (16:01:20) (in thread): > Hi,@Matthew Idungafa. You’re welcome. Kindly join the#bugsigdbchannel to get started. > > You’ll see the pinned message by@Svetlana Ugarcina PerovicOr here’s it:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539You can thereafter, check this one by@Aleru Divine:point_right:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:
Adeshile Oluwatosin (16:33:46) (in thread): > Welcome@Matthew Idungafa
Adeshile Oluwatosin (16:35:06) (in thread): > Check out#bugsigdband#molevolvrAnd join the interested channel to begin !
Daud Ahmed (17:00:53): > @Daud Ahmed has joined the channel
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2024-10-03
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Matthew Idungafa (09:46:29): > Welcome@Daud Ahmed, it’s nice to have you here. Feel free to ask questions when you feel lost
Toluwalase Abigail (10:33:11): > @Toluwalase Abigail has joined the channel
rhoda (11:15:02): > @rhoda has joined the channel
Veronicah Wags (11:55:53): > Hi everyone!:blush:My name is Veronica Waiganjo > Looking forward to connecting and learning from you all, and contributing to the community!:rocket:
Yoko C (12:58:22): > @Yoko C has joined the channel
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Adeshile Oluwatosin (14:01:35) (in thread): > Welcome@Veronicah Wags
Dan-Aletor Daniela (14:23:34): > Hello everyone! > > I’m Dan-Aletor Daniela and I’m an outreachy applicant > I’m new to Microbiome but I’m ready to learn and contribute to this awesome project, I’ll be contributing to the Microbiome Study Curation.
Himanshi Srestha (14:43:35): > @Himanshi Srestha has joined the channel
Adeshile Oluwatosin (15:26:57) (in thread): > Welcome:hugging_face:To get started, join #bugSigDB channel ! > 1. Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > 2. Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > 1. Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > 1. Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:
Jessica Oviahon (20:29:03): > @Jessica Oviahon has joined the channel
Jessica Oviahon (20:46:27): > Hello everyone,My name is Jessica, and I am an Outreachy applicant. I am excited to be part of this community and look forward to contributing to the project. I would greatly appreciate any guidance and knowledge that can help me get started and make meaningful contributions. > Thank you.
Joy (21:04:27): > Helloeveryone, > > My name is Joy, and I’m an Outreachy applicant for the December 2024 to March 2025 round. I’m excited to contribute to the MolEvolvR project and to collaborate with such a talented and diverse group! > > I have experience with R programming, bioinformatics, literature review, and I am eager to learn and grow alongside this community. I’m especially looking forward to contributing to the project’s development and learning more about bioinformatics tools. > > Looking forward to working with you all and learning from this experience!:blush:
Inimfon Ebong (21:12:15): > @Inimfon Ebong has joined the channel
abdulwasiu maryam (22:39:15): > Good day everyone, I am Maryam, I would be glad to be a contributor to theMicrobiome Study Curationproject
Teresia (23:05:20): > @Teresia has joined the channel
2024-10-04
Agnes Obianuju Anosike (02:02:46): > @Agnes Obianuju Anosike has joined the channel
Monisa Hasnain (02:03:38): > @Monisa Hasnain has joined the channel
Agnes Obianuju Anosike (02:37:48): > Hi everyone, > I am Agnes, a Python developer with research skills. > > I look forward to collaborating and making quality contributions. > > Thank you
Adeshile Oluwatosin (02:43:45) (in thread): > Welcome@Agnes Obianuju Anosike:hugging_face:Check out#bugsigdb#molevolvr
Oluwatomisin Omojokun (04:12:22): > Good morning my name is Oluwatomisin, I’m glad to be here again.:relaxed::relaxed:Looking forward to amazing contributions and collaboration.
Adeshile Oluwatosin (04:27:33) (in thread): > Welcome@Oluwatomisin OmojokunCheck out#bugsigdband#molevolvr:hugging_face:
Adeshile Oluwatosin (04:27:46) (in thread): > Join one of the channels and start contributing
Princess Rehoboth Asuelimen (05:18:06): > @Princess Rehoboth Asuelimen has joined the channel
Agnes Obianuju Anosike (05:20:04) (in thread): > Thank you
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2024-10-05
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Ochogwu Emmanuel (05:23:40): > Hello everyone, my name is Emmanuel, I am an outreachy applicant. I am excited to contribute to this project as it align perfectly with my goals. Please I will need a work through or guidance on how to contribute effectively to this project.
Adeshile Oluwatosin (05:23:56) (in thread): > Welcome@Ochogwu Emmanuel:hugging_face:
Adeshile Oluwatosin (05:24:21) (in thread): > Check out#bugsigdband#molevolvrJoin one of the channels to get started
Adeshile Oluwatosin (05:24:42) (in thread): > Which of the projects are you interested in?@Ochogwu Emmanuel
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Ifeoma Okafor (20:40:42): > Hello everyone, > > My name is Ifeoma, and I’m thrilled to be an Outreachy applicant for the December 2024 to March 2025 period. I’m eager to contribute to both the Microbiome Study Curation project. > > I am skilled in literature review, microbiome knowledge and have some public health research knowledge. I am especially excited to contribute to the development of the project while expanding my knowledge of microbiome research. > > I’m enthusiastic to get started and learn from this experience. Looking forward to working with everyone!
Adeshile Oluwatosin (20:44:29) (in thread): > Welcome:hugging_face:@Ifeoma OkaforTo get started, join#bugsigdbchannel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the#bugsigdbchannel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:
Rita Kusi-Appiah (22:24:53): > @Rita Kusi-Appiah has joined the channel
2024-10-06
Toluwalase Abigail (00:56:33): > Hello, everyone!I’m Toluwalase, and I’m excited to be an Outreachy applicant eager to contribute to theMicrobiome Study Curationproject. I can’t wait to dive in, learn from this experience, and collaborate with all of you along the way. Looking forward to a great journey together!:hugging_face:
Adeshile Oluwatosin (03:08:28) (in thread): > Welcome@Toluwalase Abigail:blush:
Toluwalase Abigail (09:58:01) (in thread): > Thank you@Adeshile Oluwatosin:pray:
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2024-10-07
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2024-10-09
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Swazi (17:11:34): > Hello, everyone! > I’m Swazi, an Outreachy applicant, and I’m thrilled to be here! I’m looking forward to contributing, learning, and collaborating with you all throughout this journey. I can’t wait to get started and make the most of this amazing opportunity!
Adeshile Oluwatosin (18:02:55) (in thread): > Welcome@SwaziCheck out#bugsigdband#molevolvrJoin one of the channels to get started
2024-10-10
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Mohamed Osman Omar (09:26:20) (in thread): > I did it@Svetlana Ugarcina Perovicthanks
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Josh Steier (13:06:10): > Hi everyone, > I have a background in computational biology(MS applied math and stats degree from Stony Brook University), and a strong background in machine learning, where I currently work as a machine learning engineer. > I’ve been working in machine learning for roughly 3-4 years, including my educational background, and programming in Python since I was younger. > I’m eager to contribute to Bioconductor and don’t know where to start, can someone help me with that? > Thank you!
Maria Doyle (13:42:32) (in thread): > Welcome, Josh, and thanks for offering to contribute!@Lori Shepherd’ssuggestions of#machine-learningand#biocpythonare great places to start—hopefully, you’ll find something that suits you there!
Josh Steier (14:18:10) (in thread): > Thank you!
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2024-11-13
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2024-11-14
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2024-11-15
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Alex Han (13:44:39): > Hello everyone! > I’m Alex, an enthusiastic undergraduate student studying data science and biology. I am deeply fascinated by bioinformatics, where I aim to combine my interests in computational tools and biological systems. My primary areas of interest include whole-genome analysis and the development of AI-driven tools for disease diagnosis. > Thank you for having me here, and I look forward to engaging with you all!
Sergius Nyah (19:48:42): > Hello! > I’m Sergius, an Undegrad Computer Science student with a strong interest for Biologically Computational systems and ML for healthcare. Previously, I interned with MIT CSAIL under the Summer Geometry Initiative program. I’m interested in Bioinformatics and how such systems are developed, and I think this is the right place to begin! > How do I begin contributing? [GSoC ’25 in view as well]!
Vince Carey (21:23:49): > Hi Sergius and welcome! Are you in the Boston area?
2024-11-16
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Sergius Nyah (19:31:10) (in thread): > I’m not. I’m abroad!
2024-11-17
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2024-11-18
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2024-11-19
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2024-11-20
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2024-11-21
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Meg Urisko (17:32:45): > Hi:wave:I’m Meg, and I’m a user researcher working at the Chan Zuckerberg Initiative, where I support tools likeCELLxGENEandCxG Census. I’ll be reaching out from time to time when we’re looking for feedback on our tools, but also always happy to hear feedback or help get support if you have questions about any of our tools.
Maria Doyle (17:49:50) (in thread): > Hi Meg, I’m Maria, the Bioconductor Community Manager. Delighted to see the Chan Zuckerberg Initiative engaging with the community here!:blush:
Maria Doyle (18:23:25) (in thread): > Hi Sergius, thanks for offering to contribute! You might find the#biocpythonchannel helpful. There are some project suggestions in there that could align well with your GSoC ’25 plans!
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2024-11-22
Gen B (10:56:48): > Hi everyone! My name is Genevieve and I’m currently a Bioinformatician at UMMS with a background in microbiology and neurobiology. My initial love of science eventually led me to pursue my BS in Biology and MS in Bioinformatics at LUC. I’m excited to be part of this community and looking forward to connect with others in bioinformatics/comp bio/data science/tech and to learn from everyone:slightly_smiling_face:
2024-11-23
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2024-11-24
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2024-11-25
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Sergius Nyah (08:11:30) (in thread): > Cool, Thanks! > Looking into it!
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2024-11-26
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2024-11-27
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2024-11-28
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2024-11-29
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2024-11-30
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2024-12-02
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2024-12-03
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2024-12-04
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2024-12-05
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2024-12-06
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2024-12-08
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2024-12-11
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2024-12-12
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2024-12-13
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Kateřina Matějková (05:15:25): > Hello everyone. I am Kateřina and I am a bioinformatician and a PhD candidate at First Faculty of Medicine, Charles University in Prague. My main focus is NGS, specifically splicing analysis in hereditary cancer syndromes. I am glad I can connect with others in the field and I hope to be able to seek some advice or guidance if needed.:relaxed:
Jan (06:15:48): > @Jan has joined the channel
Dinesh Sharma (06:57:22): > Hey hi everyone,To introduce myself I am Dinesh Sharma (final year PhD Student at IIT Delhi, India). My research area is focused on on computational genomics andbioinformatics, particularly in understanding the physicochemical properties of DNA. I am developing a universal genome annotation software pipeline using machine learning and deep learning techniques to efficiently identify and characterize genome elements such as promoters and exon-intron boundaries. Additionally, I am interested in applying these methods to better understand genomic diseases and related ailments.I am looking for some postdoc opportunities (preferably USA) to carry forward my research in Genomics and Bioinformatics. I will be grateful for any sort of leads and help.Thank you.Regards,Dinesh Sharma
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2024-12-14
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2024-12-17
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2024-12-18
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2024-12-19
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Ndukauba Oluchi (14:58:41): > Hello everyone, > My name is Oluchi a graduate of Biochemistry (B.sc.) and I am very much interested in bioinformatics, I am a data analyst as well > I am so happy to be here. > > Regards > Oluchi:hearts:
2024-12-20
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2024-12-21
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2024-12-23
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2024-12-24
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2024-12-26
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2024-12-27
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willie (08:07:23): > Hi everyone > I am Wiliiam Boateng > A bioinformatician at the Noguchi Memorial Institute for Medical Research > I am happy to be part of this group/family
Rasmus Hindström (09:31:46): > Hello! I’m Rasmus Hindström. I have a Bsc. In Biology with a major in Genetics and currently wrapping up my graduate studies in Computational Biology. Looking forward to getting my hands dirty and finding some projects to contribute to. My research interests revolve around host-microbiome interactions and am deeply enthusiastic about bayesian statistics and science communication!
2024-12-28
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Taofeecoh Adesanu (10:00:49): > Hello! > My name is Taofeecoh Adesanu, a Bio-imaging technician with a background in Human Physiology. I took a deep interest in how technology could be used to help bio-image analysis and got to know about Bio-Informatics. > I had taken a 1-year fellowship program in Data Science and currently enrolled in a Bio-Informatics bootcamp which would be rounding up in a few weeks. One of the exciting projects I’ve worked on here is building a Gene ID Converter Application with R Programming. > I am currently looking to apply my skills and contribute to open source Bioinformatics projects.
apekshya kandel (10:07:04): > Hello everyone, > I am Apekshya Kandel, a student pursuing an MSc in Bioinformatics. I completed my undergraduate studies in Agricultural Science. I have experience working on various gene information mining projects, transcriptomics, and web development. I am seeking opportunities to learn and contribute to open-source Bioinformatics projects.
megha joshi (10:11:32): > @megha joshi has joined the channel
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2024-12-29
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Innas Widiasti (00:35:53): > Hello everyone! > I am Innas Widiasti, a Research Associate in Dharmais National Cancer Center Hospital in Indonesia. I completed my graduate studies on Biomedical Sciences in Bioinformatics. I have experience working on metabolomics and cancer tertiary analysis data. I’m looking for chances to learn and participate in open source bioinformatics projects.
Yahya Jahun (03:59:07): > @Yahya Jahun has joined the channel
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2024-12-30
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2025-01-01
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2025-01-02
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Gloria Amor Arroyo (08:30:51): > Hello Everyone! I am Gloria Amor Arroyo. I am currently pursuing an MSc in Bioinformatics after completing my undergraduate studies in Biomedical Sciences. I am looking to get hands-on experience on some bioinformatics projects as well as contribute to open-source projects. I am not sure where to start with this so I would appreciate any tips!
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2025-01-03
Pariksheet Nanda (14:26:08) (in thread): > For getting experience being new to Bioconductor, usually it’s good to try and incorporate using it into things “you would need to do anyway” over the course of your masters. So if you have some other non-Bioconductor tool you’re currently using you could try to replace it with a Bioconductor equivalent and allow your self maybe 4x more time than typical to get to learn along the way. Happy to answer questions on#generalbut there’s also the support sitehttps://support.bioconductor.org/that the package authors / maintainers are subscribed to if you have any questions.
2025-01-05
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2025-01-06
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2025-01-08
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2025-01-09
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2025-01-10
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Brian Repko (09:30:55): > Hello! I’m Brian Repko - I work in Oncology Research with Novartis as well as being the Minneapolis-St Paul (MN) city captain for BitsInBio. R package developer (and more) but have only helped with some design on MultiAssayExperiment within BioC. I’m actually retiring in May 2025 and am hoping to work on spatial transcriptomics data, single-cell data, MAE in terms of engineering / scaling work (and interoperability) as well as some pharmaverse packages (for R package testing / validation).
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2025-01-11
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2025-01-13
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2025-01-14
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2025-01-16
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2025-01-17
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2025-01-21
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2025-01-24
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2025-01-27
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Heather Turner (06:25:07): > French-speaking/English-speaking R Dev Day at University of Mons, Belgium, 22 May 2025:https://pretix.eu/r-contributors/r-dev-day-rr2025/. > > Join us for this open, collaborative event for people interested in contributing to the code and documentation of base R, or to infrastructure that supports such contribution. Both new and experienced contributors are welcome! > > This is straight after Rencontres R 2025 (https://rr2025.sciencesconf.org/?lang=fr), but registration for Rencontres R is not required. Registration for the R Dev Day is free of charge (includes lunch and refreshments!). - Attachment (pretix.eu): R Dev Day @ Rencontres R 2025 > 22 Mai 2025
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2025-01-28
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2025-01-29
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2025-01-30
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2025-01-31
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Bastien CHASSAGNOL (17:02:33): > Hi Everyone, > > I’m Bastien CHASSAGNOL, and I’m interested in the following topics:
Bastien CHASSAGNOL (17:02:57): > * Development of advanced statistical methods for analysing single-cell and spatial omics
Bastien CHASSAGNOL (17:04:27): > * Better integration betweenellmerandBioChatterpackage (in other words, bring the RAGs implemented in Python for Biological use cases to R/BioConductor) > * Benchmarking cell-cell-communication inference methods, pairing single-cell and spatial omics.
Bastien CHASSAGNOL (17:05:01): > * Development of a new bulk omic deconvolution algorithm natively integrating gene regulatory networks for advanced characterisation of closely related cell types.
Bastien CHASSAGNOL (17:07:45): > Also, I used to be a R instructor for INSEE, the statistical public French agency providing with all governemental statistics and polls, from elementary data analysis tasks to hading out advanced econometric notions: > * Tidyverse ecosystem. > * ggplot2and visualisation in R > * Advanced string manipulation throughstringr > * Advanced data analysis withduckdbfor native DBMS integration ordata.table. > * Econometrics and survey sampling
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2025-02-02
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Vince Carey (11:46:21) (in thread): > Welcome@Bastien CHASSAGNOL. It looks like we need a channel for LLM discussion. I’ll create one now, but if I missed something already in use please let me know.
Bastien CHASSAGNOL (13:22:21) (in thread): > Hi Vince, > I’m quite interested in the development towards LLMs tailored to biological applications in R, starting from a Hackathon contribution to theBioChatterpackage. > However, I’m really a newbie in this field, so apart from Sebastian Lobentanzer, I do not know other R experts or channels dedicated to that topic. > > Nonetheless, I’m grateful for adding me to this prelimineary research:slightly_smiling_face:
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2025-02-03
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2025-02-05
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2025-02-06
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2025-02-07
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2025-02-09
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2025-02-10
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2025-02-11
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Juliana Kentomahun Mautin (13:28:25): > Hello everyone, My name is Mautin from Lagos Nigeria. I’m super excited to join this amazing community. I’m looking to learn, connect with amazing community members and also grow. I can also that the Microbiome Study curation community fosters and inclusive and collaborative community of developers and data scientist. > > I’m not a developer and data scientist but I have nocode skills. Is there a space for me to learn and contribute to the community regardless of my skills?
Svetlana Ugarcina Perovic (15:45:29) (in thread): > Hi Juliana, please join#bugsigdbchannel and feel free to ask questions there related to the Microbiome Study Curation project. Thanks!
2025-02-12
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Juliana Kentomahun Mautin (02:21:26) (in thread): > Ok… Thank you
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2025-02-13
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Anushka Paharia (09:29:00): > Hello everyone, > I am Anushka, a cs undergrad from India. I am enthusiastic about Data Science and open source. I’m hoping to participate in this cohort of Outreachy. I wanna know what kind of prior skills I should have before I dive into the contribution phase. I have done data science projects and programming in R. Thankyou.
Svetlana Ugarcina Perovic (09:33:04) (in thread): > Hi Anushka, please join#bugsigdbchannel and feel free to ask questions there related to the Microbiome Study Curation project. Thanks!
2025-02-14
zetianjia (03:23:31) (in thread): > Dear Anushka, > Hello! It’s great to hear from you and to know that you’re enthusiastic about data science and open source. Participating in Outreachy is an excellent opportunity to dive deeper into these areas while contributing to meaningful projects. > Before diving into the contribution phase, here are a few skills and preparations that will help you get started: > 1. Version Control with Git > > * Familiarize yourself with Git for managing code versions and collaborating with others. Many open-source projects use GitHub or GitLab. > * Resources to learn Git:Git Tutorial,Pro Git Book. > > 1. Problem-Solving Skills > > * Practice debugging and troubleshooting, as these are essential for identifying and resolving issues in code. > * Work on small projects or challenges to improve your problem-solving abilities. > > 1. Data Science Tools > > * Since you already have experience with R, consider exploring Python if not familiar—many open-source data science libraries (like NumPy, Pandas) are in Python. > * Familiarize yourself with tools like Jupyter Notebooks for prototyping and sharing your work. > > 1. Open Source Contribution > > * Start by exploring repositories on GitHub or GitLab related to your interests. Fork repositories, create branches, and submit pull requests for small fixes or features. > * Many projects have “good first issues” tagged for beginners. > > 1. Communication Skills > > * Effective communication is key in open-source collaboration. Learn how to write clear commit messages, ask questions on forums (like GitHub Issues), and engage with the community. > > 1. Learning Resources > > * Explore platforms likeKagglefor data science projects. > * Check out free online courses like those onCourseraoredXto strengthen your skills in areas like machine learning, statistics, and programming. > > 1. Time Management > > * As an undergraduate student balancing coursework and projects, managing time effectively will be crucial. Prioritize tasks and set realistic deadlines for yourself. > If you’re unsure where to start, don’t hesitate to ask the Outreachy team or your project mentor for guidance. Many open-source communities are welcoming and supportive of newcomers. > Good luck with your application and participation in Outreachy! Keep exploring and contributing—you’ll gain valuable experience and skills along the way.:blush: - Attachment (git-tower.com): Tower Git Client - Tower — The most powerful Git client for Mac and Windows > Over 100,000 developers and designers are more productive with Tower - the most powerful Git client for Mac and Windows. - Attachment (kaggle.com): Kaggle: Your Machine Learning and Data Science Community > Kaggle is the world’s largest data science community with powerful tools and resources to help you achieve your data science goals. - Attachment (Coursera): Coursera | Degrees, Certificates, & Free Online Courses > Learn new job skills in online courses from industry leaders like Google, IBM, & Meta. Advance your career with top degrees from Michigan, Penn, Imperial & more. - Attachment (edX): Build new skills. Advance your career. | edX > Discover thousands of offerings — from free courses to full degrees — delivered by world-class partners like Harvard, Google, Amazon and more.
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2025-02-16
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2025-02-17
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2025-02-19
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2025-02-20
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James Nemesh (09:28:57): > Hi! I’m Jim Nemesh, a developer of many softwarepackagesover at theBroad Institutein the US. Most of my work in recent years (since 2012) has been in the single cell RNASeq, developing new methods for data cleanup and analysis, as well as generating end-to-end pipelines to take data from raw fastq files to digital expression matrices. I’ve dropped into this slack to get feedback/advice on publishing my latest methodDropSifton Bioconductor - we wanted to create a more “official” release of the software than just directing people to some random github repo. - Attachment (broadinstitute.org): Broad Institute > Broad Institute is a multidisciplinary community of researchers on a mission to improve human health.
2025-02-21
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2025-02-22
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2025-02-25
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2025-02-27
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2025-02-28
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2025-03-02
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2025-03-03
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2025-03-04
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2025-03-05
Scott Chamberlain (13:43:48): > @Scott Chamberlain has joined the channel
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2025-03-06
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2025-03-09
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2025-03-10
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2025-03-11
Sanika Menkudale (07:09:29): > @Sanika Menkudale has joined the channel
Sanika Menkudale (07:16:27): > Hello, > I am Sanika, a computer Engineering undergrad from India. I am enthusiastic about open source. I’m looking forward to participate in this cohort of Outreachy. I wanna know what kind of prior skills I should have before I dive into the contribution phase and will you please guide me how to contribute in project. Thankyou
Svetlana Ugarcina Perovic (08:19:29) (in thread): > Hi Sanika, please join#bugsigdbchannel and feel free to ask questions there related to the Microbiome Study Curation project. Thanks!
Ying Lu (13:37:32): > @Ying Lu has joined the channel
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2025-03-12
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2025-03-13
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2025-03-14
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2025-03-15
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2025-03-16
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2025-03-17
Keenan (09:52:07): > @Keenan has joined the channel
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Shade Akinremi (12:04:33): > @Shade Akinremi has joined the channel
thebluevirtue (12:12:34): > @thebluevirtue has joined the channel
Jesulolufemi Adelanke (12:14:44): > @Jesulolufemi Adelanke has joined the channel
Eseoghene Cynthia Princewill-Ukot (12:22:59): > @Eseoghene Cynthia Princewill-Ukot has joined the channel
progress olaoye (12:28:23): > @progress olaoye has joined the channel
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Jesulolufemi Adelanke (12:55:38): > Hello everyone, > My name is Jesulolufemi Adelanke. I’m really excited to be here and contribute to this project. > Looking forward to interacting with everyone. Nice to meet y’all.
Svetlana Ugarcina Perovic (12:59:08) (in thread): > Hello, please join#bugsigdbchannel and feel free to ask questions there related to the Microbiome Study Curation project. Thanks!
Dorcas Odetayo (13:11:23): > @Dorcas Odetayo has joined the channel
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Jane Ezeala (Jannyblink’s) (14:08:11): > @Jane Ezeala (Jannyblink’s) has joined the channel
Jane Ezeala (Jannyblink’s) (14:19:32): > Hello everyone! my name is Jane Ezeala, and I’m excited to be part of this group. I look forward to learning, collaborating, and sharing insights with you all.
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Ndukauba Oluchi (14:28:58): > Hello@Jesulolufemi Adelanke@Jane Ezeala (Jannyblink’s)please search for#bugsigdband introduce yourself there > thank you so much:hearts:
Ambogo (14:30:08): > @Ambogo has joined the channel
Jane Ezeala (Jannyblink’s) (14:44:41) (in thread): > Done > Thanks
Utibe Ita (14:49:55): > @Utibe Ita has joined the channel
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2025-03-18
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Star Chukwunyerenwa (Ozi) (05:20:11): > @Star Chukwunyerenwa (Ozi) has joined the channel
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chiamaka Uche (06:00:54): > @chiamaka Uche has joined the channel
chiamaka Uche (06:10:15): > Hello Everyone, My name is Chiamaka Uche and i’m part of the outreachy contribution. I’m exicted to get started, learn and meet new people.
Mildred Anashie (06:11:05) (in thread): > Hi@chiamaka UcheWelcome > Please join#bugsigdbto get started
chiamaka Uche (06:11:39) (in thread): > Thanks.
Oladipo Abolanle (07:20:40): > @Oladipo Abolanle has joined the channel
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Munachi Elekwa (10:15:26): > Hello everyone, I’m Munachi Elekwa, an outreachy applicant and I’m excited to contribute and collaborate on this project
Taofeecoh Adesanu (10:17:08) (in thread): > Welcome@Munachi Elekwa! > Kindly join#bugsigdbchannel.
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Adebisi Adeyemi (11:49:10): > Hello everyone, I’m Adebisi Adeyemi. looking forward to contributing and learning with you all.
Anthony (13:07:57): > @Anthony has joined the channel
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Ndukauba Oluchi (13:44:38): > Welcome@Adebisi Adeyemikindly join#bugsigdbchannel and introduce yourself there.
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2025-03-19
Amaka (03:48:02): > @Amaka has joined the channel
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iniobong simeon (10:10:26): > @iniobong simeon has joined the channel
iniobong simeon (10:17:15): > Hello everyone, my name is Iniobong Simeon, i am happy to be part of this group and hope it brings the best out of me.
Mildred Anashie (10:23:56) (in thread): > Hi@iniobong simeonJoin#bugsigdbto get started
Ayomide Olugbenga Ojo (11:16:53): > @Ayomide Olugbenga Ojo has joined the channel
Oriade Adeola (11:42:24): > Hi everyone! > I am Adeola Oriade, a Product Designer with a skill in UI/UX, user research and documentation. I am excited to be contributing as an outreachy applicant.
Taofeecoh Adesanu (11:43:20) (in thread): > Welcome@Oriade AdeolaPlease join#bugsigdbchannel to get started.
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2025-03-20
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2025-03-22
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2025-03-24
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2025-03-25
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2025-03-26
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2025-03-27
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2025-03-28
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2025-03-29
Hashaam Khan (18:22:12): > @Hashaam Khan has joined the channel
Hashaam Khan (18:24:34): > Hello Everyone, My name is Meer Hashaam Khan, i am excited to work, contribute in this community and help others.
2025-03-30
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aw (13:00:56): > @aw has joined the channel
2025-03-31
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2025-04-01
Noel Okumu (07:00:14): > Hi Team, > > Noella Okumu here from Kenya. Currently looking for opportunities to help in Transcriptomicanalysis to continue refining my skills. I am etremely happy to have joined this vibrant community. I have intermediate level R knowledge and RNA-Seq data analysis.
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2025-04-02
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2025-04-03
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2025-04-04
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2025-04-07
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Precious (11:17:01): > :wave:Hello, team!
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2025-04-08
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2025-04-09
Felix Lisso (04:02:06): > Hi Team, > Felix Lisso from Tanzania. I am excited to join this community. Looking forward to learn, network and contribute.
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2025-04-10
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2025-04-11
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2025-04-13
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2025-04-14
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2025-04-17
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2025-04-18
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D. Taylor (11:08:04): > I’m a retiree that refuses to stop. > My main interests are in Micro-Biology. Mycologie - Fungi, Virus research with Phages. Any local ( to me in Stuttgart, Germany. ) individuals or groups would be ideal.
Shashwati (15:23:48): > @Shashwati has joined the channel
2025-04-20
Dr. ZUBAIDA KHATOON (06:08:58): > @Dr. ZUBAIDA KHATOON has joined the channel
Scheduled message (23:30:03): > Hallo everyone I would like to join this bioc community for my Data Science and Bioinformatics project:thread:. I would be happy with your co-operation. Thanks, team!
2025-04-21
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2025-04-22
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2025-04-23
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2025-04-24
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2025-04-25
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2025-04-27
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2025-04-28
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2025-04-29
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2025-04-30
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