#education-and-training

2020-03-05

Sean Davis (13:05:36): > @Sean Davis has joined the channel

Sean Davis (13:05:37): > set the channel description: Discuss all things Bioc education and training-related, network with folks interested

Mark Robinson (13:06:04): > @Mark Robinson has joined the channel

Jenny Drnevich (13:06:04): > @Jenny Drnevich has joined the channel

Lori Shepherd (13:06:04): > @Lori Shepherd has joined the channel

Levi Waldron (13:06:04): > @Levi Waldron has joined the channel

Ludwig Geistlinger (13:06:05): > @Ludwig Geistlinger has joined the channel

Jenny Drnevich (13:40:13): > @Sean Davis- thanks for starting this channel and adding me! We just started teaching our RNA-Seq workshop (https://go.illinois.edu/10X-rnaseq) and the R/BioC part will start after we break for an intro workshop on March 25 (https://go.illinois.edu/introR, currently pointing to last fall’s wiki)

Sean Davis (13:47:11): > Sweet!

Sean Davis (13:58:21): > Post your own materials, discuss processes, announce courses, and perhaps do some collaborative curriculum/material development.

Sean Davis (13:59:02): > Mine are a bit messy and always a work-in-progress, but:https://seandavi.github.io/ITR/

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Ruth Isserlin (14:01:37): > @Ruth Isserlin has joined the channel

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Frederick Tan (14:05:08): > @Frederick Tan has joined the channel

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Alexander Pico (14:05:54): > @Alexander Pico has joined the channel

Jenny Drnevich (14:08:07): > very nice,@Sean Davis. We should port over all our stuff to github but just haven’t gotten around to doing it. I have been doing it for our Software Carpentry/Data Carpentry workshops (latest one:https://swc-uiuc.github.io/2020-02-06-dc-illinois/) but the template was already made up. I did do my first Rmarkdown slides for our single cell workshop last fall (https://wiki.illinois.edu/wiki/display/HPCBio/10X+Single+Cell+RNA-Seq+Analysis).

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Mikhail Dozmorov (14:17:18): > @Mikhail Dozmorov has joined the channel

Dan Bunis (14:21:36): > @Dan Bunis has joined the channel

Kevin Blighe (14:21:41): > @Kevin Blighe has joined the channel

darlanminussi (14:22:01): > @darlanminussi has joined the channel

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Marcel Ramos Pérez (14:54:57): > set the channel topic: Post your own materials, discuss processes, announce courses, and perhaps do some collaborative curriculum/material development

Alexander Pico (14:59:33): > Here are a couple notebooks we use in workshops for network analysis and visualization: > 1. https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/Cancer-networks-and-data.nb.html > 2. https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/230_Isserlin_RCy3_intro.nb.html

Leonardo Collado Torres (15:17:08): > @Leonardo Collado Torres has joined the channel

Ana Beatriz Villaseñor Altamirano (15:17:54): > @Ana Beatriz Villaseñor Altamirano has joined the channel

Federico Marini (15:22:17): > @Federico Marini has joined the channel

Federico Marini (15:22:49): > Almost surprised this channel came to life only now. Well done@Sean Davis!

Sehyun Oh (15:51:34): > @Sehyun Oh has joined the channel

Stephany Orjuela (15:53:01): > @Stephany Orjuela has joined the channel

Martin Morgan (15:53:43): > @Martin Morgan has joined the channel

Vince Carey (16:29:04): > @Vince Carey has joined the channel

Teun van den Brand (16:37:20): > @Teun van den Brand has joined the channel

Peter Hickey (17:04:43): > @Peter Hickey has joined the channel

Peter Hickey (17:05:34): > FWIW i taught a 2-day scRNA-seq workshop to 40 people at my workplace last week heavily based onhttps://osca.bioconductor.org/Content herehttp://bit.ly/WEHIscRNAworkshop - Attachment (osca.bioconductor.org): Orchestrating Single-Cell Analysis with Bioconductor > Online companion to ‘Orchestrating Single-Cell Analysis with Bioconductor’ manuscript by the Bioconductor team.

Leonardo Collado Torres (18:27:41): > I’ll be teaching a 4 day workshop to undergrad students in Mexico on March 24-27 about scRNA-seq also based on the OSCA book. I haven’t started preparing my slides yet:stuck_out_tongue:

Leonardo Collado Torres (18:27:53): > (that’s what I’ll be doing this Saturday)

Matt Ritchie (19:14:36): > @Matt Ritchie has joined the channel

dave_sevenbridges (20:08:53): > @dave_sevenbridges has joined the channel

Jayaram Kancherla (21:11:29): > @Jayaram Kancherla has joined the channel

Stuart Lee (22:44:14): > @Stuart Lee has joined the channel

Sridhar N (22:59:51): > is this the most updated guide to create a BioC packagehttps://bioconductor.org/developers/how-to/buildingPackagesForBioc/

2020-03-06

Martin Morgan (01:15:53): > yes, but this could definitely be updated (e.g., to use roxygen for writing man pages and testthat for unit tests). Input as pull requests onhttps://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/how-to/buildingPackagesForBioc.mdwelcome!

Mike Smith (01:57:39): > @Mike Smith has joined the channel

Nitesh Turaga (08:59:25): > @Nitesh Turaga has joined the channel

Sridhar N (10:41:33): > thanks@Martin Morgan

Mariam Malik (15:37:08): > @Mariam Malik has joined the channel

2020-03-08

Goutham Atla (16:58:31): > @Goutham Atla has joined the channel

2020-03-09

David J. Goldstein (09:27:50): > @David J. Goldstein has joined the channel

Stephanie Hicks (14:33:32): > @Stephanie Hicks has joined the channel

2020-03-16

Shani Amarasinghe (07:16:25): > @Shani Amarasinghe has joined the channel

Jenny Drnevich (12:03:37): > Anyone have experience running remote learning for R/BioC? With all the Covid-19 shut downs, we are debating cancelling the rest of our RNA-Seq workshop vs. teaching via Zoom.

Federico Marini (12:06:29): > Not yet, but soon it might become a need

Federico Marini (12:06:43): > I was contemplating the option to use Renku as a platform for the participants

Federico Marini (12:07:58): > which would simplify (or just delete) the bunch of so many different installation errors that would pop up on every single partiicpant’s machine

Federico Marini (12:08:40): > I had a glimpse into it at the end of EuroBioc2019 and was deeply impressed - also because@Emma Jablonskigave a stellar tour to it in a few minutes

Ludwig Geistlinger (12:11:39): > Levi and I were giving an R/Bioc Intro online-only course for Columbia last year on the base of recorded youtube clips (= lectures, highly recommend camtasia for thathttps://www.techsmith.com/video-editor.html). It figured that canvas (https://canvas.instructure.com) is a great tool for structuring contents into modules and making materials available over time. It has other useful features such as focused discussion boards, integrating conference calls, quizzes, and exams. Can invite you to our canvas course page if interested. - Attachment (TechSmith): TechSmith Camtasia | Screen Recorder & Video Editor > Camtasia 2018 makes it easy to record your screen and create polished, professional-looking videos.

Jenny Drnevich (12:26:53): > @Ludwig GeistlingerYes, I’d love to see how you’ve structured your canvas course.

Ludwig Geistlinger (12:27:50) (in thread): > will need your email to be able to invite you, can send to me via direct message on slack if you prefer so

Jenny Drnevich (12:29:22) (in thread): > done! Thanks so much

Jenny Drnevich (12:30:24): > The University of Illinois just bought everyone a Zoom license and has some tutorials on running courses via Zoom. I am having a hard time imagining how it will work given how much time we spend showing them where the typos are in their codes…

Vince Carey (16:47:14): > @Ludwig Geistlinger, I would love to look at canvas too, thanks

Ludwig Geistlinger (16:50:32) (in thread): > Sure. Just sent an invitation to your channing harvard email address.

2020-03-19

Sean Davis (08:43:07): > https://dx.plos.org/10.1371/journal.pcbi.1006419

Sean Davis (08:43:41): > https://resources.rstudio.com/upcoming-webinars/webinar-registration - Attachment (Upcoming Webinars): Upcoming Webinars > A list of upcoming webinars you can register for.

Sean Davis (08:44:09): > https://twitter.com/RStudioEDU/status/1239632892759871491 - Attachment (twitter): Attachment > Upcoming webinar: Teaching Online on Short Notice > @gvwilson shares advice for moving your in-person class online in a hurry. > March 19th at 4PM EDT > Learn more and sign up at, https://resources.rstudio.com/upcoming-webinars/webinar-registration > #rstats https://pbs.twimg.com/media/ETQPi60XkAATp6k.jpg

2020-03-22

Leonardo Collado Torres (15:54:02): > So, I’m working on my slides for a scRNA-seq analysis course based on the OSCA book by@Stephanie Hicks@Rob Amezquita@Aaron Lunet al and Pete’s slides and just finished my template slide deck athttps://lcolladotor.github.io/osca_LIIGH_UNAM_2020/00-template.html. However, I’m a bit confused by licenses. The OSCA book is licensed underhttp://creativecommons.org/licenses/by-nc-nd/3.0/us/and fromhttps://creativecommons.org/faq/#when-is-my-use-considered-an-adaptationI’m not 100% sure whether making slides based on the book is considered an adaptation. If so, then under the OSCA license I won’t be allowed to make the slides (well, maybe I can, but not host them on GitHub) under BY-NC-ND instead of BY-NC-SA. In the end, I’d like to know if it’s ok for me to create these slides based on the OSCA book or not. Thx! > > Btw Pete@Peter Hickey, I couldn’t find a license for your slides.

Rob Amezquita (15:54:08): > @Rob Amezquita has joined the channel

Aaron Lun (15:54:08): > @Aaron Lun has joined the channel

Stephanie Hicks (15:55:30): > @Leonardo Collado Torresi forget where we had a similar convo in slack before, but someone else asked a similar question. my recollection was that we had no problem with others creating slides based on the book

Stephanie Hicks (15:56:23): > but@Rob Amezquita@Aaron Lunwould be able to confirm this

Leonardo Collado Torres (16:09:34): > awesome, thanks Stephanie:smiley:

Stephanie Hicks (16:11:39): > as always, thanks for leading this effort@Leonardo Collado Torres!!

Peter Hickey (18:28:03): > yeah i asked about thishttps://community-bioc.slack.com/archives/CM2CUGBGB/p1578895401047000 - Attachment: Attachment > i’m teaching a 2-day workshop next month based on https://osca.bioconductor.org/. > this is a non-commercial event for researchers at WEHI and perhaps other research institutes. > > i’m not a lawyer but this seems permitted under the ‘CC BY-NC-ND 3.0 US’ license (https://creativecommons.org/licenses/by-nc-nd/3.0/us/). > However, my reading of the license is that i can’t distribute any slides adapted from this material (the ‘no derivatives’ clause). > is that the intention? > > Finally, is it okay to include figures from OSCA in a flyer advertising the workshop?

Peter Hickey (18:28:33) (in thread): > I hadn’t planned on making them available outside the classroom, but since a few people asked i did (and based on linked discussion with Aaron and co)

Peter Hickey (18:29:01) (in thread): > will licence them when i’ve got time

Leonardo Collado Torres (22:13:14): > Thanks Pete! From Sean’s reply to your comment, it looks like BY-NC-SA instead of the current BY-NC-ND would be a better license to use in order to explicitly allow slides instead of Rob’s “we promise not to litigate” reply (due to lack of $$). Though I just read that there’s tons of issues with building the OSCA book that I was unaware of.

Leonardo Collado Torres (22:20:06): > that is, this licensehttps://creativecommons.org/licenses/by-nc-sa/4.0/(or the 3.0 one, dunno the difference between the 3.0 and 4.0, just that 4.0 is newer)

Aaron Lun (22:21:18): > Re “issues”: there have been many difficulties. It seems that@Mike Smithhas set up an environment that resolves many of them. In the meantime, I will be spending my time more productively working on my novel.

Leonardo Collado Torres (22:27:17) (in thread): > just updated my slides to that onehttps://github.com/lcolladotor/osca_LIIGH_UNAM_2020/commit/448b882331f39127a962be6f88ddef98664a5608assuming that at some point in the future OSCA will use that one (or a more permissive one) as well as Pete’s. If not, then I’ll have to shutdown my repo of slides. Anyway, gotta actually make them now:stuck_out_tongue:

Leonardo Collado Torres (22:27:30) (in thread): > aka, be more productive as Aaron put it

2020-03-23

Laurent Gatto (07:30:29): > @Laurent Gatto has joined the channel

Peter Hickey (16:22:34): > forgot to mention, there’s a github repo with the code i used for the workshop:https://github.com/WEHISCORE/scRNA-seq_workshop

Peter Hickey (16:22:42): > usesrenvto manage dependencies

Peter Hickey (16:25:43): > I spun up a BioC AWS image (https://www.bioconductor.org/help/bioconductor-cloud-ami/), ranrenv::restore()in RStudio, then saved the image. I’m sure there’s a proper way to do this was docker but this worked well enough for me

Peter Hickey (16:25:59): > I then spun that image up on a separate AWS instance for each student, got the URLs for the 40-something instances using a script a colleague wrote, and then made a google sheet containing students emails and their assigned URL which was available from the google drive (https://drive.google.com/drive/folders/1cn5d-Ey7-kkMiex8-74qxvxtCQT6o72h) during the workshop

2020-03-24

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2020-03-31

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2020-04-06

Ludwig Geistlinger (19:47:35): > These days I always recommend The Bioconductor 2018 Workshop Compilationhttps://bioconductor.github.io/BiocWorkshops/as a starting point, due to its great structure and that it starts with the very basics - Attachment (bioconductor.github.io): The Bioconductor 2018 Workshop Compilation > This book contains all the workshops presented at the Bioconductor 2018 Conference

2020-04-09

Laurent Gatto (10:39:37): > Hello. I wanted to mention this training and education initiative:https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharingIn a nutshell, we would like to get some members of the Bioconductor community trained to develop/contribute to some Carpentries/Bioconductor material. The number of trainers that can be trained is limited by the number of places available in these Carpentries instructor trainings. If more people that can enrol in the may event are interested, I am happy to gather more names and try to coordinate. - File (Google Docs): bioc-teaching

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Liz Ing-Simmons (11:48:06) (in thread): > This sounds like a great initiative! I am already a trained Carpentries instructor and have taught at a few workshops (including one that’s mentioned in that document where we included a short introduction to Bioconductor:slightly_smiling_face:). I would be happy to share my experiences or get involved with developing Carpentries-style Bioconductor material.

Laurent Gatto (12:12:03) (in thread): > Hi@Liz Ing-Simmons- your input would be very welcome, thank you (this link should allow you the edit the document -https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharing). > If you are interested in participating more closely, let me know and I will keep you in the loop. - File (Google Docs): bioc-teaching

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2020-04-10

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2020-04-13

Jenny Drnevich (12:26:38) (in thread): > @Laurent GattoI am also interested in seeing Bioconductor lessons for the Carpentries. I went through instructor training here at Univ. of Illinois (also a gold Carpentries member) several years ago although I may not be technically certified because I didn’t complete my checkout in time. But I’ve been instructing at SWC and DC workshops for the last 3 years. We modify the lessons for our local system, and here was our last one:https://swc-uiuc.github.io/2020-02-06-dc-illinois/I am a bit time crunched at the moment so I’m not sure how much I will be able to contribute, but please keep me in the loop.

Laurent Gatto (12:31:42) (in thread): > Thanks,@Jenny Drnevich- I have added your last lesson to those already listed in the google doc. I will be sharing updates here to keep the wider community in the look. Feel free to add you name to the google doc (under theAlso interestedsection if you prefer a direct feedback).

2020-04-14

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2020-04-20

saskia (20:41:42) (in thread): > Hi@Laurent Gatto, I am also interested in taking part in the training. I will submit an application today.

2020-04-21

Laurent Gatto (04:01:50) (in thread): > Hi@saskia- great! Could you add you name under ‘possible candidates’ in the google doc, please?

saskia (23:56:50) (in thread): > Done

2020-04-22

Davide Risso (09:22:31): > @Davide Risso has joined the channel

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Kelly Eckenrode (09:27:09): > @Kelly Eckenrode has joined the channel

Laurent Gatto (11:41:16) (in thread): > Thank you!

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Levi Waldron (13:39:29): > FYI we’re organizing a single-cell multimodal data journal club:https://community-bioc.slack.com/archives/C35G93GJH/p1587573511180200 - Attachment: Attachment > Hi all!  > > I am new to this community and have introduced myself here today. I am a postdoctoral researcher with @Levi Waldron. > > I’d like to invite you to a newly forming journal club about single cell multimodal (SCMM) data with @Levi Waldron and @Davide Risso’s groups . If you have experience working with SCMM or are interested in learning more about the literature, please consider joining us. Take a look at the list of article ideas here. > > Please fill out this doodle to help us schedule our first meeting time: https://doodle.com/poll/3ry8kg66yv3rsbvq > > Join us in the #education-and-training channel. This is where I will post SCMM journal club updates. > > In addition to the journal club, if you are interested in sharing a SCMM dataset of yours or one of interest, please share with us.  To streamline our database curation, please read the following guidelines here. Parties interested in contributing would have to make a pull request to the repository. > > I’m looking forward to reading with you!

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2020-04-23

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2020-04-27

Kelly Eckenrode (14:28:00): > For those of you interested in the Single-cell Multimodal (SCMM) journal club, thank you so much for filling out the Doodle poll. According to consensus,Monday at 8am - 9am EDT / 2PM - 3PM European Central Time, is the best time.  > > Our first meeting will benext Monday, May 4thon Zoom. And alsoadd the invite to your calendar here!)We will introduce ourselves and get acquainted with the meeting format. In addition to introductions, I will also present a review paper, “A secret life of cells” by Michael Eisenstein. You can find a PDF attached here and on theSCMM journal club wikiHere you can find the agenda and where the meeting notes will be recorded:SCMM meeting notesI look forward to meeting all of you and beginning a thoughtful conversation about single cell multimodal data!

Kelly Eckenrode (14:31:37): > The secret life of cells - File (PDF): Eisenstein 2020 - The secret life of cells.pdf

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2020-04-28

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Kevin Rue-Albrecht (12:00:05): > any favorite dataset fromscRNAseqorExperimentHubfor teaching pseudotime? Bonus point for accompanying exercises:grimacing:

Aaron Lun (12:02:14): > There’s a hESC dataset in there, nestorawa.

Kevin Rue-Albrecht (12:13:01): > ok, thanks - so I was on the right track, I started toying with that one

Kevin Rue-Albrecht (12:13:43): > I just wondered if there were any exercises out there. From the Bioc courses I’ve only rediscovered the bioc2018 workshop

Aaron Lun (12:16:13): > I have a half-finished chapter in the book.

Davide Risso (12:24:08): > I have thishttps://github.com/drisso/fletcher2017data

Davide Risso (12:24:22): > Which was used in the slingshot paper

Davide Risso (12:24:44): > Never found the time to put it in scRNAseq but it is a SingleCellExperiment

Aaron Lun (12:42:01): > should consider doing so.

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Dan Bunis (13:47:48): > @Kevin Rue-Albrechtthe labels in scRNAseq’s nestorawa dataset are a bit wonky, but I’d put together some code to help parse them. In case you go with that data, I’ll add the code here.

Dan Bunis (13:48:25) (in thread): > > nest <- NestorowaHSCData() > df <- as.data.frame(as.matrix(nest$cell.type))[,1:6] > # parse > nest$calls <- as.character(sapply(seq_len(nrow(df)), > function(cell) { > names(df)[as.logical(df[cell,])] > })) > # clean > nest$calls[nest$calls=="character(0)"] <- "NA" > nest$calls <- sapply(nest$calls, > function(x) strsplit(x, split = "_")[[1]][1]) > # check > table(nest$calls) > > probably could be cleaned up some as I was just going for something quick:man-shrugging:

Dan Bunis (13:50:26) (in thread): > @Aaron Lun, lemme know if this calls metadata is something that should be added to the dataset. The current labeling system is a table with many overlapping calls.

Aaron Lun (13:50:43) (in thread): > probably couldn’t hurt.

Aaron Lun (13:50:47) (in thread): > You know the drill.

Kevin Rue-Albrecht (13:58:53): > thanks all - i gotta log off for now but i’ll take the advice > 1. @Davide Rissoi spotted that from the bioc2018 workshop, I’ve considered it, but I find the workflow a bit too complex for first-timers > 2. @Dan Bunisindeed the nested data structure and overlapping calls surprised me a bit, but I do like this dataset at first glance - I’m aiming to take students through 1 - maybe 2 - alternative ‘simple’ trajectory inference workflows with it, e.g. slingshot and monocle.

Kevin Rue-Albrecht (14:01:26): > i’ll admit that it’s a bit ambitious as I haven’t practiced this type of analysis recently - which is why i was looking for a refresher myself

Dan Bunis (14:03:09): > :+1:Sounds great!dittoSeq’s dittoDimPlot can help show the trajectories btw.add.trajectory.lineagestakes a list of cluster paths and the cells’s cluster identities to map onto any dim reduction, oradd.trajectory.curvestakes the curves spit out by slingshot but only makes sense in the original reduction used for the calculation.

Kevin Rue-Albrecht (14:04:11): > since the time that I see frequent mentions ofdittoSeqaround here, that is an excellent reminder to look it up for this class/workshop, thanks!

Dan Bunis (14:05:22): > mostly by me? its ambitious creator lol

Dan Bunis (14:06:12) (in thread): > Actually, maybe I don’t… but simple PR?

Aaron Lun (14:07:07) (in thread): > yes, that’s the drill.

Dan Bunis (14:07:08) (in thread): > (I haven’t handled any of the SingleR reference updates nor actually contributed a dataset toscRNAseqyet. Send more deets in#sc-signatureif needed? probs the better spot for this)

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2020-04-29

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2020-04-30

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2020-05-01

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2020-05-03

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Levi Waldron (17:00:05) (in thread): > @channelReminder we are starting the single-cell multimodal data journal club tomorrow morning at 8am EDT / 2pm CET, with@Kelly Eckenrodeleading discussion of “The Secret Life of Cells.”

Dan Bunis (17:06:03) (in thread): > Will these be recorded? I won’t be able to join from San Francisco at this time. (Just wondering, not complaining; I certainly could have spoken up when the planning was happening, but I did not.)

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2020-05-04

Levi Waldron (02:57:18) (in thread): > I was surprised by how many people liked the Monday 8am ET time! We’ll see today how folks feel about recording. At least, we’ll keep slides and notes in this directory.

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Aedin Culhane (12:40:17): > @Aedin Culhane has joined the channel

2020-05-05

Kelly Eckenrode (10:47:39): > Hi thereSingle Cell Multimodal Journal club! Thank you for the people who signed up to present papers in the upcoming weeks. We still need someone for next Monday. Can we ask for a volunteer?https://github.com/waldronlab/data-science-seminar/wiki/Single-cell-multimodal-data

2020-05-06

Levi Waldron (09:21:59): > <!channel>reminder that although there are volunteers for the following several weeks of single-cell multimodal journal club, there’s still no presenter fornextweek May 11. I think we’re hesitant to start random assignments on this short notice, so if there’s no volunteer we’ll have to skip a week.https://github.com/waldronlab/data-science-seminar/wiki/Single-cell-multimodal-data

Sanchit Saini (11:04:19): > @Sanchit Saini has joined the channel

Shani Amarasinghe (18:16:39) (in thread): > Hey@Kelly Eckenrodeand@Levi Waldron… I am thinking of inviting someone not in this group but who has recently developed a R package on multimodal analysis to present their work. Is that OK? Also, can I ask them to prepare for a presentation for 30 minutes or less?

2020-05-07

Levi Waldron (01:10:15) (in thread): > Sounds good to me!

Shani Amarasinghe (19:59:41) (in thread): > I received the following from the authors of scAI (https://github.com/sqjin/scAI) whom I contacted to see whether they are available for a talk (I shared the GitHub speaker list). They can’t present next Monday (:( ) + they have time zone issues…. if you could let me know how I should respond, it would be great! > ———————- > Dear Shani, > > Thank you so much for your kindly invitation. I would love to present our work at this club. However, I am sorry that I am not able to do it next Monday as I have a deadline this week.  > > It seems that there is no available slot until late June. Can I do it on 2020-07-06? I noticed that the event is held on 8am EDT, which is 5am PDT at my local time. Is it possible to postpone two hours? If this change causes much inconvenience, I am fine to do it on 5am PDT.  > > Thanks! > > Best, > Suoqin > > ———————–

2020-05-09

Preethy (16:05:19): > @Preethy has joined the channel

2020-05-10

Sangram Keshari Sahu (09:29:51): > @Sangram Keshari Sahu has joined the channel

Levi Waldron (10:23:59) (in thread): > Thanks for doing this legwork@Shani Amarasinghe!

Levi Waldron (10:24:59) (in thread): > Seems to me it would be OK to have one session later to accommodate a special guest speaker, but I’ll leave scheduling to@Kelly Eckenrode.

Levi Waldron (10:27:16) (in thread): > We will skip tomorrow but start up again the following Monday May 18 @Dominik Szabowould you post the paper you’re presenting (“Integrative single-cell analysis”)?

Dominik Szabo (15:51:23) (in thread): > Hi all, I’m excited to present an article by Tim Stuart and Rahul Satija (author of the scRNA-seq package Seurat) about integrative single-cell analysis. Please find the paper here:https://doi.org/10.1038/s41576-019-0093-7It’s quite long, but I’ll do my best to condense it down to a couple of slides. See you next week!

Shani Amarasinghe (18:58:40) (in thread): > Not a problem! I’ll add@Kelly Eckenrodeto the email… so she can communicate with them directly… :)

2020-05-13

Nadine Bestard-Cuche (10:23:53): > @Nadine Bestard-Cuche has joined the channel

Nadine Bestard-Cuche (10:49:48) (in thread): > Hi, I had a look to your wiki page and the project seems really interesting but I don’t see how to join the talks

Kelly Eckenrode (10:53:04) (in thread): > Hi Nadine! Here is the Google Drive folder where you can find the Zoom details and meeting notes.https://drive.google.com/drive/u/0/folders/1aRpIQjDHYOMOH7MFdrRUCmSPwe2kMnkA

2020-05-14

saskia (07:15:35) (in thread): > @Laurent GattoI thought I missed the deadline and applied to general carpentries courses. I am no longer free on the 19th and 20th, will there be another course this year?

Laurent Gatto (08:03:46) (in thread): > I don’t know, but I will enquire given that you are the second person asking me. In the meantime you can register your interest here -https://carpentries.org/community/#instructors - Attachment (The Carpentries): Join our Community > Find ways to engage with the global Carpentries Community, including taking part in committees and taskforces.

2020-05-15

Giuseppe D’Agostino (05:13:35): > @Giuseppe D’Agostino has joined the channel

jhawe (05:27:25): > @jhawe has joined the channel

2020-05-17

Kelly Eckenrode (14:21:43): > <!channel>As a reminder, the Single Cell Multimodal journal club will meet tomorrow, Monday May 18 at 8am EDT/2pm CET.@Dominik Szabowill lead a conversation on “Integrative single-cell analysis” byTim Stuart&Rahul Satija(https://www.nature.com/articles/s41576-019-0093-7)  > > Please check out the journal club website for meeting informationhttps://github.com/waldronlab/data-science-seminar/wiki/Single-cell-multimodal-data - Attachment (Nature Reviews Genetics): Integrative single-cell analysis > The functional interpretation of single-cell RNA sequencing (scRNA-seq) data can be enhanced by integrating additional data types beyond RNA-based gene expression. In this Review, Stuart and Satija discuss diverse approaches for integrative single-cell analysis, including experimental methods for profiling multiple omics types from the same cells, analytical approaches for extracting additional layers of information directly from scRNA-seq data and computational integration of omics data collected across different cell samples.

2020-05-18

saskia (04:25:17) (in thread): > I have registered my interest.

Levi Waldron (07:40:10) (in thread): > PDF for anyone with paywall issues - File (PDF): Stuart and Satija 2019 - Integrative single-cell analysis.pdf

Levi Waldron (07:58:21) (in thread): > Zoom made me create a new meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09

Mikhael Manurung (08:23:42) (in thread): > I would like to join, but at this moment I don’t have anything to bring onto the table as I am still very new to this field (but eager to learn). Would that be okay?

Kelly Eckenrode (09:07:58) (in thread): > Hi@Mikhael Manurung! We will be meeting next week, so please feel free to join us then. We welcome any level of experience.

Dario Righelli (09:21:41) (in thread): > For the new ones, we created a dedicated section into thegdoc_notes filefor adding your name. > This will help us to keep track of the attendees. :)

Mikhael Manurung (09:23:14) (in thread): > Thanks! I will definitely join the upcoming session.

Huipeng Li (11:04:23): > @Huipeng Li has joined the channel

Laurent Gatto (11:43:19) (in thread): > Excellent, thank you.

Kelly Eckenrode (13:47:10) (in thread): > Thank you@Dario Righelli!

2020-05-19

Dominik Szabo (03:38:07): > Hi all, there will be a virtual talk by Eileen Furlong on ‘Dissecting regulatory trajectories during embryonic development at single cell resolution’ this Friday, May 22nd, 1 pm (CEST). It’s the second seminar of the lecture series ‘Recent Advances in Single Cell Omics’ from the German single cell omics network. Thought that some of you might find this interesting. It’s free, but you need to register in advance (https://www.singlecell.de/index.php/events/scog-vls-eileen-furlong/).

Katie Hughes (09:26:02): > @Katie Hughes has joined the channel

2020-05-20

Benjamin Reisman (18:25:58): > @Benjamin Reisman has joined the channel

2020-05-24

Kelly Eckenrode (15:36:35): > As a reminder, the Single Cell Multimodal journal club will meet tomorrow, Monday May 25 at 8am EDT/2pm CET.@Dario Righelliwill lead a conversation on Mirjana Efremova and Sarah A. Teichmann’s “Computational methods for single-cell omics across modalities”.  > > Please check out the journal club website for meeting informationhttps://github.com/waldronlab/data-science-seminar/wiki/Single-cell-multimodal-data(edited)

Kelly Eckenrode (15:37:19): - File (PDF): TeichmannEfremova.pdf

2020-05-25

Levi Waldron (03:06:33): > <!channel>learn how to search cBioPortal and to download data as @Bioconductor MultiAssayExperiment objects, the result of a collaboration between cBioPortal with@Marcel Ramos Pérezand myself. cBioPortal developer@Ino de Bruijnpresents the API & R client webinar this Thursday May 28 11am-12pm EDT, register athttps://www.cbioportal.org/tutorials

Levi Waldron (07:54:41) (in thread): > Here’s the shortcut to the Zoom meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09Meeting ID: 989 3746 9133 > Password: 112918 > One tap mobile+16465588656,,98937469133#US (New York)+13126266799,,98937469133#US (Chicago) > > Dial by your location+1 646 558 8656US (New York)+1 312 626 6799US (Chicago)+1 301 715 8592US (Germantown)+1 346 248 7799US (Houston)+1 669 900 9128US (San Jose)+1 253 215 8782US (Tacoma) > Meeting ID: 989 3746 9133 > Find your local number:https://zoom.us/u/abVvVAMpjz

Sean Davis (08:18:30): > https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854 - Attachment (journals.plos.org): Ten simple rules for making training materials FAIR > Author summary Everything we do today is becoming more and more reliant on the use of computers. The field of biology is no exception; but most biologists receive little or no formal preparation for the increasingly computational aspects of their discipline. In consequence, informal training courses are often needed to plug the gaps; and the demand for such training is growing worldwide. To meet this demand, some training programs are being expanded, and new ones are being developed. Key to both scenarios is the creation of new course materials. Rather than starting from scratch, however, it’s sometimes possible to repurpose materials that already exist. Yet finding suitable materials online can be difficult: They’re often widely scattered across the internet or hidden in their home institutions, with no systematic way to find them. This is a common problem for all digital objects. The scientific community has attempted to address this issue by developing a set of rules (which have been called the Findable, Accessible, Interoperable and Reusable [FAIR] principles) to make such objects more findable and reusable. Here, we show how to apply these rules to help make training materials easier to find, (re)use, and adapt, for the benefit of all.

Kevin Rue-Albrecht (09:03:20): > Great meeting everyone at the scMMJC! I’ll miss next weekend again because of teaching duties.

Kelly Eckenrode (09:12:12) (in thread): > It was great to meet you and thanks you for adding to our discussion. See you in 2 weeks :)

Kevin Rue-Albrecht (09:14:54) (in thread): > Argh. Did I really just write “weekend”? My notion of working days is completely messed up:rolling_on_the_floor_laughing:

Dario Righelli (09:54:23) (in thread): > for the ones interested, I uploaded the presentation with the references in the github wiki.:slightly_smiling_face:(also available here:slides)

2020-05-26

Lucy (08:16:12) (in thread): > I am excited to get to come to this soon. Currently teaching with Kevin so won’t make it for the next couple of weeks

2020-05-28

Shila Ghazanfar (14:27:24): > @Shila Ghazanfar has joined the channel

2020-05-31

Kelly Eckenrode (14:44:32): > <!channel>As a reminder, the Single Cell Multimodal journal club will meet tomorrow, Monday June 1 at 8am EDT/2pm CET.@Isaac Virshupwill lead a conversation on “CiteFuse enables multi-modal analysis of CITE-seq data” by Hani Jieun Kim, Yingxin Lin, Thomas A. Geddes, Jean Yee Hwa Yang  and Pengyi Yang. PDF is attached. > > Please check out the journal club website for meeting information:https://github.com/waldronlab/data-science-seminar/wiki/Single-cell-multimodal-dataHere’s the shortcut to the Zoom meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09Meeting ID: 989 3746 9133 > Password: 112918 > One tap mobile+16465588656,,98937469133#US (New York)+13126266799,,98937469133#US (Chicago) > > Dial by your location+1 646 558 8656US (New York)+1 312 626 6799US (Chicago)+1 301 715 8592US (Germantown)+1 346 248 7799US (Houston)+1 669 900 9128US (San Jose)+1 253 215 8782US (Tacoma) > Meeting ID: 989 3746 9133 > Find your local number:https://zoom.us/u/abVvVAMpjz - File (PDF): CiteFuse.pdf

2020-06-01

Lucy (03:38:24) (in thread): > Shame I’m going to miss this. Keen to hear people’s thoughts on this paper/method.

John Lawson (11:34:44): > @John Lawson has joined the channel

2020-06-03

Kirk Reardon (06:36:31): > @Kirk Reardon has joined the channel

2020-06-04

Yingxin Lin (09:22:09): > @Yingxin Lin has joined the channel

Almut (10:32:15): > @Almut has joined the channel

2020-06-06

Olagunju Abdulrahman (19:57:19): > @Olagunju Abdulrahman has joined the channel

2020-06-07

Kelly Eckenrode (12:00:54): > <!channel>As a reminder, the Single Cell Multimodal journal club will meet tomorrow, Monday June 8 at 8am EDT/2pm CET.@Zhiyuan Huwill lead our conversation on “Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity” Angermueller et al, 2016. PDF is attached. > > Here’s the shortcut to the Zoom meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09Meeting ID: 989 3746 9133 > Password: 112918 > One tap mobile+16465588656,,98937469133#US (New York)+13126266799,,98937469133#US (Chicago) > > Dial by your location+1 646 558 8656US (New York)+1 312 626 6799US (Chicago)+1 301 715 8592US (Germantown)+1 346 248 7799US (Houston)+1 669 900 9128US (San Jose)+1 253 215 8782US (Tacoma) > Meeting ID: 989 3746 9133 > Find your local number:https://zoom.us/u/abVvVAMpjz - File (PDF): nmeth.3728.pdf

Juan Ojeda-Garcia (12:20:07): > @Juan Ojeda-Garcia has joined the channel

2020-06-09

Mark Tefero Kivumbi (15:41:07): > @Mark Tefero Kivumbi has joined the channel

cigdemak (16:50:09): > @cigdemak has joined the channel

2020-06-10

Davide Risso (05:48:11): > Hi<!channel>since next Monday our journal club overlaps with the BIRS online conference, I propose we skip next week and meet again the 22nd

Davide Risso (05:48:41): > I was scheduled to speak next week and we have no speaker for the 22nd, so I could simply give my presentation the 22nd

Davide Risso (05:50:46): > In case you don’t know what I’m talking about, there is a free, online BIRS conference on single-cell multi-omics (co-organized by@Aedin Culhane)https://www.birs.ca/events/2020/5-day-workshops/20w5197 - Attachment (birs.ca): 20w5197: Mathematical Frameworks for Integrative Analysis of Emerging Biological Data Types (Online) | Banff International Research Station > Workshop at the Banff International Research Station in Banff, Alberta between Jun 14 and Jun 19, 2020: Mathematical Frameworks for Integrative Analysis of Emerging Biological Data Types (Online).

Robert Castelo (06:08:31): > Hi@Davide Rissodo you know if it’s possible to attend the workshop online (watch some of the talks)?

Davide Risso (06:10:47): > @Aedin Culhaneshould be able to provide a link to register for the online conference, I believe it is free and open to everyone interested (am I right@Aedin Culhane?)

Kelly Eckenrode (07:58:28) (in thread): > Yes–great idea Davide. I’ll update the journal club page with the changes.

2020-06-11

Davide Risso (02:36:13): > Hi@Robert Castelothe talks will be streamed online athttp://www.birs.ca/live - Attachment (birs.ca): BIRS Live Stream > Live video stream from BIRS

Aedin Culhane (17:58:24): > Yes they will be live-streamed on the BIRS websitewww.birs.ca/live. The workshop schedule ishttps://www.birs.ca/events/2020/5-day-workshops/20w5197/schedule - Attachment (birs.ca): 20w5197: Mathematical Frameworks for Integrative Analysis of Emerging Biological Data Types (Online) | Banff International Research Station > Workshop at the Banff International Research Station in Banff, Alberta between Jun 14 and Jun 19, 2020: Mathematical Frameworks for Integrative Analysis of Emerging Biological Data Types (Online).

2020-06-16

Izaskun Mallona (09:57:08): > @Izaskun Mallona has joined the channel

2020-06-21

Kelly Eckenrode (15:57:30): > <!channel>As a reminder, the Single Cell Multimodal journal club will meet tomorrow, Monday June 8 at 8am EDT/2pm CET.@Davide Rissowill lead our conversation on “Joint profiling of chromatin accessibility and gene expression in thousands of single cells” (Science), Cao, J., Cusanovich, D. A., Ramani, V., Aghamirzaie, D., Pliner, H. A., Hill, A. J., … Shendure, J. (2018).  PDF is attached. > > Here’s the shortcut to the Zoom meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09Meeting ID: 989 3746 9133 > Password: 112918 > One tap mobile+16465588656,,98937469133#US (New York)+13126266799,,98937469133#US (Chicago) > > Dial by your location+1 646 558 8656US (New York)+1 312 626 6799US (Chicago)+1 301 715 8592US (Germantown)+1 346 248 7799US (Houston)+1 669 900 9128US (San Jose)+1 253 215 8782US (Tacoma) > Meeting ID: 989 3746 9133 > Find your local number:https://zoom.us/u/abVvVAMpjz - File (PDF): cao2018.pdf

2020-06-22

Devika Agarwal (08:26:39): > @Devika Agarwal has joined the channel

2020-06-24

Marisa Isabell Metzger (05:16:49): > @Marisa Isabell Metzger has joined the channel

Kelly Eckenrode (10:56:09): > <!channel>The Single Cell Multimodal journal club will have a change of format next week. There will be no presentation but rather an open discussion on “Eleven grand challenges in single-cell data science” (2020). There is a lot of material here , so please read and join our conversation nextMonday June 29 at 8am EDT/2pm CET. PDF attached. > > Here’s the shortcut to the Zoom meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09Meeting ID: 989 3746 9133 > Password: 112918 - File (PDF): 11_grand_scRNA.pdf

Kevin Rue-Albrecht (11:28:08) (in thread): > 29 June:slightly_smiling_face:Looking forward!

Kelly Eckenrode (13:53:31) (in thread): > Thank you!

2020-06-30

Chris Vanderaa (10:23:33): > @Chris Vanderaa has joined the channel

2020-07-01

Frank Rühle (04:22:05): > @Frank Rühle has joined the channel

2020-07-02

Kayla Interdonato (08:50:07): > @Kayla Interdonato has joined the channel

Laurent Gatto (09:01:52) (in thread): > For those interested in a Bioconductor curriculum, there is now a google group. We are also preparing a first discussion to get started with the planning. Details in the google group:https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharing - File (Google Docs): bioc-teaching

Peter Hickey (21:07:22) (in thread): > added my details to the doc . would you please add me to the google group?

2020-07-03

Laurent Gatto (03:36:54) (in thread): > Done. After fixing some settings, it should be possible for anyone to register now - sorry for the inconvenience.

Marco Chiapello (05:54:49): > @Marco Chiapello has joined the channel

2020-07-04

Umar Ahmad (08:20:52): > @Umar Ahmad has joined the channel

2020-07-05

Kelly Eckenrode (17:31:34): > <!channel>Please join the Single Cell Multimodal JC for aspecial presentation from Suoqin Jin from the Nie lab at the University of California Irvine. > > “scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles”at a different time: 7AM PST / 10AM EDT / 4PM CET.Here’s the shortcut to the Zoom meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09Meeting ID: 989 3746 9133 > Password: 112918 (edited)

2020-07-06

Pablo Latorre-Doménech (11:30:03): > @Pablo Latorre-Doménech has joined the channel

2020-07-07

Mehdi Pirooznia (09:27:15): > @Mehdi Pirooznia has joined the channel

2020-07-10

Veronica Jimenez Jacinto (20:09:06): > @Veronica Jimenez Jacinto has joined the channel

2020-07-12

Kelly Eckenrode (17:12:03): > <!channel>The Single Cell Multimodal journal club will meetMonday July 13th at its normal time (8AM EDT / 2PM CET).We will continue with “Eleven grand challenges in single-cell data science” (2020); however, with a presentation by@Simone Tiberi. Please join us! PDF attached. > > Here’s the shortcut to the Zoom meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09Meeting ID: 989 3746 9133 > Password: 112918

Simone Tiberi (17:12:09): > @Simone Tiberi has joined the channel

2020-07-13

Dana Silverbush (10:20:41): > @Dana Silverbush has joined the channel

2020-07-14

Kelly Eckenrode (14:04:48): > <!channel>The Single Cell Multimodal journal club will meetMonday July 20th at 8AM EDT / 2PM CET.**** ****@Robert Castelo**** ****will share**** ****“MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.” Argelaguet, R., Arnol, D., Bredikhin, D.et al.Genome Biol21, 111 (2020).https://doi.org/10.1186/s13059-020-02015-1Important note:**** this will be our last journal club until the week of September 14.****I will re-poll everyone for the fall semester to see if there’s a new time that could work for everyone. > > Here’s the shortcut to the Zoom meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09Meeting ID: 989 3746 9133 > Password: 112918 - Attachment (Genome Biology): MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data > Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational strategies to analyze data from complex experimental designs that include multiple data modalities and multiple groups of samples. We present Multi-Omics Factor Analysis v2 (MOFA+), a statistical framework for the comprehensive and scalable integration of single-cell multi-modal data. MOFA+ reconstructs a low-dimensional representation of the data using computationally efficient variational inference and supports flexible sparsity constraints, allowing to jointly model variation across multiple sample groups and data modalities.

2020-07-15

wmuehlhaeuser (09:21:54): > @wmuehlhaeuser has joined the channel

2020-07-19

Hyun-Hwan Jeong (22:54:17): > @Hyun-Hwan Jeong has joined the channel

2020-07-20

Dr Awala Fortune O. (02:35:21): > @Dr Awala Fortune O. has joined the channel

Dr Awala Fortune O. (02:36:14): > Hello everyone

2020-07-21

Carl McIntosh (12:50:21): > @Carl McIntosh has joined the channel

2020-07-23

Bishoy Wadie (03:00:26): > @Bishoy Wadie has joined the channel

Biljana Stankovic (05:10:44): > @Biljana Stankovic has joined the channel

2020-07-24

Rajiv Kumar Tripathi (14:55:57): > @Rajiv Kumar Tripathi has joined the channel

Rajiv Kumar Tripathi (14:56:21): > Hello Everyone

2020-07-25

Levi Waldron (02:12:56): > Welcome@Rajiv Kumar Tripathi!

Levi Waldron (02:13:25): > And welcome@Dr Awala Fortune O.!

2020-07-26

Reza Rezaei (09:57:23): > @Reza Rezaei has joined the channel

2020-07-27

Triin (03:37:47): > @Triin has joined the channel

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2020-07-28

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2020-07-29

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2020-07-30

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2020-07-31

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2020-08-03

Kevin Rue-Albrecht (06:41:26) (in thread): > Sorry I missed the party, but I’ve added my name under****“Also interested?”****and in the “Working group participants” even though I missed the early July meeting.

Kevin Rue-Albrecht (06:41:36) (in thread): > To me the Google Group still says - File (PNG): image.png

Kevin Rue-Albrecht (06:42:33) (in thread): > Let me know how I can catch up:slightly_smiling_face:

Jenny Drnevich (10:21:28) (in thread): > I also would like to be added to the Google Group.drnevich@illinois.edu

Jenny Drnevich (10:24:11): > Hello Carpentries community! > > Did you really enjoy your Instructor Training workshop? Have you found yourself sharing things you learned there with other friends and colleagues? Consider joining our team of Instructor Trainers and co-teaching that curriculum yourself! > > Instructor Trainers (‘Trainers’) are certified to teach at all authorized Carpentries Instructor Training workshops, onboarding new Instructors who may in turn become certified to teach Data Carpentry, Library Carpentry, and Software Carpentry workshops. Trainers also play a role in the Instructor checkout process, evaluating trainees’ teaching demonstrations. The Trainer community plays a leading role in The Carpentries, maintaining our flagship Instructor Training Curriculum, contributing to relevant policies, and bringing instructional practices to bear in leadership roles across our local and global communities. > > Trainers benefit from being part of a global community of pedagogically trained professionals with a shared interest in promoting robust teaching practices and propagating data skills worldwide. Trainers continually build on their own pedagogical and communication skills through co-instruction and monthly community discussions about Instructor training. Trainers have opportunities to influence what we teach, through curriculum maintenance, and to steer the progress of this community, through leadership roles. Trainers often play leadership roles in their home communities, mentoring local Instructors, and modeling best practices. > > We recommend that Trainer applicants either have experience as Carpentries Instructors or prior training in education. However, there are no strict requirements – each application is reviewed individually and anonymously by a panel of current Instructor Trainers and Core Team members. For this cohort, we will be prioritizing in applicants who can help us meet demand for training in US time zones. > > For more details, see this blog post:https://carpentries.org/blog/2020/07/trainer-training-fall-2020/Applications are here:https://forms.gle/X2jmLm5xPkUmja5Y8Please emailteam@carpentries.orgwith questions! > > Best, > > Karen Word > Director of Instructor Training - Attachment (The Carpentries): Carpentries Trainer Training Fall 2020 > Apply to become an Instructor Trainer and shape the next generation of Carpentries Instructors! - Attachment (Google Docs): Carpentries Instructor Trainer Application > This is the application form for The Carpentries Instructor Trainer training programme. Instructor Trainers on-board new Carpentries Instructors by teaching Instructor Training workshops and hosting online teaching demonstration sessions. The Trainers’ group meets regularly to prepare and reflect on teaching experiences, share thoughts on best practices, and discuss improvements to policies, procedures, and the Instructor Training curriculum (https://carpentries.github.io/instructor-training/). Carpentries Instructor Trainers are leaders in The Carpentries community. We are collecting and processing personal data collected with this form in accordance with our Privacy Policy (https://docs.carpentries.org/topic_folders/policies/privacy.html). Each Instructor Trainer brings something different to the community. Some have formal training in pedagogy; some are highly engaged Carpentries Instructors. Some participate as part of their jobs, while others contribute their own free time. We all share a commitment to helping new Instructor trainees to become familiar and comfortable with The Carpentries teaching practices and community principles. More detailed information about the Instructor Trainer role and responsibilities can be found in our Handbook: https://docs.carpentries.org/topic_folders/instructor_training/duties_agreement.html Thank you for your interest in joining the Trainer community!

Kevin Rue-Albrecht (10:33:25) (in thread): > I’ll throw in my email here too then:slightly_smiling_face:kevin.rue-albrecht@imm.ox.ac.uk

Junyan Xu (12:56:58): > @Junyan Xu has joined the channel

Jenny Drnevich (15:49:23): > Another repost from Life Science Trainers slack that I thought people on this channel could be interested in. Note that the call for volunteers is open until Aug 7th. am happy to announce that the Steering Committee has approved the creation of a global survey for everyone doing training in the life sciences. We need your help to refine a draft and ultimately collect data and publish a manuscript. Please read about this effort and consider signing up. We have scoped out time and effort and would look forward to administering in September. If you know anyone not on the Slack who this would be interesting to please circulate the blog post. Thanks - Attachment (Life Science Trainers): Call For Volunteers: Global trainers survey > The Steering Committee has formulated a proposal for a survey of trainers across the globe and we need your help.

2020-08-04

rohitsatyam102 (14:29:09): > @rohitsatyam102 has joined the channel

2020-08-05

Hans-Rudolf Hotz (03:22:24): > @Hans-Rudolf Hotz has joined the channel

shr19818 (13:46:18): > @shr19818 has joined the channel

2020-08-11

Laurent Gatto (10:46:50) (in thread): > Hi@Jenny Drnevichand@Kevin Rue-Albrecht- I missed your messages and just saw them now. You should have been added to the group.

Kevin Rue-Albrecht (10:47:13) (in thread): > Awesome thanks!

Jenny Drnevich (10:51:44) (in thread): > @Laurent GattoI just got the confirmation email - thank you!

Kevin Rue-Albrecht (10:55:41) (in thread): > On a related note, I’ve contacted both the Carpentries directly through their “application for instructor training” form, and “Reproducible Research Oxford” (RROxford) who’s in the process of restoring their organisation membership. > Carpentries have suspended non-member training at the moment, so I’m waiting on updates from Oxford… except if there’s any online training coming up any time soon?

Kevin Rue-Albrecht (11:07:45) (in thread): > Nevermind, having joined the group I can see there’s a meeting schedule for next Monday. I can get the answer then

2020-08-17

Laurent Gatto (08:04:45): > The Bioconductor teaching working group had their second meeting today. Notes available on the shared google group (https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharing). - File (Google Docs): bioc-teaching

Nitesh Turaga (08:05:56): > https://github.com/Bioconductor/bioconductor-teaching

2020-08-18

Will Macnair (09:08:24): > @Will Macnair has joined the channel

Jenny Drnevich (14:19:53): > Great blog post about experiences in teaching remote workshops:https://www.ccdatalab.org/blog/2020/8/17/how-we-train-going-remote - Attachment (Childhood Cancer Data Lab): How we train: Going remote — Childhood Cancer Data Lab > When the CCDL (along with everyone else) realized that we would have to conduct our bioinformatics training workshops remotely, we had to make some quick decisions about how we were going to do it. Here’s what we decided to do.

2020-08-26

rohitsatyam102 (16:02:25): > @Jenny Drnevichdidn’t get selected for the Carpentries Instructor Trainer. Please keep us updated through this channel so that those who didn’t get through it could apply again next time…

Jenny Drnevich (16:32:42): > @rohitsatyam102sorry to hear that! I’ll check to see when they might do it again.

2020-09-06

Tyrone Chen (22:32:27): > @Tyrone Chen has joined the channel

2020-09-09

Kelly Eckenrode (08:22:06): > <!channel>The Single Cell Multimodal journal club is back! We will meetMonday September 14th at 8AM EDT / 2PM CET.**** ****@Rajiv Kumar Tripathi****  ****will lead our conversation on**** ****““Single-cell multimodal omics: the power of many”. DOI: 10.1038/s41592-019-0691-5 > > I’m looking forward to our discussion!:shuffle-parrot:Here’s the shortcut to the Zoom meeting:https://zoom.us/j/98937469133?pwd=SWFrbE10NGY2WVBITzJab0F3N29JQT09Meeting ID: 989 3746 9133 > Password: 112918 - File (PDF): Single-cell multimodal omics.pdf

2020-09-10

Charlotte Soneson (14:55:07): > https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008090

2020-09-11

Jenny Drnevich (11:02:16) (in thread): > Nice article! Too bad it doesn’t including anything about how to also do this remotely…

2020-09-14

Ilir Sheraj (06:28:14): > @Ilir Sheraj has joined the channel

Kelly Eckenrode (09:41:01): > Thank you@Rajiv Kumar Tripathifor a great presentation on a recent single cell multimodal survey paper. > > Interested in presenting at SCMM journal club? Maybe you or a lab member?Please sign up hereat the SCMM journal club wiki or contact me. The wiki also has videos of all previous presentation and papers.

Rajiv Kumar Tripathi (09:46:35) (in thread): > Thanks@Kelly Eckenrode.

2020-09-18

Chris Cheshire (05:42:14): > @Chris Cheshire has joined the channel

2020-09-20

Kelly Eckenrode (19:37:51): > The SCMM journal club will not be meeting tomorrow. However, we are still actively looking for people to share articles. Let me know if you are interested!

2020-09-28

Qirong Lin (06:54:06): > @Qirong Lin has joined the channel

2020-10-01

Friederike Dündar (16:21:12): > @Friederike Dündar has joined the channel

Friederike Dündar (16:22:25): > Hello!

Friederike Dündar (16:23:08): > How are you all preparing your remote-only classes? I like the edX format, hence my pinging of@Michael Lovein the#randomchannel, but happy to hear about other solutions, too

Michael Love (16:23:13): > @Michael Love has joined the channel

Simina Boca (16:49:29): > I’m worried mine are a disaster:joy:

Simina Boca (16:49:36): > I mean maybe they’re fine who knows?

Simina Boca (16:49:44): > (Getting even less student feedback than usual)

Simina Boca (16:50:23): > But I try to have breakout rooms and/or Zoom polls every lecture and I worry students hate it (but again, no idea whether they actually do)

Friederike Dündar (16:51:16): > I really don’t think that zoom is the best solution for lectures (or presentations in general)

Friederike Dündar (16:52:13): > I’ve attended a symposium recently that had a much better platform – just small details such as having the chat open per default (and not another window that keeps on vanishing) made a huge difference

Simina Boca (16:52:30): > Yes, Zoom has all the options in random places

Friederike Dündar (16:53:52): > I really like the edX format because I think at the heart of the problem with zoom lectures is that they MUST be much shorter than in-person sessions where the energy of the presenter is much more palpable and infectious (as well as the peer shaming of nodding off)

Friederike Dündar (16:54:20): > so, I’ll definitely switch to a mix of prerecorded, tightly scripted lectures that the students can do at their own time and pace

Friederike Dündar (16:55:02): > but especially for pre-recording of lectures that involve coding I keep on coming back to the edX format – I don’t really see how to gracefully do that with zoom

Friederike Dündar (16:55:14): > have you done coding demos in zoom,@Simina Boca?

Michael Love (16:55:24): > My experience with edx is from 2013 so maybe out of date

Friederike Dündar (16:55:36): > how bad was it?

Michael Love (16:56:00): > For me it was problematic, everything had to be done withaGUI, and the repetitive actions of adding questions didn’t do wellwith my wrists

Friederike Dündar (16:56:33): > so, how are you handling your lectures these days?

Simina Boca (16:56:56): > I just have them download the code and then write small parts during some of the breakout rooms

Simina Boca (16:57:07): > it’s very hard to gauge how much time to give them in the breakout rooms

Simina Boca (16:57:34): > I’m also not sure people are actually running the code at the same time I am, since that would involve multiple open windows and split attention

Friederike Dündar (16:57:58): > right

Friederike Dündar (16:59:23) (in thread): > that does not sound enticing, indeed

Friederike Dündar (16:59:43) (in thread): > any non-GUI solution you’re preferring these days?

Friederike Dündar (17:00:29): > I feel like one external monitor (or two screens or split screen) are a minimum requirement, but I don

Friederike Dündar (17:00:36): > ’t think many students will have that

Friederike Dündar (17:01:27): > I’ve got to go now, but happy to hear and discuss more about this

Aaron Lun (17:01:42): > even I don’t have two monitors.

Aaron Lun (17:01:45): > in fact, I don’t even have one monitor.

Friederike Dündar (17:03:16): > I’ll edit

Simina Boca (17:06:07): > I feel like I’m already spendingso much timepreparing for class that I’m not willing to make any radical changes at this point

Simina Boca (17:06:14): > my semester is almost halfway done

Michael Love (17:14:29) (in thread): > I haven’t rolled a MOOC since then

Michael Love (17:14:35) (in thread): > Only in person stuff

Michael Love (17:14:53) (in thread): > So grading exams one by one :-)

Marcel Ramos Pérez (17:14:55) (in thread): > are you already using neuralink?:grin:

2020-10-02

Paul Harrison (03:23:15): > @Paul Harrison has joined the channel

Friederike Dündar (04:32:13) (in thread): > and Covid hasn’t derailed that? Or are you currently off the hook?

Friederike Dündar (04:34:52): > @Simina BocaI feel ya. I’m feeling nauseous just thinking about the amount of time it will take me to overhaul my classonce again, but it seems that I’ll be teaching remotely for at least another year, so…

Friederike Dündar (04:35:46): > ugh. so annoying that there’s been close to no support from the colleges though, I mean, all they are saying is, use zoom and perhaps buy a good microphone (on your own dime, of course)

Will Arnold (07:40:34): > @Will Arnold has joined the channel

Kasper D. Hansen (07:50:51): > @Kasper D. Hansen has joined the channel

Michael Love (08:15:53) (in thread): > oh, i was doing that in Spring but i teach one semester / academic year so i will start again in Jan

Geet (09:12:04): > @Geet has joined the channel

mirna (10:12:00): > @mirna has joined the channel

hcorrada (10:50:06): > @hcorrada has joined the channel

Jenny Drnevich (11:51:27): > We did pre-recorded lectures to finish up our Spring workshop series and offered zoom “office hours” and a slack channel to help with any questions, but only got ~3 questions total which told me no one watched them and tried to work through them. We are doing live zoom for our Fall workshop series, 2 hrs chunks, 2 days a week. It’s going OK but it’s like teaching to the void - there is very little feedback. We do a mix of follow along with the instructor live-coding and then breakout rooms for them to work on problems in small groups with a helper present. If participants are really short on monitor space, we tell them to log into zoom a second time with a tablet or even a phone and keep the presenter on there and use all their monitor space for slides & coding.

Jenny Drnevich (11:51:44): > Luckily we don’t have to grade anything!

Frederick Tan (12:06:09): > With regards to real time feedback, we had reasonable success implementing Software Carpentry’s “pink sticky” / “green sticky” via Slack - File (PNG): slack-stickies.png

Friederike Dündar (14:09:41): > > breakout rooms for them to work on problems in small groups with a helper present

Friederike Dündar (14:10:08): > how big are those groups? do they select one person that does the coding and the others critique them or how does that work?

Jenny Drnevich (14:14:46): > No more than 4-5 people. As helper I usually ask if someone will share their desktop. Sometime no one volunteers and say they want to work on their own. Or I’ve shared mine and ask them questions as I work through the problem using their answers. Again, mixed success but it is the only time they will unmute and interact.

Jenny Drnevich (14:16:42) (in thread): > Where do you get those sticky reactions? I’d like to add them to our workshop slack channels…

Friederike Dündar (14:22:05) (in thread): > slack is def 1000% better than zoom’s prehistoric chat

Friederike Dündar (14:22:30) (in thread): > do you make use of it throughout the class?

Frederick Tan (14:29:40) (in thread): > I haven’t had a chance to google how to add reactions to Slack … grateful that a TA did it:slightly_smiling_face:

Frederick Tan (14:30:56) (in thread): > This was for a five day bootcamp. We used it for all the live coding sessions. Again, similar cadence as a Software Carpentry workshop (particularly troublesome spots, results that are a dependency for a following step)

Frederick Tan (14:31:38): > Ditto on the 4-5 people … we started our five day bootcamp with Zoom breakout rooms of 2 and it was super awkward.

Jenny Drnevich (14:45:38) (in thread): > We are still using Zoom

Jenny Drnevich (14:45:44) (in thread): > Zoom

Jenny Drnevich (14:47:34) (in thread): > Darn it, I keep hitting enter instead of apostrophe! I meant to say we are still using zoom’s chat and I agree it is horrible. But we haven’t convinced everyone to get on Slack and it’s one more window they have to have open so that is why we haven’t shifted to slack

Simina Boca (14:56:08): > I do 2-3 and ask them to figure it out by for example sharing a screen

Simina Boca (14:56:13): > I have 7 students total in my class though

Simina Boca (14:56:32): > I’ve also had the occasional non-coding “write 3 bullet points” on Google slides

Simina Boca (15:00:54): > I usually give them very specific things to do, but tell them it’s OK if they don’t finish and that we’ll discuss as a group

Simina Boca (15:01:16): > However, I got the feedback that I wasn’t giving them enough time so now try to increase the time and decrease the number of things

Friederike Dündar (15:12:34): > can you give an example of such a problem?

Roye Rozov (15:29:51): > @Roye Rozov has joined the channel

Simina Boca (15:32:56): - File (PNG): image.png

Simina Boca (15:34:02): > I’m teaching data analysis not programming though

Simina Boca (15:34:21): > And I provide them with a file that they can download and write into

Simina Boca (15:34:47): > It could be better organized, like I could upload the files the night before, but I always want to do a “final check” like 1 hour before class starts

Simina Boca (15:35:51): > This was a Google slides one - again it’s not programming related - File (PNG): image.png

Simina Boca (15:36:15): > This was earlier in the semester and they told me later that I didn’t give them enough time (I had just introduced confounders in class)

Sean Davis (15:38:48): > Nice to see some examples,@Simina Boca.

Simina Boca (15:39:53): > I read part of this bookhttps://www.amazon.com/Teaching-Effectively-Zoom-practical-students-ebook/dp/B08CBG9GRH

Simina Boca (15:40:24): > And being able to work on collaborative documents in breakout rooms was listed as one benefit of remote classes

Simina Boca (15:40:36): > But it can be a hassle because you have to prepare it all in advance

Simina Boca (15:41:25): > The author of that book recommends having a document that then leads into the next part of the class in a meaningful way - not sure I’m achieving that but:shrug:- can only do so much

Frederick Tan (15:49:56) (in thread): > Yes, screen management is fun … we recommended thishttps://docs.google.com/presentation/d/1yvp4Z_PwnBDsCbAAV2eWr2vlK4o0Rs_11gr1ikbV–c/edit#slide=id.g926bfc514f_0_22

Nur-Taz Rahman (16:07:40): > @Nur-Taz Rahman has joined the channel

2020-10-04

Giuseppe D’Agostino (22:06:22): > a very nice example from earlier this year was Neuromatch Academy’s interactive track. They pre-recorded short lectures on Youtube, and embedded them in Google Colab Python notebooks. These notebooks had (relatively easy and short) coding exercises with easy access to solutions, and an expected output just below. Since it was a global workshop, groups were divided by time zones, and every group had a TA. During every day of the workshop, every group was divided into breakout rooms in Zoom, with the TA cycling through every breakout room to check the progress. People took turns to share their screen and solve the coding exercise live while discussing what was going on. The downside is obviously that you need to invest a huge amount of time and resources in preparing the material and triple checking it. Even then, some exercises had bugs and some lectures were clear outliers in terms of difficulty.

2020-10-05

David Sims (06:46:43): > @David Sims has joined the channel

Friederike Dündar (07:13:02): > @Simina Bocathanks a lot, that’s all really useful advice and feedback

Charlie George (11:55:03): > @Charlie George has joined the channel

2020-10-06

Jordan L. (10:51:18): > @Jordan L. has joined the channel

Maria Doyle (22:21:52): > @Maria Doyle has joined the channel

2020-10-08

Aedin Culhane (12:01:59) (in thread): > Actually I see it with my kids remote school. They put all of the students into small group or individual breakout rooms and the instructor then visits them one by one. At any time the students can “invite” the host into the breakout room if they have questions

B P Kailash (15:45:02): > @B P Kailash has joined the channel

2020-10-09

Nathan (00:14:16): > @Nathan has joined the channel

Susan Holmes (05:02:42): > @Susan Holmes has joined the channel

2020-10-10

Meeta Mistry (20:54:52): > @Meeta Mistry has joined the channel

2020-10-12

Jenny Drnevich (09:54:56): > @Charlotte Sonesonsorry I missed the bioc-teaching meeting today - I didn’t have it on my calendar for some reason and was still asleep when your email reminder came through. Is the next one going to be Nov 9? I’ll have to double check what time that will be for me because we set our clocks back one hour on Nov. 1.

Charlotte Soneson (10:01:36): > @Jenny Drnevichno worries (sorry for sending the reminder only today, it fell off my mind) - you can follow our discussion in the Google Doc, and we’ll try to set up a follow-up meeting later this week to further condense and formulate the learning goals that we were discussing. Yes, the next meeting should be on November 9. We set our clocks back on the last weekend of October here, so I would think that on November 9 we should again have the same time difference as now:slightly_smiling_face:

Jenny Drnevich (10:29:55) (in thread): > I read through the Google Doc - my target audience is much like yours, Nitesh’s and Robert’s, which are different from Laurent’s. It will be interesting to see how we can put together an intro lesson that can cover a wide range of target audiences but all of whom are learning R so they can use Bioconductor packages. I’ll put Nov’s meeting on my work AND personal calendar. Let me know about the follow up meeting this week.

Martin Morgan (17:28:20): > Is ‘the google doc’ meant for public consumption? Can it be pinned to this channel?

2020-10-13

Laurent Gatto (01:41:40) (in thread): > done

Laurent Gatto (08:03:41): > Hello - for those that are interested, a group of us are working on developing a Bioconductor Carpentries-like curriculum. We have agoogle docwhere we keep notes (also clipped to this channel) and meet monthly (2nd Monday). Meeting reminders and general info is posted on thebioc-teaching google group. - File (Google Docs): bioc-teaching

Laurent Gatto (08:04:58): > For those interested in becoming Carpentries instructors, please complete the application form linked from this page:https://carpentries.org/become-instructor/. There is currently a long waiting list; you might thus also investigate on an individual basis whether you belong to a Carpentries member organisation and, if so, reach out within that organisation to enquire about upcoming training. - Attachment (The Carpentries): Become an Instructor > The Carpentries is a fiscally sponsored project of Community Initiatives, a registered 501(c)3 non-profit organisation based in California, USA. We are a global community teaching foundational computational and data science skills to researchers in academia, industry and government.

Laurent Gatto (08:10:30): > (Here’s a list of member organisationshttps://carpentries.org/members/) - Attachment (The Carpentries): Our Current Member Organisations > The Carpentries is a fiscally sponsored project of Community Initiatives, a registered 501(c)3 non-profit organisation based in California, USA. We are a global community teaching foundational computational and data science skills to researchers in academia, industry and government.

Lukas Weber (09:47:42) (in thread): > Hi@Laurent Gatto@Charlotte Soneson, I would be interested in joining these meetings and seeing what I could contribute. I agree that having Bioconductor modules in Carpentries would be very useful for learners. My expertise is more on downstream analyses e.g. single-cell, spatial, flow - not sure if you want to go that far in the modules, but would be great to join the discussion. (I am also a Carpentries instructor, although it has been a while now since I last taught.)

Charlotte Soneson (09:55:19) (in thread): > Hi Lukas - sounds great! I think you can join (or at least ask to join, can’t remember the settings) the google group via the link above, and you’ll get all the communications. The next planned meeting will be on November 9 at 2pm Central European time.

Lukas Weber (09:56:23) (in thread): > Thanks! Hmm the link just says “Content unavailable”, you might need to add me manually.lukas.weber.edu@gmail.com

Charlotte Soneson (09:57:51) (in thread): > Hm, strange. I added you manually

Lukas Weber (09:58:06) (in thread): > thanks, it’s working now

Lukas Weber (09:59:22) (in thread): > added it to my calendar for Nov 9 (8am our time) - I’ll have a look through the previous notes and messages to catch up

Laurent Gatto (11:27:44) (in thread): > Thank you for your interest, Lukas!

Laurent Gatto (11:30:29) (in thread): > @Charlotte Soneson- we missed one point on last Monday’s agenda, which was running a workshop at EuroBioc, which we should add to the next meetings agenda. Maybe also discuss whether we want to embark already now with the development of more specialised courses like those suggested by Lukas. I’m sure others also have ideas. I certainly consider proposing mass spec/proteomics material once we have set up the first lessons.

Charlotte Soneson (11:34:43) (in thread): > Yes, I agree! Re: EuroBioc, I just realized that we may need to take a decision before next meeting, since the submission deadline is Oct 30…

Laurent Gatto (11:38:13) (in thread): > See my note in the google doc regarding what kind of workshop you mean.

Ilir Sheraj (14:33:11) (in thread): > Hello, I’m not that professional with analysis but would like to get in touch with other people in the field. Should I join or is it only for professionals?

Laurent Gatto (15:08:23) (in thread): > Dear@Ilir Sheraj- there is no requirement to be a professional, but the effort refered to above isn’t related to analysis: it’s about creating teaching material.

2020-10-14

Laurent Gatto (16:52:34) (in thread): > FYI - I have received some further details regarding the instructor training backlog: > > We are doing all we can to work through our backlog! While it is possible that a highly ranked applicant might be invited as soon as 1-2 months from now, most should expect a minimum wait of 3-6 months at this point.

2020-10-15

Federico Marini (04:10:06): > For the ones that knew her from Coursera: Daphne Koller just launched the Engageli platform

Federico Marini (04:10:07): > https://www.forbes.com/sites/susanadams/2020/10/14/coursera-founder-launches-zoom-challenger-for-higher-ed/#74cc2ea5a45a - Attachment (Forbes): Coursera Founder Launches Zoom Challenger For Higher Ed > Engageli, cofounded by Daphne Koller, has raised $14.5 million to launch a learning platform for real-time online higher ed courses

Federico Marini (04:11:25): > As the name says, it seems to focus on engaging students, and this is a big component of what we’d like to have (apart from 1st class contents, of course)

Pariksheet Nanda (21:47:33) (in thread): > @Laurent GattoI think the bioc-teaching Google group is private? When I load the page I see “This group either doesn’t exist, or you don’t have permission to access it. If you’re sure this group exists, contact the Owner of the group and ask them to give you access.”

2020-10-16

Paul Harrison (00:03:00) (in thread): > @Laurent GattoHi, I’m also interested in being involved. I’ve done a few workshops in the past covering the basics of Bioconductor types using GRanges and DNAStringSet as examples. ie, things you need to understand to make sense of a typical bioconductor vignette. Seeing lots of people needing to get up to speed with SummarizedExperiment, SingleCellExperiment, etc now. > > I would like to join the google group. I’m getting similar errors to other people.

Laurent Gatto (01:34:42) (in thread): > @Pariksheet Nanda@Paul Harrison- The group really isn’t meant to be private, sorry about this. Could you try again, please. Otherwise, if you message me you email address, I’ll add you directly.

Laurent Gatto (01:37:28) (in thread): > @Paul Harrison- thank you for your suggestion. We are currently putting a lot of effort on the pedagogy rather than the content itself, so not quite yet focusing on objects such as GRanges and DNAStringSets. The first lesson we are working on, defining the learning objectives, is focused on beginners, and the end point would indeed be SummarizedExperiments. All our notes are in the google doc.

Laurent Gatto (01:37:55) (in thread): > We also have monthly meetings, and both of you welcome to join.

Paul Harrison (21:00:59) (in thread): > Great! I’ll try to make it to the next meeting.

2020-10-18

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2020-10-20

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2020-10-22

Federico Marini (07:38:23): > Welcome@Christa Toenhake:wink:This should get you to the right channel

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Christa Toenhake (08:52:55): > Thanks@Federico Marini! I had somehow missed this channel:flushed:

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2020-10-23

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2020-10-26

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2020-10-30

Kevin Rue-Albrecht (08:17:16): > Hello community! > > The#eurobioc2020submission deadline is extended toMonday, November 16th! > > The organising committee welcomes submissions for: > * talks > * workshops > * posters > * birds-of-a-feather session topics > The scope for submissions is far from limited to Bioconductor packages; we welcome contributions as workflows, live demonstrations, interactive Shiny applications, data visualisations, new concepts, packages in development, calls for feedback and collaborations, … and all the many more hidden gems produced by the community; surprise us! > > Submit your contribution hereWe look forward to seeing you all online for this stimulating and community-driven conference! - Attachment (OpenReview): EuroBioC 2020 Conference > Welcome to the OpenReview homepage for EuroBioC 2020 Conference

2020-11-02

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2020-11-12

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2020-11-13

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2020-11-18

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2020-11-19

Aedin Culhane (12:15:16): > At the CZI HCA meeting, there was a great talk on data visualization approaches by Katy Boner. If your interested in beyond UMAP … check out this coursehttps://expand.iu.edu/browse/sice/cns/courses/visual-analytics-0121-open… its $950 to register though

2020-11-22

Vince Carey (02:00:32): > @Aedin Culhaneare there any other online resources related to the talk you mention?

Stuart Lee (17:54:44): > Something cheaper if you’re looking for an intro / overview of data vis is Tamara Munzner’s Visualization Analysis and Design bookhttps://www.cs.ubc.ca/~tmm/vadbook/

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2020-11-23

rohitsatyam102 (06:18:13) (in thread): > Thanks for sharing it here@Stuart Lee

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2020-11-27

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2020-11-30

Jenny Drnevich (13:21:55): > The Carpentries has put out their 2021 Instructor Training schedule:https://carpentries.github.io/instructor-training/training_calendar/index.html - Attachment (The Carpentries - Instructor Training): Instructor Training Calendar > Lesson episode summary - keypoints?

2020-12-01

Aedin Culhane (13:48:05): > Thanks Jenny, Did we do a Bioc membership or is there a central Bioc Carpentries application, or “code” etc. Or do we just apply independently.

Laurent Gatto (15:44:42) (in thread): > There is no Bioc membership yet. Planning to do this first thing next year.

2020-12-02

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Konstantinos Geles (Constantinos Yeles) (05:57:46): > Hello! I would like to ask if there are any workflows regarding ways to annotate small RNA sequences in a recently sequenced genome. > I’ve also made a question inBiostarswebsite.

Pariksheet Nanda (13:49:53) (in thread): > One way would be to use a nascent RNA sequencing technology like PRO-seq or NET-seq to find active transcriptional regions. mirSTP isn’t in Bioconductor but finds micro-RNA:http://bioinfo.vanderbilt.edu/mirSTP/ - Attachment (bioinfo.vanderbilt.edu): mirSTP > miRNA; TSS; PRO-seq; GRO-seq; prediction

Amarinder Singh Thind (18:49:11): > Hello! is there anyone working on circular RNA annotation?https://www.biostars.org/p/476599/

2020-12-03

Dario Righelli (03:49:39) (in thread): > @Antonio Federicomaybe knows something! But I’m not sure he’s using this slack… Try to reach him via email.

Konstantinos Geles (Constantinos Yeles) (05:54:34) (in thread): > Thank you for the suggestion, but this would mean to do a new sequencing on the samples that we have, which is not possible at the moment. > Furthermore, I am interested in piRNAs precisely, which complicates the things even more I believe.

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2020-12-04

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Kate (09:22:36) (in thread): > Hi Konstantinos - I’m working on something similar with a non-model and am also finding this difficult. I have done something similar to you in terms of filtering reads based on length to kind of split up the miRNAs and piRNA pools. I havent done this yet but because piRNAs are not typically conserved among species my thought with piRNAs is to use my repeat annotations to identify them since they come from transposons. I think that would be clearer and easier than looking at alignments straight to the genome. I’m hoping to really dig into this soon and happy to chat more if that would be helpful.

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2020-12-06

Amarinder Singh Thind (17:56:42) (in thread): > Ok, thanks@Dario RighelliI will write..

2020-12-11

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2021-01-29

Aaron Lun (02:40:34): > does anyone have students that I can farm out development work to?

Aaron Lun (02:40:46): > They get development experience. I get some time off. It’s a win-win.

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Leo Lahti (05:11:18) (in thread): > Hi@Aaron Lun- do you have a specific class or package in mind, or any of the ones you’re developing?

Aaron Lun (11:29:30) (in thread): > Couple of SingleCellExperiment issues, for example, involve expanding on the class structure.

Aaron Lun (11:30:44) (in thread): > Various issues with BiocSingular.

Aaron Lun (11:30:53) (in thread): > Reorganizing some of the OSCA book contents

2021-02-02

Leo Lahti (10:07:51) (in thread): > Ok good to know. I will check what the chances are. Would be good.

2021-02-12

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2021-02-24

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2021-03-01

rohitsatyam102 (13:50:40): > Isn’t SARSCoV2 already a model organism to teach student Bioinformatics in university coursework on which all sort of Genomics/Proteomics and other sorts of Omics analysis has been done. Wouldn’t it be interesting to use it as a starting point when instructing them. I am saying this because I, as a student struggled a lot to find out all sort of inferences one can derive with data in hand. Say what all sort of analysis can be performed with total RNASeq data in hand. How differently we can use the VCF files to derive novel information!!

2021-03-03

Pariksheet Nanda (09:24:34) (in thread): > The choice of data I think usually depends on the instructor: how well they understand it, how meaningful they personally find it, how excited they are to talk about it, and how useful the visualizations are in explaining the concepts. The data set might be something to look at after deciding learning objectives and goals, looking at the teaching schedule, and how much time one wants to spent on retooling. For a broad audience, sure, SARSCoV2 might be a great way to make the teaching material more interesting. In a mathematical modeling class I attended in the fall, the professor mentioned we would be working our way up to the SIR model which can be applied to the spread of disease and it gave us something to look forward to.

rohitsatyam102 (12:20:44) (in thread): > Great to hear that u are already using it. And I will buy it all that u said

2021-03-11

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Jenny Drnevich (14:15:06): > I won’t be able to attend but thought others might be interested:https://www.cineca-project.eu/news-events-all/how-to-make-training-fair - Attachment (CINECA): How to make training FAIR — CINECA - Common Infrastructure for National Cohorts in Europe, Canada, and Africa > During this webinar, we will give you some tips and suggestions on how you can make more of the training materials you produce and encourage others to do the same. FAIR is not just for data - we can make our training materials FAIR too. Join us to find out the benefits of sharing your FAIR materials

2021-03-16

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2021-03-20

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2021-03-23

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2021-03-26

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2021-03-31

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2021-04-02

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2021-04-07

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2021-04-13

rohitsatyam102 (12:41:07): > https://australianbiocommons.github.io/?s=09

2021-04-15

rohitsatyam102 (13:43:41): > https://quovidi.github.io/ - Attachment (quovidi.github.io): QuoVidi > QuoVidi (previously known as BioGO) is an interface to manage large (and small) scale treasure hunt. It was intially designed to organise a biological treasure hunt, but can be adapted to any situations.

2021-04-16

rohitsatyam102 (09:15:41): > Any good resources to teach systems biology??

Pariksheet Nanda (12:27:40) (in thread): > Before suggesting resources it depends on what your teaching goals our. Here’s the syllabus of my introductory systems biology class last semester with the weekly objectives: > 1. Introduction to Systems Biology > > 1. Course overview: topics to be covered, software tools, databases, and algorithms > 2. Relationships and interactions among biological parts at different levels and scales > 3. Math and computer science in biology; models, simulations, data analysis and data-driven science > 4. Definitions and history, notable achievements, basic science vs. translational research > 5. Assignment: install and test core software tools - VCell, Copasi, CellDesigner, Cytoscape, MatLab > > 1. Introduction to Kinetic Modeling Using Virtual Cell > > 1. Introduction to molecular interaction networks: cartoon diagrams, pathways and databases > 2. Introduction to reaction kinetics: species & reactions, kinetic laws, mass-action, deriving ODEs > 3. Example: kinetic modeling of signal-receptor interactions > 4. Tutorial on VCell > 5. Assignment: do several theoretical and modeling exercises using VCell > > 1. Whole Cell Modeling > > 1. Discussion of a paper by Karr et al “A whole-cell computational model predicts phenotype from genotype” (http://www.ncbi.nlm.nih.gov/pubmed/22817898) > 2. Discussing modeling concepts behind the paper > 3. Introduction to MatLab > 4. Assignment: prepare discussions of several parts of the paper > > 1. Experimental techniques used in Systems Biology > > 1. Techniques for obtaining in vitro binding kinetics > 2. Fluorescence-based biosensors for analyzing molecular reaction kinetics in vivo > 3. High Content and High Throughput analysis of interaction networks > 4. Assignment: short presentations about experimental techniques. Compare them to the techniques used to obtain data for the whole cell modeling paper. > > 1. Kinetic modeling using different modeling tools > > 1. Different types of reactions: unimolecular/state transitions, binding/unbinding, transport, production/degradation > 2. Different kinetic laws: mass action, Michaelis-Menten, Hill > 3. Tutorial on Copasi software > 4. Assignment: create a compartmental model of reaction kinetics in VCell and one other tool; find papers that describe models developed using specific software > > 1. Spatial modeling & Parameter estimation > > 1. Deterministic vs. stochastic simulations > 2. Taking care of units, conversion factors > 3. Spatial modeling: shape topology vs. actual geometry, reaction-diffusion in 1D, 2D, 3D > 4. PDEs and boundary conditions > 5. Parameter Estimation > 6. More tools: VCell (spatial), Smoldyn, MCell > 7. Assignment: extend previous model to include stochastic and spatially-resolved applications; compare simulations > > 1. Rule-based modeling > > 1. Description of molecular interactions using rules and patterns > 2. Rule-based network generation; examples: FceRI and EGFR signaling > 3. Rule-based network-free simulations; examples: multivalent ligand-receptor binding, actin filaments > 4. Review of tools: BioNetGen, Kappa, Simmune > 5. Assignment: recast previous model using rule-based description; compare simulations > > 1. Standards, repositories and visualization in Systems Biology > > 1. Model description languages and exchange standards: SBML, CellML > 2. Ontologies and controlled vocabularies: MIRIAM, BioPAX, SBO, KiSAO > 3. Reproducibility of simulation experiments: MIASE, SED-ML, SBRML > 4. Graphical representations: entity-relationship diagrams, process diagrams, the Systems Biology > 5. Graphical Notation (SBGN) > 6. Rule-based descriptions > 7. Tools for drawing biological diagrams > 8. Databases: pathways & interactions, metabolic, proteins motifs & compounds, kinetics, BioNumbers > 9. Tools: Cytoscape, CellDesigner > 10. Assignment: annotate model; find papers using data from databases, compare data in different databases > > 1. Metabolic analysis > > 1. Introduction to enzymes: structure, nomenclature, thermodynamics > 2. Metabolic pathways & databases > 3. Metabolism vs. signal transduction > 4. Analysis of metabolic network properties: stoichiometry matrix, flux balance analysis, metabolic control analysis > 5. Assignment: analyze metabolic pathway in Whole Cell paper, simulate and do FBA, MCA > > 1. Network analysis > > 1. Graph representation of networks > 2. Structural parameters of large scale network - Attachment (PubMed): A whole-cell computational model predicts phenotype from genotype - PubMed > Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all …

Pariksheet Nanda (12:27:40) (in thread): > 1. Connectivity degree distribution; scale free networks > 2. Average path length > 3. Node centrality and network centrality > 4. Global connectivity of the network (network hubs and bow-tie structure) > > 1. Modularity and network decomposition > 2. Software and tools for network structure analysis > 3. Assignment: install Cytoscape and analyze pathway models. > > 1. Stochastic Modeling > 2. Logic Modeling > 3. Signal transduction & examples of complex models > > 1. Introduction to multi-scale models > 2. Examples: calcium dynamics, circadian clock, cell cycle > 3. Parameter sensitivity, parameter sweeps, fitting/optimization > 4. Signal-response analysis: linear vs. non-linear response curves, positive and negative feedback, hysteresis, oscillations > 5. Special cases: perfect adaptation, one way switch, toggle switch > 6. Assignment: signal-response analysis of signaling model > > 1. Reproducing published modeling studies

rohitsatyam102 (13:19:31) (in thread): > Precisely Topics covered in 1, 3 8 and 10 right now since the course is introductory. The rest of it has been kept as an Elective under Advanced Systems Biology, shall students be interested.

rohitsatyam102 (13:24:09): > Btw there was a server used for designing 3D biological graphics/ cells. It used Unity in the backend. I forgot its name. It was really a wonderful tool, though a bit laggy, to produce scientific illustrations and publication ready pictures. It was opensource. Also could you suggest something opensource for generating mindmaps (a server or suite that’s free)?

rohitsatyam102 (13:31:19) (in thread): > Any alternative opensource for Biorender?

rohitsatyam102 (13:36:03): > https://mit6874.github.io/ - Attachment (mit6874.github.io): Spring 2021 6.874 Computational Systems Biology: Deep Learning in the Life Sciences > Course materials and notes for MIT class 6.802 / 6.874 / 20.390 / 20.490 / HST.506 Computational Systems Biology: Deep Learning in the Life Sciences

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2021-04-23

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2021-04-30

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2021-05-01

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2021-05-03

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2021-05-10

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2021-05-11

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2021-05-12

rohitsatyam102 (13:28:22): > I was wondering if there is a slack plugin (Gant chart plugin) or entirely any other app (free) that can be used to monitor an ongoing project progress and assign task in no time…?

Jared Andrews (13:36:13): > trello kind of fits the bill

Alan O’C (13:36:13): > github or gitlab projects?

Jared Andrews (13:36:22): > Or that.

Jared Andrews (13:36:51): > ToDoist has similar functionality

Sean Davis (15:22:29): > I use Zenhub in combo with github. Private repo with no code works fine for general project management.

2021-05-14

rohitsatyam102 (00:49:43) (in thread): > The project is related to bioconductor package development.

rohitsatyam102 (00:52:57): > Thanks everyone. I will look into it which one works best. Hopefully ToDoist or Zenhub will be helpful.

2021-05-21

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2021-05-25

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2021-05-27

Sean Davis (00:13:12): - Attachment: Attachment > @Casey Greene and I are looking for an “Informatics and Data Science Training and Education Coordinator” in the Colorado Comprehensive Cancer Center and the Center for Health Artificial Intelligence. https://cu.taleo.net/careersection/2/jobdetail.ftl?job=21020&lang=en

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2021-05-28

saskia (00:42:46): > Australian Biocommons is interested in producing a workshop/webinar called “Getting started with Bioconductor and R”. It is supposed to be a 15min overview of why you should care to use Bioconductor or R in your life science research. I am happy to make some material but I was wondering whether this would fit in more broadly with our education efforts.

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Charlie George (10:34:10): > We have a Computational Biology /Data Science trainer position available at the University of Oxford, I’d be really grateful if you could circulate to anyone who might be interested. Many thankshttps://my.corehr.com/pls/uoxrecruit/erq_jobspec_version_4.display_form?p_company=1[…]display_apply_ind=Y&p_refresh_search=Y&p_recruitment_id=150861

Amarinder Singh Thind (10:43:16): > Hi, Is there any tool with motive similar to mutsigcv/oncodrivfml that can work on RNAseq based variant data

2021-06-04

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2021-06-09

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2021-08-05

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Elisabetta Mereu (02:52:55): > Hi! For those interested in doing a PhD insingle-cellandspatial transcriptomics, we offer a nice computational position in Barcelona:https://www.carrerasresearch.org/en/phd-student-cellular-systems-genomics-endothelial-pathobiology-and-microenvironment_185615. Contact with me atemereu@carrerasresearch.orgfor informal requests or apply directly.

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2021-08-06

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2021-08-18

Aedin Culhane (09:41:09): > If you have developed a Bioconductor Package and learned the challenges along the way If you have tips and tricks for would-be developers. Please consider joining the new Bioconductor Mentorship program to help new would be developers get from R scripts to Bioconductor package. Expression of interest form athttps://forms.gle/fya5JEArTT5kNEGr9 - Attachment (Google Docs): Bioconductor Developer Mentorship Program - Expression of Interest > Please indicate your interest to learn more and potentially become a mentor in the Bioconductor Developer Mentorship program. The Bioconductor Developer Mentorship Program will form a part of the Bioconductor “welcome mat” that the Bioconductor Community Advisory Board are developing. It will be a group-mentorship/buddy program for would-be, new, or hesitant developers or for developers who wish to refresh their skills. The goal of the program is to welcome and onboard new developers, develop educational material to assist new developers, improve the quality of packages submitted to Bioconductor, and strengthen community and interactions between Bioconductor developers. Mentors should have at least 1 package either in the release or accepted in the development branch of Bioconductor. Each program cycle would run for 6 months (or the development cycle of Bioconductor package release). For more information about the program see the Bioconductor Website [link].. or Google doc [https://docs.google.com/document/d/1Q-Hxmy0ZcKzKSbB-dtg02gJRlZ0Vi6WNOTF-W3bwjmY/edit?usp=sharing]

2021-08-19

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2021-08-20

Jenny Drnevich (09:29:09): > This could go in several different slack channels but I decide to put it here. “Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries”.https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009218

2021-09-06

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2021-11-08

Paula Nieto García (03:26:56): > @Paula Nieto García has joined the channel

Elisabetta Mereu (06:52:06): > Please, consider join my group inBarcelonaas acomputational PhD student onIntegrative #singlecell Biologyearly next year with this greatinternational programcalled InPhINIT:https://www.mereulab.org/post/join-us-as-a-phd-student-within-the-inphinit-program-deadline-27-january-2022 - Attachment (mereulab.org): Join us as a PhD student within the INPhINIT program (deadline: 27 January 2022). > The INPhINIT-Incoming doctoral program consists of 35 fellowships for early-stage researchers of any nationality to pursue their PhD studies in the best Spanish and Portuguese research centres and units with excellence distinction. This frame is addressed exclusively to PhD research projects on STEM disciplines. Our group has a position for 1 PhD in Integrative Single Cell Biology for Personalized Medicine. Job position description: We propose a computational PhD in which the candidate will have

kent riemondy (10:57:22): > @kent riemondy has joined the channel

2021-11-09

Julia Philipp (15:10:14): > @Julia Philipp has joined the channel

2021-11-19

Ramon Massoni-Badosa (03:41:14): > @Ramon Massoni-Badosa has joined the channel

2021-11-24

Helge Hecht (13:15:45): > @Helge Hecht has joined the channel

Heather Bouzek (14:46:26): > @Heather Bouzek has joined the channel

2022-02-10

mirna (11:25:51): > Hi, y’all!  I am planning a workshop in Mexico:flag-mx:focusing on metagenomics (genome reconstruction and metabolism discovery).  I want to include a section of the Bioconductor packages used in metagenomics:microbe:.  Do you have any recommendations?

Kozo Nishida (17:43:48): > Hi@mirna. > I’m not familiar with metagenomics, but I can suggest the candidates. > Since there are 30 packages, I think it is not impossible to read all the vignettes. > How about choosing the packages suitable for your workshop (based on the impression you received from the vignettes)? - File (PNG): image.png

Kozo Nishida (17:49:31): > Also add biocViews for the data. - File (PNG): image.png

Kozo Nishida (17:53:21): > I will also add information about what is dealing with metagenomics in Orchestra workshop platform.https://waldronlab.io/curatedMetagenomicAnalyses/index.html - Attachment (waldronlab.io): Analyses using curatedMetagenomicData > This package is a home for significant analyses using curatedMetagenomicData. - File (PNG): image.png

Kozo Nishida (18:06:03): > @mirnapathviewis not in metagenomics biocViews, but it may be suitable for you. I found the following in the vignette of pathview.Notebaly, it can be directly used for metagenomic, microbiome or unknown species data when the data are mapped to KEGG ortholog pathways (Subsection 8.5).I think there are other cases like this, so it would be nice to have some advice from other people.

2022-02-13

Vince Carey (08:06:34): > @Levi Waldron^^

Levi Waldron (23:05:08) (in thread): > Thanks for the note@Kozo Nishida!@mirna, if you want to include some statistical analysis of already processed taxonomic and inferred metabolic functional data, curatedMetagenomicData provides uniformly processed profiles with manually curated metadata for >20,000 samples, and there are a number of analyses demonstrated in the repo and Orchestra container@Kozo Nishidamentioned. One other data package from my lab is HMP16SData, which provides processed 16S data from the Human Microbiome Project phase 1 (shotgun data are in curatedMetagenomicData). Other Bioconductor packages relied on in those analyses are TreeSummarizedExperiment (for representation), mia (for taxonomic analysis like aggregation), phyloseq (for all kinds of things), and SIAMCAT (for machine learning).

Levi Waldron (23:05:42) (in thread): > Thanks for the tag, Vince!

2022-02-14

Sean Davis (17:52:20): > https://www.ccdatalab.org/blog/2022/2/8/data-lab-single-cell-rna-seq-workshop-virtual-march-14-18-2022 - Attachment (Childhood Cancer Data Lab): Data Lab Single-Cell RNA-Seq Workshop, Virtual, March 14-18, 2022 — Childhood Cancer Data Lab > The Data Lab will hold our first virtual workshop of the year from March 14-18, 2022! In this workshop, we will introduce researchers studying pediatric cancer to the R programming language , the Tidyverse R packages for data science, single-cell RNA-seq data analysis, and pathway a

2022-02-21

Kowo Cyril (02:35:17): > @Kowo Cyril has joined the channel

2022-02-23

Paulina Paiz (10:45:24): > @Paulina Paiz has joined the channel

Susanna (12:07:24): > @Susanna has joined the channel

2022-02-25

Joshua Sodicoff (16:20:17): > @Joshua Sodicoff has joined the channel

2022-03-02

Avani Bhojwani (23:03:46): > @Avani Bhojwani has joined the channel

2022-04-29

Leo Lahti (14:58:45): > We will run an introductory course on microbiome analysis with R/Bioconductor using the TreeSummarizedExperiment / MultiAssayExperiment framework. In Oulu, Finland on June 20-23, 2022https://microbiome.github.io/course_2022_oulu/-> Feedback, questions welcome.

2022-05-02

Elisabetta Mereu (05:21:07): > Hi everyone! My lab is looking for a Marie Sklodowska-Curie postdoc candidate to work on single-cell genomics applied to personalized medicine. Read more here:https://www.mereulab.org/post/marie-sklodowska-curie-postdoctoral-fellowship-msca-fellow - Attachment (mereulab.org): Marie Sklodowska-Curie Postdoctoral Fellowship (MSCA-Fellow) > The Cellular Systems Genomics Group at the Josep Carreras Research Institute is looking for a postdoc candidate of a MSCA fellowship! If you are interested in Single-Cell Genomics, Machine Learning and their application to Personalized Medicine, get in touch at mailto:emereu@carrerasresearch.org|emereu@carrerasresearch.org. What do we look for? The ideal candidate is eligible for a MSCA individual fellowship and has the following characteristics: - PhD in Computational Biology, Genomics or any similar field with strong analytical

Laurent Gatto (08:08:00) (in thread): > I think you are more likely to hit the right audience in the#jobschannel

2022-05-09

Raoul Kamadjeu (17:21:39): > @Raoul Kamadjeu has joined the channel

Paul Villafuerte (22:04:34): > @Paul Villafuerte has joined the channel

2022-05-10

Daniel Adediran (05:02:26): > @Daniel Adediran has joined the channel

Madelyn Carlson (10:14:19): > @Madelyn Carlson has joined the channel

Sean Davis (14:50:41): > A little off-topic, but might be of interest to#clinicalor#cancer-relatedfolks. - Attachment (events.cancer.gov): Machine Learning and Health Outcomes in Cancer Care Delivery Research (Overview) | Events Registration > Overview The National Cancer Institute is conducting a Machine Learning and Health Outcomes in Cancer Care Delivery Research virtual workshop from May 16-17, 2022 focused on research in machine learning, cancer care delivery, and health outcomes. The goals are to identify scientific gaps, barriers, and opportunities in this emerging area of cancer-focused healthcare research.

2022-05-14

Elisabetta Mereu (08:26:09) (in thread): > Thanks@Laurent Gatto! I’ll do that:slightly_smiling_face:

2022-05-29

Kozo Nishida (08:56:52) (in thread): > Hi@Leo LahtiCan I ask you to apply to add this course to Bioconductor’s event calendar?https://bioconductor.org/help/events/To add an event, submitthis form.(To view the form, you have to be signed in to GitHub.)Any questions or if you do not have a github account please email events atbioconductor.org

2022-05-31

Leo Lahti (08:22:47) (in thread): > Done!

2022-06-12

Karat Sidhu (12:36:44): > @Karat Sidhu has joined the channel

2022-06-23

Batool Almarzouq (07:53:35): > Hi Everyone, we are happy to introduce new tutorial byJoel Nitta:blossom:, under the tittle “Modular, reproducible bioinformatics workflows with the targets R package :dna:****” in the ISCB.****Modern bioinformatics pipelines can be incredibly complex, but all tend to follow a common pattern: they start with raw data, then pass the data through various programs until arriving at a final result. If this is done in an ad-hoc, unorganized fashion, the results may never be reproducible or even worse, unreliable and/or wrong. Pipeline management software is therefore essential to obtain results that are robust and reproducible. The targets R package is a recently developed workflow manager that comes with many excellent features for bioinformatics, including data caching, pipeline-level parallelization, and HPC support. In this hands-on workshop, I will demonstrate how targets can be used in concert with other tools like docker and conda to orchestrate modular, reproducible bioinformatics pipelines. The workshop will feature variant-calling as an example, but the concepts and tools can be applied to nearly any analysis.Pre-requisites :computer:****:****Basic familiarity with R. Installations of recent versions of R, conda, and docker.Duration :clock2:****:****2 hoursRegister :point_down:https://www.iscb.org/iscbacademy > > We offer waiver for individuals who are unable to pay, if you are unable to pay, please feel to contact me! - Attachment (iscb.org): Main > ISCB - International Society for Computational Biology

2022-07-07

Clara Pereira (14:27:12): > @Clara Pereira has joined the channel

2022-07-09

Kozo Nishida (07:33:06): - Attachment: Attachment > I will be holding this document translation event two and a half hours from now. > If you like, please feel free to join us. > The introduction slide is https://docs.google.com/presentation/d/1yvC6ylG2eK6qnwv9MRPrRUJ0pfYc-7H4zbkhSWnlEos/edit?usp=sharing.

Xueyi Dong (12:06:02): > @Xueyi Dong has joined the channel

2022-07-11

Laurent Gatto (08:54:16): > The Carpentries are hiring a Director of Technology -https://carpentries.org/blog/2022/07/director-of-technology/ - Attachment (The Carpentries): We are Hiring a Director of Technology. Join Our Team. > Applications received before 20 July at 11:59 PM (anywhere on earth) will receive full consideration.

2022-07-15

Ashley Robbins (15:23:42): > @Ashley Robbins has joined the channel

2022-07-26

Sean Davis (14:40:53): > A little off-topic, but data sharing and management is a core value for Bioconductor, so here you go:https://sharing.nih.gov/about/learning/DMS-Update - Attachment (sharing.nih.gov): REGISTER NOW! NIH Data Management and Sharing Policy Webinar Series | Data Sharing > REGISTER NOW! NIH Data Management and Sharing Policy Webinar Series | Data Sharing - Learn about NIH data sharing policies and how to share and access scientific data

Jenny Drnevich (17:13:31) (in thread): > Thanks! This is going to be a big change at NIH.

Sean Davis (17:14:40) (in thread): > I think so. If your institution is not already planning and socializing, it’s probably time to start.

Jenny Drnevich (17:19:22) (in thread): > We are, except we are trying to get it standardized across the entire University instead of different institutions doing their own thing.@Chris Fields:point_up:

Chris Fields (17:19:31): > @Chris Fields has joined the channel

Chris Fields (17:25:29) (in thread): > Yep! This is one of the reasons a few key institutes are panicking at the moment. BTW hi@Sean Davis!

Chris Fields (17:27:57) (in thread): > And I’m guessing@Jenny Drnevichmade it to Seattle:slightly_smiling_face:

Jenny Drnevich (17:28:32) (in thread): > I’m at OHare at the moment but on my way!

2022-07-27

rohitsatyam102 (10:57:34): > Hi I registered for BioC2022 (Virtual Mode) but I didn’t get an email to join. Whom to contact

Jenny Drnevich (11:01:33) (in thread): > You can use this link and sign in with the email you registered with.Click this link

rohitsatyam102 (11:02:02) (in thread): > Thanka

2022-07-28

Krithika Bhuvanesh (13:50:33): > @Krithika Bhuvanesh has joined the channel

Aedin Culhane (17:47:26) (in thread): > @Qian LiuRcwl and Rcwlpipelineshttps://bioconductor.org/packages/release/bioc/html/RcwlPipelines.html - Attachment (Bioconductor): RcwlPipelines > A collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language.

Aedin Culhane (17:48:59): > In person course Introduction to genomic data analysis with R and Bioconductorhttps://bioconductor.github.io/2022-09-12-BiocIntro-Heidelberg/BioQuant Heidelberg > September 12-13, 2022

2022-07-29

Alexandra Emmons (12:07:52): > @Alexandra Emmons has joined the channel

Jenny Drnevich (12:36:54): > Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010220

Aedin Culhane (20:08:22): > Posted before.. but adding again as its worth reading . Great article from CAB member@Janani Ravihttps://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010164 - Attachment (journals.plos.org): Ten simple rules to host an inclusive conference > Conferences are spaces to meet and network within and across academic and technical fields, learn about new advances, and share our work. They can help define career paths and create long-lasting collaborations and opportunities. However, these opportunities are not equal for all. This article introduces 10 simple rules to host an inclusive conference based on the authors’ recent experience organizing the 2021 edition of the useR! statistical computing conference, which attracted a broad range of participants from academia, industry, government, and the nonprofit sector. Coming from different backgrounds, career stages, and even continents, we embraced the challenge of organizing a high-quality virtual conference in the context of the Coronavirus Disease 2019 (COVID-19) pandemic and making it a kind, inclusive, and accessible experience for as many people as possible. The rules result from our lessons learned before, during, and after the organization of the conference. They have been written mainly for potential organizers and selection committees of conferences and contain multiple practical tips to help a variety of events become more accessible and inclusive. We see this as a starting point for conversations and efforts towards building more inclusive conferences across the world. * Translated versions of the English abstract and the list of rules are available in 10 languages in S1 Text: Arabic, French, German, Italian, Japanese, Korean, Portuguese, Spanish, Tamil, and Thai.

2022-07-31

Arda Keles (04:15:02): > @Arda Keles has joined the channel

2022-08-02

Alvaro Sanchez (05:09:45): > @Alvaro Sanchez has joined the channel

2022-08-09

Laurent Gatto (10:29:20): > Bioconductor is now a Carpentries member organization and opportunities to join an instructor training:https://bioconductor.github.io/biocblog/posts/2022-07-12-carpentries-membership/ - Attachment (bioconductor.github.io): Bioconductor community blog - Bioconductor becomes a Carpentries member organization > Starting from August 1, 2022, Bioconductor will be a member of The Carpentries. Among other things, the membership enables us to allow 15 individuals to follow the Carpentries’ Instructor Training program and become certified Carpentries Instructors.

2022-08-17

Laurent Gatto (10:01:17): > Join us during theBioconductor Teaching Weekto discuss the teaching and education needs of the Bioconductor community and how to plan our future activities and efforts accordingly. > > Everybody welcome! No teaching experience required.https://support.bioconductor.org/p/9146055/

2022-08-18

Frederick Tan (08:46:34) (in thread): > Thank you for organizing this! We’ve started a tiny “book club” to work through bioc-intro over the course of the next four weeks so the timing is perfect. Will try and make the Thu Sep 8th session!

2022-08-22

Batool Almarzouq (18:22:33) (in thread): > Thank you@Aedin Culhane!

2022-08-27

Kozo Nishida (12:21:49) (in thread): > I am already a Carpentries instructor. > If I want to teach a lesson using the bioc-intro teaching material, > do I need to submit the form in the blog post? > (even if I’m already an instructor.)

Kozo Nishida (12:27:36): > I have set up a Crowdin translation project forbioc-intro. > Please reply me if you are interested. > Due to storage limitations in Crowdin, it currently only have 4 translation target languages. > Please let me know if there is no language you want to translate. > I can add your language to the target (upon your request).

Charlotte Soneson (14:03:51) (in thread): > Hi Kozo - no, you don’t have to do that. The form is for people who want to become certified Carpentries instructors. Anyone can use the material for teaching (it’s licensed under CC-BY).

2022-08-30

Lisa Breckels (07:12:44): > @Lisa Breckels has joined the channel

2022-09-01

Indrik Wijaya (21:39:27): > @Indrik Wijaya has joined the channel

2022-09-04

Gurpreet Kaur (15:00:01): > @Gurpreet Kaur has joined the channel

2022-09-07

Hugo Tavares (08:58:10): > @Hugo Tavares has joined the channel

2022-09-12

Mervin Fansler (18:23:30): > @Mervin Fansler has joined the channel

2022-09-14

Aedin Culhane (19:18:36): > Upcoming MAQC meeting on reproducibility and explainable AI maybe of interesthttps://themaqc.org

Aedin Culhane (19:19:33) (in thread): > AGENDA > > FDA/NCTR-MAQC 2022 Conference > (5th Annual Meeting of the MAQC Society) > > Venue: U.S. FDA White Oak Campus Great Conference Room (Silver Spring, MD) > Note: All times are shown in Eastern Time Zone. > > Monday September 26, 2022 > 8:00am-8:45am > Registration > > 8:45am-9:00am > Welcome and Introduction > • Dr. Wendell Jones > Q2 Solutions > • Dr. Tucker Patterson FDA/NCTR (virtual) > > 9:00am-9:10am > Opening Remarks > • Dr. Namandjé BumpusFDA Chief Scientist > 9:10am-9:30am > “From Genomics to AI – Reflections on the MAQC’s Journey to Improve Reproducibility in Life and Health Science” > • MAQC Panel > • Dr. Leming Shi > Fudan Univ. (virtual), > Dr. Benjamin Haibe-Kains, Princess Margaret Cancer Center (virtual) > 9:30am-10:15am > Special Invited Speaker – “Leakage and the Reproducibility Crisis in ML-based Science” > • Sayash Kapoor Princeton University > 10:15am-10:25am > Q&A > > > 10:25am-10:40am > Break > > 10:40am-12:01pm > Parallel Sessions I-A and I-B > > > > Session I-A: XAI Programs > Session Chair: > Dr. Cesare Furlanello, > HK3 Lab > 10:40am-11:20am > Special Invited Speaker – “DARPA’s explainable AI (XAI) program: A retrospective” > • Dr. Matt Turek > DARPA (virtual) > 11:20am-11:50am > “Drug repurposing for COVID-19 using explainable machine learning and mechanistic models of signal transduction circuits related to SARS-CoV-2 infection with real world data validation” > • Drs. Loucera & Dopazo Andalusian Public Foundation Progress & Health (virtual) > 11:50am-12:01pm > Q&A > > > Session I-B: Real World NGS Challenges > Session Chair: > • Dr. Joshua Xu, FDA/NCTR > 10:40am-11:10am > “Beyond SEQC2 – Next Phase with Real World Data” > • Dr. Don Johann > UAMS Health (virtual) > 11:10am-11:40am > “Some nonobvious factors that enhance or diminish observed and theoretical Illumina library complexity” > • Dr. Wendell Jones > Q2 Solutions > 11:40am-11:50am > Q&A > > 12:01pm-1:15pm > Lunch Break > > > 1:15pm-3:00pm > Parallel Sessions II-A and II-B (Monday, September 26) > > Session II-A: Reproducible AI/ML in Toxicology > Session Chair: > • Dr. Shraddha Thakkar > FDA/CDER > > 1:15pm-1:40pm > “AI or Animal – A reproducibility perspective” > • Dr. Weida Tong > DBB Director,FDA/NCTR > > 1:40pm-2:05pm > “Reproducible AI for supporting regulatory applications – a case study” > • Dr. Ting Li > FDA/NCTR/DBB > > 2:05pm-2:30pm > “Enhancing reproducibility of language models in BERTox” > • Dr. Leihong Wu > FDA/NCTR/DBB > > 2:30pm-2:55pm > “Improving preclinical pathology analysis with PathologAI” > • Dr. Cesare Furlanello > HK3 Lab > 2:55pm-3:00pm > Q&A > > > > Session II-B: Tools and Methods for Reproducibility + “Hot Topics” (Posters) > Session Chair: > 1:15pm-1:40pm > “An automated bioinformatic software testing and benchmarking platform to standardize the development of accurate, reproducible, and scalable omics analysis tools” > • Gwenn Berry > Magna Labs, Inc. > 1:40pm-2:05pm > “Reproducible toxicogenomics analysis in the three-sample scenario” > • Dr. Dongying LiFDA/NCTR/DBB > 2:05pm-2:10pm > Q&A > > 2:10pm-2:25pm > “LeaSH: a High-Throughput COVID-19 Test to Profile Viral and Host Transcriptomes by Next Generation Sequencing” (Poster) > • Dr. Oswaldo Lozoya > NIH/NIEHS (virtual) > 2:25pm-2:40pm > “Evaluation of mutagenic susceptibility of different stages in germ cell development of Caenorhabditis elegans using next generation sequencing”(Poster) > • Dr. Tao Chen FDA/NCTR/DGMT(virtual) > 2:40pm-2:55pm > “Explainable approach for species identification using LIME” (Poster) > • Dr. Aarti Milind KarandeS.P.I.T. (virtual) > 2:55pm-3:00pm > Q&A > > 3:00pm-3:20pm > Break and Posters > > 3:20pm-5:20pm > Session III > > > Session III: precisionFDA NCTR Indel Challenge > Session Chair: > • Dr. Samir Lababidi, FDA/ODT > > 3:20pm-3:40pm > “NCTR indel calling challenge from oncopanel sequencing data” > • Dr. Binsheng Gong FDA/NCTR/DBB > > 3:40pm-3:55pm > Winner presentation #1 > • in-person > 3:55pm-4:10pm > Winner presentation #2 > • virtual > 4:10pm-4:25pm > Winner presentation #3 > • virtual > 4:25pm-4:40pm > Winner presentation #4 > • virtual > 4:40pm-4:55pm > Winner presentation #5 > • virtual > 4:55pm-5:10pm > Winner presentation #6 > • virtual > 5:15pm-5:20pm > Closing Announcements and Adjourn > > > Tuesday September 27, 2022 > 8:00am-8:45am > Registration > > 8:45am-8:50am > Introduction > • Dr. Wendell Jones > Q2 Solutions > > 8:50am-9:30am > Keynote: “Reproducibility and Transparency in Medical AI” > • Dr. Hugo Aerts > Dana-Farber, Harvard(virtual) > 9:30am-9:35am > Q&A > > 9:35am-10:40am > Session IV MAQC Society Awards > > 9:35am - 9:40am > Award announcements – MAQC Society Award and Outstanding Reproducibility in Science Award > • Dr. Becky Kusko Immuneering > • Dr. Cesare Furlanello HK3 Lab > > MAQC Society Award – Dr. Ira Deveson, Garvan Institute of Medical Research > Outstanding Reproducibility in Science Award – Dr. Marzyeh Ghassemi, MIT > • > 9:40am-10:10am > Outstanding Reproducibility in Science Award – “Reproducibility Challenges in AI/ML” > • Dr. Marzyeh GhassemiMIT > > 10:10am-10:40am > Outstanding Reproducibility in Science Award Runner-up – “Reproducibility Issues with Pre-Clinical Data” > > • Dr. Brian Nosek > University of Virginia > 10:40am-10:50am > Break > > > 10:50am-12:01pm > Parallel Sessions V-A and V-B > > Session V-A: Single Cell Annotation and Inference > Session Chair: > • Dr. Becky Kusko Immuneering > > 10:50am-11:20am > “De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution” > • Dr. Jie Liao > Zhejiang University, China (virtual) > 11:20am-11:50am > “A signaling-informed neural network for scRNA-seq annotation of known and unknown cell types” > • Drs. Joaquin Dopazo & Carlos LouceraAndalusian Public Foundation Progress & Health (virtual) > > 11:50am-12:01pm > Q&A > > > Session V-B: Enhancing Reproducibility of and Confidence in Studies > Session Chair: > > 10:50am-11:20am > “Systematizing Confidence in Open Research and Evidence (SCORE)” > • Dr. Brian Nosek > University of Virginia > 11:20am-11:50pm > “The FAIR Cookbook: pharmas and academics join forces to make data FAIR” > • Dr. Susanna Sansone University of Oxford > 11:50am-12:01pm > Q&A > > 12:01pm-1:00pm > Lunch Break > > 1:00pm-1:45pm > Keynote: “Interpretable AI” > • Dr. Zachary Lipton > CMU > 1:45pm-2:00pm > Q&A and Break > > > 2:00pm-3:45pm > Parallel Sessions VI-A and VI-B (Tuesday, September 27) > > > Session VI-A: SEQC2 Targeted RNA-seq > Session Chair: > • Dr. Wendell Jones > Q2 Solutions > > 2:00pm-2:30pm > “Targeted RNA-seq for small variant detection to enhance precision medicine” > • Dr. Dan Li > FDA/NCTR/DBB (virtual) > > 2:30pm-3:00 pm > “Integrated Calling and Evaluation of Gene Fusion Detection by Targeted RNA Sequencing of Reference Samples with Long and Short Reads” > > • Dr. Joshua Xu FDA/NCTR/DBB > 3:00pm-3:30pm > “Resolving complex gene expression and splicing with targeted long-read RNA sequencing” > • Dr. David P Kreil > Boku University, Austria(virtual) > • Dr. Paweł P ŁabajJagiellonian University, Poland (virtual) > > 3:30pm-3:35pm > Q&A > > > > Session VI-B: New Single-Cell Assays and Tools + “Hot Topics” (Posters) > Session Chair: > > 2:00pm-2:30pm > “Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk” > • Dr. Xin Shao > Zhejiang University, China (virtual) > 2:30pm-3:00pm > “Mutual genome and transcriptome enrichment and sequencing in single cells with ResolveOME amplification chemistry to illuminate complex biological mechanisms” > • Dr. Isai Salas-Gonzalez > BioSkryb Genomics > 3:00pm-3:05pm > Q&A > > 3:05pm-3:20pm > “Using Inherently Interpretable Models to Understand Sources of Variant Calling Errors” (Poster) > • Dr. Justin Zook > NIST > 3:20pm-3:35pm > “Radiological heterogeneity of intrapatient lesion-specific responses to chemotherapy is associated with survival in advanced leiomyosarcoma (Poster)” > • Caryn Geady > Princess Margaret Cancer Center (virtual) > 3:35pm-3:45pm > Short Break and Posters > > 3:45pm-4:00pm > Plans for 6th Annual Meeting of the MAQC Society in 2023 > > 4:00pm-5:00pm > Discussion for new MAQC Society Working Groups > > 5:00pm-5:05pm > Closing Remarks

2022-09-16

Matteo Calgaro (06:43:09): > @Matteo Calgaro has joined the channel

2022-09-17

Abdul Saboor Khan (07:03:37): > @Abdul Saboor Khan has joined the channel

2022-09-27

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2022-10-04

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2022-10-06

Fabricio Almeida-Silva (03:31:26): > @Fabricio Almeida-Silva has joined the channel

Fabricio Almeida-Silva (03:48:44): > Hello, everyone! I’d like to thank Bioconductor for the invitation to become a certified Carpentries instructor!:tada::bioc-load::male-technologist:I’ve just signed up for the training event on December 19-20. If anyone here is also attending on this date, please let me know!

Olly Crook (05:19:35): > @Olly Crook has joined the channel

Olly Crook (05:32:26): > Hi, I’m Olly - a researcher at the university of Oxford. I’m also grateful to Bioconductor for the Carpentries instructor support. I’ve signed up for the event 5 - 8th of December:smile:

Almut (08:06:07): > Hello from my side as well. I’m Almut, a PhD student at the University of Zürich and I’m excited and grateful to get the chance to become a Carpentries instructor as well:tada:! I have also signed up for the event 5 - 8th December:slightly_smiling_face:!

Kasper D. Hansen (08:43:14): > Actually, we (everyone in Bioc) are grateful to every future instructor for putting the time and effort into providing(better)training to new and existing users.

Kevin Rue-Albrecht (10:45:24): > Speaking of putting in time and effort, in the spirit ofHacktoberfest 2022, I’ve added the#hacktoberfesttag tohttps://github.com/carpentries-incubator/bioc-project, the Carpentries lesson that I’ve been developing about the BioC project. > This means that contributions to the repository count towards your Hacktoberfest progress (which itself leads to free stickers and t-shirts:smile:) - Attachment (hacktoberfest.com): Hacktoberfest 2022 > Hacktoberfest: a month-long celebration of open-source projects, their maintainers, and the entire community of contributors.

Martin Morgan (11:31:09): > @Martin Morgan has left the channel

ChiaSin (11:59:54): > Hello everyone, I am Chia Sin. I would like to thank the Bioconductor teaching committee for the chance to become certified Carpentries instructor:tada::star2:. I’ve also signed up for the training on Dec 5-8. Looking forward to meet some of you during the event:simple_smile:!

Devika Agarwal (13:10:45): > @Devika Agarwal has joined the channel

Maria Doyle (16:58:48) (in thread): > @Kevin Rue-Albrechtgood idea, maybe we could do for bioc-intro, bioc-rnaseq too. I’ve added this into the agenda for Monday’s teaching meeting in the Google notes herehttps://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit#

Kevin Rue-Albrecht (17:00:23) (in thread): > Thanks.I’m…teaching…on Monday so probably will miss that one

2022-10-07

Leo Lahti (12:30:08): > Hi all - I have been hanging around on this channel already but now was accepted to become certified Carpentries instructor with the others. Thanks! I have signed up for the Dec 19-20 training session.

Frederick Tan (12:41:47) (in thread): > +1 for bioc-intro:slightly_smiling_face:

Sehyun Oh (15:23:48): > Hi all - I’m Sehyun Oh, a postdoc at the City University of New York. I’m very thankful to Bioconductor Teaching Committee for the opportunity to become a certified Carpentries instructor! I signed up for the Dec 5-8th Training.:slightly_smiling_face:

2022-10-10

Mercilena Benjamin (13:55:47): > @Mercilena Benjamin has joined the channel

2022-10-12

Maria Doyle (07:05:07) (in thread): > To update here, we decided to add the 3 Bioconductor Carpentries lessons into Hacktoberfest (along with the Bioconductor blog)https://twitter.com/Bioconductor/status/1580122161221496832Feel free to ask any questions here or in the repos! - Attachment (twitter): Attachment > Bioconductor is participating in @hacktoberfest! A worldwide celebration :partying_face: of open-source projects in Oct. Get PRs accepted in these repos https://bit.ly/biochack for chance to win tshirt :shirt: or tree :deciduous_tree: planted in your name :sunglasses: #hacktoberfest #rstats @R_Contributors @_R_Foundation

Kevin Rue-Albrecht (12:53:43) (in thread): > Btw,@Maria Doyle, I’ve created a meetup for this herehttps://www.meetup.com/boston-r-bioconductor-for-genomics/events/289042169/It will take place next Thursday 20 Oct, so we should prepare a post/tweet about it soonish. > I was waiting for Aedin to promote me in the NYC meetup group to post both at the same time, but that hasn’t happened yet, so perhaps we should just go ahead with promoting it in the Boston group already - Attachment (Meetup): Contributing to The Carpentries lesson about the Bioconductor project, Thu, Oct 20, 2022, 11:00 AM | Meetup > Hello! Hola! Bonjour! 你好! こんにちは! In this meetup, we will describe how to contribute to lesson “The Bioconductor project” in The Carpentries incubator. This is a Hacktober

2022-10-13

Umar Ahmad (04:12:41): > Hello everyone, I amUmar Ahmad. I am excited to be part of this community as a trainee for Bioconductor Certified Carpentry Instructor. I have signed up to participate in the training on15-18 November. I gladly appreciated the Bioconductor Teaching Committee for offering this opportunity to me to be trained through your Carpentries membership. Looking forward to learn from your wealth of knowledge and experience.

Maria Doyle (17:39:32) (in thread): > @Kevin Rue-AlbrechtI’ve drafted a tweet at the top of the Google doc here, see what you thinkhttps://docs.google.com/document/u/0/d/1j-n8ZtGYyXI2yHqp0NIr0JMYsK2gKvuCeMaYCHufwC4/mobilebasicDid you say you had an image that you couldn’t add to the meetup as if so, want to add it to the Tweet?What about adding a link to the rendered lesson in the meetup description?

2022-10-18

Frederick Tan (14:55:02): > Two questions aboutgithub.com/carpentries-incubator/bioc-intro > 1. Is there an updated schedule on demonstrating how the material could be spread across two days? The only one I can find isbioconductor.github.io/2022-09-12-BiocIntro-Heidelbergwhich doesn’t reflect “remove the joins chapter #a57bb1” > 2. Any preference for having discussions about this material in this channel or a new channel?

Frederick Tan (15:50:35) (in thread): > @Jenny Drnevich@Laurent Gatto@Maria DoyleBased on the times listed in the current Schedule it looks to be 10h 30m of content so splitting into two 5-hour days would > * End day 1 with dplyr - part 1 > * Start day 2 with dplyr - part 2 > … which leaves a nice amount of time for breaks, lunch, and perhaps ending an hour early:slightly_smiling_face:

2022-10-19

Laurent Gatto (00:07:53) (in thread): > * From recent experience (Heidelberg and local workshop) is that day 1 finishes with of just before group_by/summarise. > * Indeed, the joins chapter was removed and a short section was added at the end of the dplyr chapter. > * The duration seems of the overall course seems good now. I think the tidySummarizedExperiment that we have could be considered optional at this stage.

Laurent Gatto (00:09:24): > For discussion, my preference would be to > * open an issue on Github > * live discussion during our monthly calls

Jenny Drnevich (08:59:40) (in thread): > It also depends on the groups of learners and the format. I am teaching parts of the workshop now, and after two 2hr sessions, we are just starting the Starting with data (est. 3:30) AND I skipped most of the spreadsheet stuff. But we are doing zoom and have 5-6 people actively asking tons of questions, which is good but slows things down. Also what would take ~5 sec to solve a problem in person takes ~5 min on zoom!

Frederick Tan (10:34:12) (in thread): > Great feedback! For what it’s worth, we’re working to offer it in person Nov 3/4 and online Dec 5/6

Frederick Tan (10:35:10) (in thread): > Regardless, hope your workshop goes well today/tomorrow!

2022-10-20

Kevin Rue-Albrecht (05:12:47): > In preparation for themeetupthis evening, I’m practicingmake sitefor the first time in a while. > I notice a warning I don’t remember seeing before.https://github.com/carpentries-incubator/bioc-projectI’ve identified that within challenges/solutions the triple backticks with r specification{r} `markup is triggering the error. > In other challenges, I use the simple backtiks alone and they don't cause any issue. > In both cases, it renders fine, but adding the{r}`makes the solution runnable with output automatically embedded, while the backticks alone require manual execution of the code and pasting+formatting the result. > Am I missing a trick? Have we set best practices? - Attachment (Meetup): Contributing to The Carpentries lesson about the Bioconductor project, Thu, Oct 20, 2022, 11:00 AM | Meetup > Hello! Hola! Bonjour! 你好! こんにちは! In this meetup, we will describe how to contribute to lesson “The Bioconductor project” in The Carpentries incubator. This is a Hacktober - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

Alan O’C (05:23:16) (in thread): > This is a known issue with the current carpentries lesson format. You can ignore the warning but be aware that any dependencies declared within those blocks won’t be picked up

Kevin Rue-Albrecht (05:23:41) (in thread): > ouch - thanks for the warning!

Maria Doyle (06:27:44) (in thread): > @Alan O’Cdo you know if it’s also an issue with the new Carpentries lesson format?

Alan O’C (06:28:18) (in thread): > No idea but I’m told most things will be fixed whenever that rolls out

Maria Doyle (06:37:07) (in thread): > ok thanks, Toby recommended at last teaching meeting to roll over to new format.@Kevin Rue-Albrechtthis is the info > > To initiate transition, Toby recommends tagging @zkamvar in an issue on each of your lesson repositories, requesting that the lesson be transitioned to the workbench. You may need to wait a short while for him to be able to do that - he is currently very busy planning the Workbench Beta Phase - but I hope he will be able to make it work for you. Otherwise/if you do not want to wait, you can studyhttps://carpentries.github.io/workbench/transition-guide.htmland try to reformat the content/reorganise the files and folder on your own

Alan O’C (06:41:05) (in thread): > Seems like it doesn’t use > for callout/challenge blocks any more so yeah this error wouldn’t pop up

Kozo Nishida (12:38:11) (in thread): > Discussions from this Hacktoberfest meetup can be continued here.https://github.com/carpentries-incubator/bioc-project/discussions

2022-10-21

John Ogata (16:05:53): > @John Ogata has joined the channel

2022-10-28

Brian Schilder (08:30:55): > @Brian Schilder has joined the channel

2022-10-31

Chenyue Lu (10:04:42): > @Chenyue Lu has joined the channel

2022-11-01

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2022-11-08

Nicolas (20:44:22): > @Nicolas has joined the channel

2022-11-09

Selin Jessa (22:03:48): > @Selin Jessa has joined the channel

2022-11-21

Maria Doyle (09:02:27): > Webinar that may be of interest to this grouphttps://www.addevent.com/event/Kq14516694 - Attachment (addevent.com): R at AstraZeneca: upskilling our workforce through education, experience, and exposure > Join us on November 29th at 12PM EST to hear Gabriella Rustici & Guillaume Desachy share their experience about the R journey AstraZeneca is currently on.The use of R continues to become more and more important at AstraZeneca. It is a true paradigm shift that we have embarked on! This shift has required upskilling our workforce to make them proficient R users. To do so, we are leveraging the 3Es of learning: education, experience and exposure. Learn more about their team’s Data Science Educational Program and how the team at AstraZeneca has built their own strong community of R users - where learning takes place through experience and exposure.  Speaker bios:Gabriella is Data Science Learning Senior Director in Astrazeneca’s R&D Data Science & AI where she is responsible for developing a strategy for, and creating a centralised approach to, data science learning for R&D. Gabriella completed her PhD at the Wellcome Sanger Institute and previously run bioinformatics training programs at the University of Cambridge and the European Bioinformatics Institute, in the UK. She is passionate about designing, implementing and evaluating effective and scalable solutions to educate scientists and data science practitioners at all career stages.Guillaume is passionate about helping bring new medicines to patients by leveraging the power of statistics and precision medicine. Since October 2020, he has been doing so at AstraZeneca where he works as a Statistical Science Director.In addition, since March 2022, he have been leading a team of 15 collaborators focusing on building the community of R users at AstraZeneca, called R @ AZ.

2022-11-23

Maria Doyle (06:12:27): - Attachment: Attachment > @stefano mangiola and I have been discussing doing an tidy-in-Bioc online tutorial in mid-December. Details cross-posted to birdsite and oldelephantsite > • https://twitter.com/mikelove/status/1595038783371706369 > • https://genomic.social/@mikelove/109387583769396088

2022-11-25

Olly Crook (10:25:21): > @Olly Crook has joined the channel

2022-11-29

Zuguang Gu (06:46:34): > @Zuguang Gu has joined the channel

Zuguang Gu (07:48:27): > Hi everyone! My name is Zuguang Gu. I am a staff scientist in German Cancer Research Center, Heidelberg Germany. Thanks for the opportunity of being a Bioconductor instructor. Current all the tickets for the Instructor Training slots are sold out, I will keep my eyes on the next open training slot.

Jenny Drnevich (08:31:03) (in thread): > Not sure when they will schedule/open ones in Jan, but I am also keeping an eye out!

Javier Carpinteyro Ponce (13:02:33): > @Javier Carpinteyro Ponce has joined the channel

Javier Carpinteyro Ponce (13:07:07): > Hello everyone! My name is Javier and I am a bioinformatician at Carnegie Institution for Science, Department of Embryology, Baltimore USA. Thank you for the opportunity of being a Bioconductor instructor. Looking forward to signing up on the next available training course.

2022-11-30

rodrigo arcoverde (07:29:37): > @rodrigo arcoverde has joined the channel

rodrigo arcoverde (07:31:46): > 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:

David Shih (09:07:38): > @David Shih has joined the channel

David Shih (09:12:06): > Hi, I am David Shih. I am an assistant professor at the University of Hong Kong. I did my postdoc in the Biostatistics (now Data Sciences) department at DFCI. I also applied for the Carpentry instructor training course on Feb 7-8, 2023.

Stephany Orjuela (09:26:33): > @Stephany Orjuela has left the channel

Jenny Drnevich (09:35:55) (in thread): > And they just opened up a bunch in 2023:https://carpentries.github.io/instructor-training/training_calendar/index.html

Himel Mallick (09:42:32): > @Himel Mallick has joined the channel

Zuguang Gu (09:51:53) (in thread): > great! thanks!

Zuguang Gu (09:52:22): > I have applied for the training onJanuary 19-20, 2023.

Javier Carpinteyro Ponce (10:49:25): > Registered for the Instructor Training on January 19-20, 2023

Antonio Cembellin Prieto (17:34:50): > @Antonio Cembellin Prieto has joined the channel

2022-12-01

irem Kahveci (01:38:53): > @irem Kahveci has joined the channel

Koji Yoshida (05:47:55): > @Koji Yoshida has joined the channel

2022-12-07

Aedin Culhane (20:23:55): > So exciting to meet so many soon-to-be Bioconductor carpentry instructors:fast_parrot::fiesta_parrot::party_parrot::parrotconga::dealwithit-parrot:

Belinda Phipson (23:22:52): > @Belinda Phipson has joined the channel

2022-12-08

Givanna Putri (01:56:58): > @Givanna Putri has joined the channel

Givanna Putri (06:51:19): > Hi everyone! My name is Givanna. I am a postdoc at Walter and Eliza Hall Institute of Medical Research (WEHI) in Melbourne, Australia. I have been using Bioconductor packages for a long time, and am looking to contribute one in the very near future! I’m still looking out for an instructor training course which time slot is more suited to Australian timezone. If nothing better turns up, I’ll attend the one on Feb 21-24 which starts at 5am for me. I’m excited to be part of the Bioconductor education and training community, and am looking forward to work with everyone!

2022-12-12

Zainab Ashimiyu-Abdusalam (04:52:12): > @Zainab Ashimiyu-Abdusalam has joined the channel

Zainab Ashimiyu-Abdusalam (04:52:41): > 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.

Kozo Nishida (05:22:16): > Hi@Zainab Ashimiyu-Abdusalam, > I recommend working on this “good first issue” firsthttps://github.com/carpentries-incubator/bioc-intro/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22(to get started to contributing).

Kozo Nishida (05:24:58): > @Zainab Ashimiyu-AbdusalamAlso, I recently made some slides about community contributions. Take a look.https://docs.google.com/presentation/d/1Wgs6y2ZMmbYGFk3WhEQ7Vc3NbvQxXjRFuyimidM1JxA/edit#slide=id.p - File (Google Slides): BioCAsia2022 - 5mins

Zainab Ashimiyu-Abdusalam (05:30:49) (in thread): > Thank you@Kozo Nishida, I’d definitely check them out

Kevin Rue-Albrecht (10:21:53): > Curious to hear if this may be of interest to anyone teaching differential expression:slightly_smiling_face:https://isee.github.io/iSEEde/articles/methods.html#live-appFeedback welcome before a likely submission to BioC in early 2023 - Attachment (isee.github.io): Supported differential expression methods > iSEEde - File (PNG): image.png

Ibra Lujumba (10:24:51): > Hi everyone. My name is Ibra Lujumba. I am a graduate student at Makerere University. I have applied for the Instructor Training on January 19 -20.

Jared Andrews (10:39:02) (in thread): > This is interesting, I have something kind of similar here:https://github.com/j-andrews7/iBET/blob/main/R/DESeq2.R

Jared Andrews (10:40:09) (in thread): > Created mostly so I could deploy Rmd’s explaining the process and provide interactive figures to which labels could be easily added and aesthetics tweaked without me having to do it.

Jared Andrews (10:40:47) (in thread): > …needs some polish after all I’ve learned from iSEE in terms of shiny code packaging.

Kevin Rue-Albrecht (10:41:06) (in thread): > Neat! I haven’t reviewed existing tools lately, as I was asked to specifically develop an add-on for iSEE apps.

Kevin Rue-Albrecht (10:41:42) (in thread): > Good to know about others out there, comparisons are always a good source of inspiration in both directions:slightly_smiling_face:

Jared Andrews (10:42:53) (in thread): > My previously posted Shiny tool for CRISPR stuff I posted has come a long way thanks to your guidelines for Bioc contribution. Hopefully I’ll get it into the next release - it’ll be a good candidate for fleshing out the review guidelines:wink:

Kevin Rue-Albrecht (10:43:53) (in thread): > Awesome. Glad to hear it helped, and that more can be added from your experience !

Kevin Rue-Albrecht (10:46:19) (in thread): > At times, iSEE can feel a bit limiting due to the requirements for communicating between panels (everything must be refer to rows/columns in the SummarizedExperiment to fit in the framework). Quite curious to know if/how bespoke shiny apps like iBET can reach functionality inaccessible to iSEE.

Jared Andrews (10:47:53) (in thread): > I keep going back and forth on the actual best way forward with iBET. It’s tempting to just make a series of fully interactive Shiny modules for generic figure types via plotly and get that into Bioc.

Jared Andrews (10:48:31) (in thread): > And then potentially just provide a gallery of examples for how they can be used in common analysis pipelines.

Kevin Rue-Albrecht (10:48:32) (in thread): > Still haven’t made any Shiny module myself.:sweat_smile:How’s that going for you?

Jared Andrews (10:49:14) (in thread): > I used them in a hackathon last year, and it was more simple than I expected:https://github.com/stjude-biohackathon/peakPeekeR/tree/main/R

Jared Andrews (10:49:47) (in thread): > I imagine the biggest thing would be trying to keep the input UI flexible enough to fit into various apps.

Jared Andrews (10:50:40) (in thread): > I also went pretty off-label for basilisk-usage in that project, abusing it to set up conda environments and run CLI tools.

Kevin Rue-Albrecht (10:57:09) (in thread): > Interesting

Umran (17:57:55): > @Umran has joined the channel

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2022-12-13

Melody Jin (03:43:23): > @Melody Jin has joined the channel

2022-12-14

Givanna Putri (00:22:30): > I’ve registered for the instructor training course on March 20-23. Anyone else doing the course at the same time?

Umar Ahmad (13:52:37) (in thread): > Nice to meet you here@Zainab Ashimiyu-Abdusalam. I am also from Nigeria passionate about genomics, bioinformatics and computational biology. I am the founder ofOSCNand maintaining a bioinformatics slack channel for Nigerians. Feel free to reach out should you be interested in joining the workspace.

Zainab Ashimiyu-Abdusalam (16:09:27) (in thread): > Hi@Umar Ahmadthanks for reaching out. I’d definitely love to join the workspace and look forward to collaborating with other members > Thanks

Zainab Ashimiyu-Abdusalam (16:16:53) (in thread): > I’m unable to access the url

Zainab Ashimiyu-Abdusalam (16:36:50) (in thread): > Hi@Umar Ahmadcheck this out since you run an open source organization .https://accelerator.github.com/application

Zainab Ashimiyu-Abdusalam (16:37:29) (in thread): > https://accelerator.github.com/It’d be of great use to the community

Lijia Yu (19:37:59): > @Lijia Yu has joined the channel

2022-12-17

Umar Ahmad (15:07:16) (in thread): > Thank you so much@Zainab Ashimiyu-Abdusalam

2022-12-19

Renuka Potbhare (08:11:01): > @Renuka Potbhare has joined the channel

Rumeysa Fayetörbay (12:59:56): > @Rumeysa Fayetörbay has joined the channel

2023-01-09

Frederick Tan (08:38:49): > Is there a bioc-teaching meeting today? I have it down for 2nd Mondays but notice that the Google Doc lists the 3rd Monday this month.

Charlotte Soneson (08:40:05) (in thread): > It was moved to next week exceptionally this month.

Frederick Tan (08:40:19) (in thread): > Thanks for the confirmation:slightly_smiling_face:

Frederick Tan (08:41:09) (in thread): > Note that next Monday is a US federal holiday:open_mouth:

Charlotte Soneson (08:43:46) (in thread): > Oh no, sorry about that! There were probably mostly Europe-based people there last meeting…:grimacing:

Frederick Tan (08:45:02) (in thread): > No worries, it’s been pretty fun learning how intercontinental meetings are organized. I can only imagine how fun it is when even more continents are involved.

2023-01-10

Atuhurira Kirabo Kakopo (11:28:48): > @Atuhurira Kirabo Kakopo has joined the channel

2023-01-12

Aedin Culhane (11:55:59): > Will the carpentries courses be built as bioconductor packages and deployed on orchestra?

Aedin Culhane (11:56:40): > Are you working with ELIXIR or an ELIXIR Institute in the EU. Are you thinking of attending the ELIXIR all-hands meeting 5-8th June in Dublin. If so let me know as we are thinking of proposing a Bioconductor session. I created an elixir channel to discussion this and other connections to elixir

Jenny Drnevich (12:00:20) (in thread): > Hadn’t really thought about it yet. We could, as a back-up. One of the Carpentries principles is to get people working on their own machines

Frederick Tan (12:04:03) (in thread): > Does Data Carpentry have different guidelines? I ask asdatacarpentry.org/shell-genomicsis cloud-based

Jenny Drnevich (12:39:39) (in thread): > Probably because the setup requires specific bioinformatics software packages (FastQC, Trimmomatic, BWA, SAMtools, BCFtools) that don’t run on Windows. Although the shell-genomics lesson you linked to (“Introduction to the Command Line for Genomics”) doesn’t seem to use these at all. The Data Wrangling and Processing for Genomics lesson in the Genomics Curriculum series does use them and they are meant to be all taught together in a 2-day workshop.

Frederick Tan (13:19:14) (in thread): > Has there been discussion on whether Bioconductor Carpentries will encourage mostly “on their own machines” or if some/many of the lessons will be on the cloud? The bioc-intro dependencies are relatively mild but it does tend to get complicated quickly …

Laurent Gatto (13:50:00) (in thread): > I think we shouldn’t encourage anything in particular and leave it to the organiser’s/instructor’s depending on their needs and goals. I think we should focus on providing the material, the experience and the advice if needed. We could prepare or help preparing pre-build containers, but I don’t think these should become part of any ‘official’ setup (especially as this would increase our maintenance burden).

Sean Davis (14:46:56) (in thread): > The Carpentries really heavily encourages folks to use their own machines. For Windows folks, Docker Desktop is an option if necessary. For genomics (primary processing), part of the workflow is using something OTHER THAN your own laptop since that is the way that genomics analyses are typically done, so I think that is a special case….

Sean Davis (14:48:42) (in thread): > And just to note that while Orchestra can support light-weight analysis, I wouldn’t want to scale up instances to include genome alignment or other applications that wouldn’t otherwise run on a laptop. In other words, Orchestra is a laptop replacement, which kinda goes against what Carpentries espouses.

2023-01-13

Jenny Drnevich (09:26:55) (in thread): > @Fabricio Almeida-Silva- here is the slack thread you should see.

2023-01-16

Laurent Gatto (10:22:37): > Are you a carpentries instructor, are part of the Bioconductor community, and would like to be listed in the forthcoming list? Please provide you name and location to thisissueeither to this issue, or add yourself directly tobioc-instructors.mdwith a PR.

2023-01-20

Aedin Culhane (17:43:33): > We started a channel#elixirto discussion education and training at the EU ELIXIR meeting in June

2023-01-21

Hien (16:02:13): > @Hien has joined the channel

2023-01-23

Maria Doyle (11:05:30): > @Fabricio Almeida-Silvais the first instructor to be certified through our Bioconductor Carpentries CZI-supported program:partying_face::raised_hands: - Attachment: Attachment > Hello, everyone. I’ve completed all my checkout steps today, which means I will soon be a Carpentries-certified instructor (just waiting for the certificate to make it official)! :tada: > > Once again, I’d like to thank Bioconductor for the scholarship, and I look forward to teaching and contributing to Bioc material to expand our community. :bioc-load:

Laurent Gatto (14:44:33) (in thread): > Congratulation@Fabricio Almeida-Silva!

2023-01-24

Imad Abugessaisa (22:59:26): > @Imad Abugessaisa has joined the channel

2023-01-26

Ibra Lujumba (03:02:23) (in thread): > Congratulations@Fabricio Almeida-Silva. Well deserved. I am doing a Data Carpentries’ training and today will be the second day

Aedin Culhane (06:21:37): > General Abstract call for ISCB/ECCB in Lyon July 23-27 is open

Aedin Culhane (06:21:38): > ISCB/ECCB deadlines Abstract Submissions (for talks and posters) > Monday, January 23, 2023 Call for Abstracts Opens (for talks and posters) > Thursday, April 20, 2023 Abstracts Submission Deadline (for talks and posters) > Monday, April 24, 2023 Late Poster Submissions Open (posters only).https://www.iscb.org/ismbeccb2023-submissions/abstracts - Attachment (iscb.org): Abstracts > ISCB - International Society for Computational Biology

Aedin Culhane (06:27:29): > https://www.embl.org/about/info/course-and-conference-office/events/can23-01/#vf-tabs__section-53de8397-0f08-449c-b4a4-0fdca47249f2

Aedin Culhane (06:27:55): > EMBL Cancer Genomics Conference. Date: 15 - 17 Nov 2023 > Location: EMBL Heidelberg and Virtual

Yu Zhang (12:32:01): > @Yu Zhang has joined the channel

2023-01-28

Aedin Culhane (10:05:29) (in thread): > I think a backup on orchestra is a good idea.If only to provide a platform if there are laptop issues (more likely in low income countries)

2023-01-29

Aedin Culhane (09:31:31): > Are carpentries programs accredited (or could they be) within the EU micro-credential programhttps://education.ec.europa.eu/education-levels/higher-education/micro-credentials#:~:text=Micro%2Dcredentials%20certify%20the%20learning,their%20personal%20and%20professional%20development.

2023-01-30

Laurent Gatto (02:27:45) (in thread): > No idea. It’s the first time I hear about EU micro-credits.

Laurent Gatto (02:33:09) (in thread): > I have added it for discussion on the next teaching group agenda

2023-01-31

Rebecca Butler (15:08:08): > @Rebecca Butler has joined the channel

2023-02-01

Francesc Català-Moll (04:15:32): > @Francesc Català-Moll has joined the channel

2023-02-02

Jenny Drnevich (13:53:05): > Re-posted from the Life Science Trainers slack: > We will have a focus group(s) on the Bicycle Principles this month (https://www.bikeprinciples.org). Please complete this poll by February 8th to confirm your interest and ability to attend. We will need at least 3-4 people for any given session to be viable (bringing or forwarding to a friend also involved in training is encouraged!); we are especially interested in reaching trainers in Asia, Latin America, and Africa. We will also have a thank you for your time.https://doodle.com/meeting/participate/id/az6l3pyaThese focus groups will be held in English on Zoom (approximately 1.5 hours and would be conducted as described below. Attendees should be significantly involved in delivering training workshops to folks in the life and health sciences (i.e., not just undergraduate educators). > > Protocol > 1. Before the focus group attendees look the Bicycle Principles website (https://www.bikeprinciples.org/), especially the video there which has helpful background (https://youtu.be/18dub7jGeQ8). > 2. Attendees browse the recommendations (at least the titles and summaries); we would not expect anyone to read through all the material. > 3. At the focus group (held based on participant time zones) we would vote on 3 recommendations to cover in a moderated discussion (a few open-ended questions). > 4. For participation, we can provide an online/digital gift card as a thank you (valued at about US $75). - Attachment (bikeprinciples.org): The Bicycle Principles > Community developed priniciples and recommendations for improving short-format training and professional development in the life sciences - Attachment (doodle.com): Doodle > Doodle is the simplest way to schedule meetings with clients, colleagues, or friends. Find the best time for one-to-ones and team meetings with our user-friendly calendar tool. Get started today! - Attachment (bikeprinciples.org): The Bicycle Principles > Community developed priniciples and recommendations for improving short-format training and professional development in the life sciences - Attachment (YouTube): Effective, inclusive, and scalable training in the life sciences, clinical education and beyond

2023-02-06

Doug Joubert (18:37:07): > @Doug Joubert has joined the channel

Ying Chen (21:35:49): > @Ying Chen has joined the channel

2023-02-07

Rishi (04:32:55): > @Rishi has joined the channel

Beryl Kanali (06:32:27): > @Beryl Kanali has joined the channel

Deena Gendoo (08:43:37): > @Deena Gendoo has joined the channel

Iris van ’t Erve (14:09:07): > @Iris van ’t Erve has joined the channel

2023-02-09

Ana Cristina Guerra de Souza (03:45:00): > @Ana Cristina Guerra de Souza has joined the channel

2023-02-10

Aedin Culhane (14:51:19): > our elixir workshop was accepted. See the#elixirchannel for info

2023-02-13

Maria Doyle (11:42:55): > Bioc-rnaseq lesson hackathonWe will be having a hackathon to develop thebioc-rnaseq lesson. We’ll have a planning meeting onMonday February 27th 3-5pm CET. Meeting linkhttps://meet.jit.si/BioconductorTeachingPlease join the meeting if you’d like to teach this lesson in the future and/or if you’re interested in contributing to it.

Jenny Drnevich (16:38:47) (in thread): > Ironically, after our meeting today I get an email with meeting minutes from a professional education group I’m in on campus that had “Discussed microcredential vendors.”. They are looking at Accredible and Badgr. That’s about all I know on it…

2023-02-14

Dr Nay (02:15:09): > @Dr Nay has joined the channel

Dr Nay (02:16:03): > I would like to study Human identification of bioinformatics

2023-02-15

Sean Davis (00:36:03): > Hi, all. I have some survey results from before/after/6-months after a 2-week-long data science/bioinformatics course taught over several years and we’d like to write up the curriculum and survey results. Any suggestions on good journals for this type of work?

Jeroen Gilis (03:17:44) (in thread): > F1000 has a collection on that, which could be interesting if you’d like to link it to the F1000 bioconductor gatewayhttps://f1000research.com/collections/bioinformaticsedu. If you don’t want to go the full publication route but something more blog-like, I also know of apaper.lipage specifically for bioinformatics training, but I don’t think it’s reaching many people yethttps://paper.li/f-1334858808.

Fabricio Almeida-Silva (04:39:28) (in thread): > I’ve seen similar papers in PLOS Comp Bio.

Federico Marini (05:36:48) (in thread): > +1 to Fabricio’s point. There were some on that line recently

Federico Marini (05:39:50) (in thread): > plus, I recall something on Briefings in Bioinfo

Federico Marini (05:48:15) (in thread): > quick scanning in my ref manager, > * older: 10.1371/journal.pcbi.1003496 > * specific from Goblet: “The GOBLET Training Portal: A Global Repository of Bioinformatics Training Materials, Courses and Trainers”, Bioinformatics (Corpas 2014) > * different perspective, but maybe giving you some pointers to harp upon :https://doi.org/10.1371/journal.pcbi.1009218 > * integration of bio & comp subjects: 10.1515/jib-2019-0005

Fabricio Almeida-Silva (05:50:41) (in thread): > This came out last month:https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010752

Maria Doyle (06:08:27) (in thread): > Yes Plos Comp Bio was the first one that springs to mind for me, another recent onehttps://pubmed.ncbi.nlm.nih.gov/36780436/

Frederick Tan (08:07:17) (in thread): > Depending on the audience you’re trying to reach, another possibility islifescied.org

2023-02-16

Sean Davis (14:25:35) (in thread): > Wow! Loving the Bioconductor Ed community!!! Thanks a bunch for the ideas and for doing my homework….:smile:

Min Zhang (14:30:17): > @Min Zhang has joined the channel

2023-02-17

William Rodriguez (10:54:29): > @William Rodriguez has joined the channel

2023-02-20

Aedin Culhane (12:13:07) (in thread): > @Fabricio Almeida-Silvaexactly the article I was thinking.

2023-02-21

Sean Davis (19:29:33): > The deadline to apply for the Argonne Training Program on Extreme-Scale Computing (ATPESC) is approaching fast.Applications are due Wednesday, March 1, 2023. > * For an overview of the program and guidance on applying, check out theslides and video from the recent ATPESC 2023 webinar. > * For additional information, and to apply, please visithttps://extremecomputingtraining.anl.gov/ - Attachment (alcf.anl.gov): ATPESC 2023 Application Webinar | Argonne Leadership Computing Facility > The Argonne Training Program on Extreme-Scale Computing (ATPESC) provides intensive, two-week training on the key skills, approaches, and tools to design, implement, and execute computational science and engineering applications on current high-end computing systems and the leadership-class computing systems of the future.  Renowned computer scientists and high-performance computing (HPC) experts from U.S. national laboratories, universities, and industry serve as lecturers and guide hands-on training sessions.

2023-02-22

Sue McClatchy (19:34:00): > @Sue McClatchy has joined the channel

2023-02-23

Claire Seibold (15:49:03): > @Claire Seibold has joined the channel

2023-02-27

Maria Doyle (05:46:23): > :writing_hand:New blog post - An update on the Bioconductor Carpentries global training program - applicants selected for Year 1:tada::mortar_board:https://bioconductor.github.io/biocblog/posts/2023-02-24-carpentries-update/ - Attachment (bioconductor.github.io): Bioconductor community blog - Bioconductor Carpentries instructors Year 1 > An update on the Bioconductor Carpentries global training program - applicants selected for Year 1

2023-02-28

Ramin (15:29:55): > @Ramin has joined the channel

2023-03-02

Umar Ahmad (17:37:12) (in thread): > Very excited to be part of this Bioconductor carpentries instructor training. Looking forward to learning from your wealth of knowledge and experience n pedagogical skills that could apply in genomics and bioinformatics workshops. Thank you once again@Maria Doyle, and the Bioconductor team for the opportunity.

2023-03-08

Ayantika Sen (01:36:28): > @Ayantika Sen has joined the channel

2023-03-10

Edel Aron (15:27:56): > @Edel Aron has joined the channel

2023-03-13

Frederick Tan (08:47:32): > > a reminder about the bioc-teaching call on Monday, March 13, 3-4pm CET (please check the time, as we are in the period where some parts of the world are in daylight saving time and others are not). > … just to check, is it 1:47pm CET right now?:slightly_smiling_face:

Charlotte Soneson (08:48:03): > Yep!

Frederick Tan (08:48:25) (in thread): > Thank you! See you in 72 min:slightly_smiling_face:

Frederick Tan (08:48:42) (in thread): > … and daylight savings begins for CET on March 26th?

Charlotte Soneson (08:49:07) (in thread): > Yes, correct

Frederick Tan (08:49:29) (in thread): > :thumbsup:

2023-03-14

Laurent Gatto (03:13:44): > The new Carpentries Instructor Training Calendar is out:https://carpentries.github.io/instructor-training/training_calendar/index.html

Hans-Rudolf Hotz (03:50:46): > As the overlap is more and more increasing…you might be interested in this: > The next Galaxy Admin workshop is happening in April. The official website is:https://galaxyproject.org/events/2023-admin-training/Please register as soon as possible, we have limited capacity and forward it to anyone that might be interested. We can sponsor up to 3 people from Low and Middle Income Countries. Thanks to EOSC for sponsoring this event. - Attachment (galaxyproject.org): 2023 Galaxy Admin Training > The ins and outs of setting up your own production quality Galaxy server

Jean Yang (04:05:04): > @Jean Yang has joined the channel

2023-04-03

Jenny Drnevich (11:10:29): > @Laurent Gatto@Charlotte Sonesonor anyone else: I have forked the carpentries-incubator/bioc-intro repo, and then I assume I should create a branch to do my work in. For the branch source, it’s giving me the option of my fork (only have main branch so far) or the upstream repository’s many branches. Should I use the upstream repository’s main branch?

Almut (11:28:30) (in thread): > Hi Jenny, I think so - at least if this is the equivalent of setting upstream as remote via CLI. I found this resource from the carpentries very useful for contributions via pull request:https://github.com/carpentries-incubator/swc_github_flow/blob/main/for_novice_contributors.md

Jenny Drnevich (12:16:56) (in thread): > Thanks,@Almut! This does look very useful

2023-04-13

Frederick Tan (08:23:07): > On Mon Apr 17th The Carpentries is hosting a Community Discussion about the Workbenchcarpentries.org/blog/2023/04/dovetail-17 > > These sessions are an opportunity to learn more about the new infrastructure, ask any questions you have - from the perspective of an Instructor, Maintainer, lesson contributor, lesson developer, or any other role in the community - and to hear about the experiences of other community members who have been working with the Workbench.

2023-04-18

Jermiah Joseph (16:58:31): > @Jermiah Joseph has joined the channel

2023-04-20

Chris Vanderaa (04:34:50): > @Chris Vanderaa has left the channel

2023-04-26

Maria Doyle (12:02:36): > Please share with anyone who you think may be interested > Twitter -https://twitter.com/Bioconductor/status/1651252499368517633Mastodon -https://genomic.social/@bioconductor/110265924876536622 - Attachment (Twitter): Bioconductor on Twitter > :tada: Exciting news! Bioconductor joins GTN Smörgåsbord online training event, May 22-26, 2023! > > :mortar_board:Embark on a free, self-paced, learning journey with Galaxy RStudio! > :question:Get help from instructors on Slack > Register now & join the fun! > :arrow_right: https://t.co/yXZ7tiwRXh… > > #biocsmorgasbord - Attachment (genomic.social): Bioconductor (@bioconductor@genomic.social) > :tada: Exciting news! Bioconductor joins GTN Smörgåsbord online training event, May 22-26, 2023! > > :mortar_board:Embark on a free, self-paced, learning journey with Galaxy RStudio! > :question:Get help from instructors on Slack > Register now & join the fun! > :arrow_right: https://gallantries.github.io/video-library/modules/bioconductor > > @gtn@mstdn.science @gallantries@mstdn.science #biocsmorgasbord

Vince Carey (12:49:56): > Are there any knowledge assessment instruments available for use at, e.g., CSAMA?

2023-04-27

Maria Doyle (16:46:27) (in thread): > :loudspeaker:Calling all Bioconductor wizards! Have a tutorial you want to include in the biggest online, bioinformatics training week globally? Now’s your chance! We’re inviting you to include your Bioconductor tutorial in Smörgåsbord 2023, happening May 22-26.Why join?Your tutorial gets more visibility and can be tried out by anyone worldwide, in an RStudio session launched via Galaxy, without any installation hassles.What you need to do?If you have a Bioconductor tutorial in a Docker container (and if it’s usingthe Bioconductor workshop templateeven better!), > it’s just two simple steps::white_check_mark:Let us know you’re in!:white_check_mark:Ensure someone from your team can answer questions on Slack during the training week. > > Feel free to get in touch with me with any questions.

Maria Doyle (16:47:45) (in thread): > I don’t know of any but that would be great if there were

2023-04-28

Maria Doyle (16:15:32): > > 1. Registration is now open for the ELIXIR-GOBLET Train-the-Trainer (TtT) online course which takes place on 22-26 May 2023, 9am – 12:30pm (UK time). This course is aimed at everyone who is interested in becoming a better teacher, and on the last day there is a particular emphasis on training aspects of systems biology and single-cell omics. Registration closes on the 1st of May, so please find more info and register athttps://elixiruknode.org/events/2023/elixir-goblet-train-the-trainer-may-2023/.2.The materials (including slides and videos) of the ELIXIR-GOBLET workshop for single-cell omics data analysis trainers are now available at theworkshop website.

2023-05-04

Maria Doyle (10:24:09): > We would appreciate your support in spreading the word about the BioC2023 pre-conference Carpentries RNA-seq workshop. Please consider sharing the following text and posts with your networks to help us reach a wider audience. Thank you for your help in making this workshop a success! > ———- > Are you ready to dive into the world of RNA-seq data analysis and elevate your research to new heights? Join ourBioC2023 pre-conference workshopin Boston, Jul 31-Aug 1, on RNA-seq analysis with Bioconductor and master the essential tools and techniques to make sense of your gene expression data! > > In this hands-on workshop, you will: > * Learn from leading experts in the field of bioinformatics and genomics > * Acquire a solid understanding of the RNA-seq analysis pipeline using Bioconductor’s state-of-the-art tools > * Gain insights into best practices for processing and analyzing RNA-seq data > * Explore a variety of methods for identifying differentially expressed genes, pathway analysis, and functional enrichment > * Develop the skills to interpret and visualize your results effectively > * Engage in interactive sessions and group discussions to address your specific questions and challenges > * Network with fellow researchers, bioinformaticians, and industry professionals > Whether you’re a graduate student, a bioinformatics analyst, or a researcher looking to expand your expertise in RNA-seq data analysis, this workshop is designed for you. Prior experience with R programming is required, but all levels of RNA-seq expertise are welcome. > > Don’t miss this fantastic opportunity to enhance your skills and stay at the forefront of cutting-edge genomics research. Spaces are limited, soapply before May 31 to secure your spotand unlock the full potential of your RNA-seq data with Bioconductor! > ———- > Twitterhttps://twitter.com/Bioconductor/status/1654097829420302337Mastodonhttps://genomic.social/@bioconductor/110310382788316790

Aedin Culhane (15:10:04): > Congrats mariahttps://www.siliconrepublic.com/innovation/bioinformatics-university-limerick-maria-doyle - Attachment (Silicon Republic): Bioinformatics, data and the value of open science > Dr Maria Doyle demystifies bioinformatics and explains just some of the many applications for this multidisciplinary field.

2023-05-12

Frederick Tan (08:59:21): > @Jenny Drnevichlooks like this failedhttps://github.com/carpentries-incubator/bioc-rnaseq/actions/runs/4937620274

Jenny Drnevich (09:00:51) (in thread): > That happened on Wed when I pushed some changes. Thought it was part of the GitHub problems…

Frederick Tan (09:04:09) (in thread): > Looks like Zhian’s started failing last week > * https://github.com/carpentries-incubator/bioc-rnaseq/actions/runs/4856575668 > cc:@Charlotte Soneson@Maria Doyle

Jenny Drnevich (14:05:24) (in thread): > @Laurent Gattoseems to have gotten this fixed today - thanks!

Frederick Tan (14:51:17) (in thread): > Nice! Great job:slightly_smiling_face:

2023-05-15

Michael Lynch (07:57:06): > @Michael Lynch has joined the channel

Rebecca Butler (17:15:41): > Hello! Do y’all know of any ewas short courses/ workshops? Preferably based in North America or online? > > I am aware of two recent courses through the University of Bristol (introandadvanced) but haven’t been able to find anything else similar. > > Thank you! And big apologies if this is not the appropriate venue for this question - Attachment (bristol.ac.uk): Advanced Epigenetic Epidemiology > This course aims to build on the knowledge and skills acquired in ‘Epigenetic Epidemiology’ by introducing students to more advanced approaches in epigenetic epidemiology and to provide students with the knowledge and skills necessary to design, execute and interpret more advanced epigenetic epidemiological analyses.

2023-05-17

Hassan Kehinde Ajulo (12:16:02): > @Hassan Kehinde Ajulo has joined the channel

2023-05-18

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2023-05-31

Alyssa Obermayer (14:14:42): > @Alyssa Obermayer has joined the channel

2023-06-01

Aedin Culhane (13:01:16): > if you would like to contribute (either in-person in Dublin or remotely) to the Elixir All Hands workshop “Opportunities for Bioconductor and ELIXIR communities to co-develop training infrastructure” on June 6th 11-12.30pm GMT please let@Maria Doyleknow or comment in the#elixirchannel

2023-06-06

Gil Poiares-Oliveira (06:13:30): > @Gil Poiares-Oliveira has joined the channel

Lisanna Paladin (06:24:03): > @Lisanna Paladin has joined the channel

2023-06-07

Alyssa Obermayer (18:29:34): > @Alyssa Obermayer has joined the channel

2023-06-09

Matt Paul (12:21:44): > @Matt Paul has joined the channel

2023-06-12

Natasha (10:51:04): > @Natasha has joined the channel

Krithika Bhuvanesh (15:13:32): > @Krithika Bhuvanesh has joined the channel

Krithika Bhuvanesh (16:41:07): > This might be an old question. Are there any end to end workflows that showcase analysis on single cell and spatial sequencing ?

Laurent Gatto (16:52:20): > The OSCA book is as end-to-end as it gets for single cell analysis -https://bioconductor.org/books/release/OSCA/ - Attachment (bioconductor.org): Orchestrating Single-Cell Analysis with Bioconductor > Or: how I learned to stop worrying and love the t-SNEs.

Laurent Gatto (16:53:23): > And the OSTA, Orchestrating Spatially-Resolved Transcriptomics Analysis -https://lmweber.org/OSTA-book/ - Attachment (lmweber.org): Orchestrating Spatially-Resolved Transcriptomics Analysis with Bioconductor > Online book ‘Orchestrating Spatially-Resolved Transcriptomics Analysis with Bioconductor’

Krithika Bhuvanesh (16:56:45): > Thank you !

2023-06-19

Maria Doyle (14:21:07): > :writing_hand:New Bioconductor blog post on the Smorgasbord online training weekhttps://bioconductor.github.io/biocblog/posts/2023-06-16-smorgasbord-recap/ - Attachment (bioconductor.github.io): Bioconductor community blog - Bioconductor’s Participation in Galaxy Smorgasbord 2023: A Recap > Bioconductor made its first appearance at the Galaxy Smorgasbord this year. This post provides a summary of our successful participation.

2023-06-25

Leo Lahti (19:30:31): > Just checking, if we would like to use preinstalled Bioc packages in a workshop, should we go for Docker containers from here, or are there better recommended options:https://www.bioconductor.org/help/docker/

2023-06-26

Vince Carey (14:35:37): > @Leo Lahtithat page seems old (referring to 3_14) though it may be accurate.@Alex Mahmoudany comments here? Leo what details about preinstalled packages are of concern? One can make a fat container that has lots of packages and data, or a thin container that “knows about” binary repositories of packages to simplify package installations, and if shared storage is possible, then the data components might be “mounted” to reduce container size.

Alex Mahmoud (14:35:43): > @Alex Mahmoud has joined the channel

Alex Mahmoud (14:41:00): > Hey@Leo Lahti, could you clarify your scenario? You can use the latest containers from Dockerhub (bioconductor/bioconductor:RELEASE_3_17) or Github registry (ghcr.io/bioconductor/bioconductor:3.17). You can also use this repository templatehttps://github.com/Bioconductor/BuildABiocWorkshopwhich contains a basic Dockerfile and some github action checks. Is this for the Bioc2023 conference or another scenario?

Leo Lahti (16:00:37): > Thanks,@Vince Carey&@Alex Mahmoud- thanks for the very informative and helpful responses. The scenario is to teach Bioconductor methods in a European summer school. We encourage to preinstall the packages on personal laptops but would like to provide a pre-installed system as a backup option. If this seems like a good idea. > > There is no option for shared storage in this particular workshop, so perhaps a fat container for Bioc 3.17 or the workshop template would be something to test here?

Leo Lahti (16:01:21) (in thread): > also pinging@Giulio Benedettihere

Alex Mahmoud (16:10:44) (in thread): > For a bring-your-own-laptop scenario, even if using containers, you should be aware that now people on M chip macs and some others (arm64) will have to either use a different container or a version of docker that supports an emulator (which slows down computation significantly), vs most other computers (amd64 chips). How long is the workshop and what is the format/timeline if you don’t mind me asking? If you’re interested in collaborating a bit closer, Bioconductor hasworkshop.bioconductor.org, where we could add a section for you for students to launch personal RStudio environments with packages pre-installed and running in the cloud so they have the same environment. If using their own laptops is advantageous, I can potentially provide an updated github workflow to build both arm64 & amd64 containers with all your packages pre-installed

Leo Lahti (18:27:30) (in thread): > Right, good to know. > > Workshop is 5 days, with half of each day dedicated to the practical sessions; timing is July 10-14. > > The cloud solution could be optimal. Would it be available with this time frame? > > I do not see specific advantages with containers in this case, installing the containers would require more effort from the students and teachers than login to a ready-made cloud environment.

2023-06-29

Lisanna Paladin (04:28:23): > Data analysis, especially for biological data, is a job in high demand and therefore especially attractive for job seekers. Do you want to learn how to perform a bioinformatics data analysis? We (BioNT) are offering a:moneybag:free &:earth_africa:online 5 half-days data analysis workshop with a focus on RNA-seq data analysis using Galaxy, a web-based platform for FAIR data analysis requiring no programming skills or previous biology training****.****This workshop will end with**** ****a general overview of data types and data bases used in bioinformatics. All material will stay online so you can train your skills even after the workshop.Click here**** to learn more and register**

2023-07-02

Leo Lahti (16:49:01) (in thread): > – and btw, even if the July 10-14 comes too soon, this option would be useful also later this and next year, in other forthcoming trainings. We do primarily support personal installations but this does not always work.

2023-07-06

Vikash Sharma (14:50:01): > @Vikash Sharma has joined the channel

Jenny Drnevich (14:53:04): > I saw this post by Andrew Severin on the Life Science Trainers slack and thought people here might be interested: > Hey all! I just published an ebook on Amazon ‘ChatGPT 4 Professors’http://a.co/d/jlqEQLjand its free until Friday. Learn step-by-step to craft great prompts using the P.E.E.R.S method. Grab a copy and tell your friends. It is geared toward faculty and postdocs and activities where ChatGPT will be useful. Let me know what you think!

2023-07-10

Kevin Stachelek (12:39:49): > @Kevin Stachelek has joined the channel

2023-07-21

Laurent Gatto (05:11:07): > Registrations open for the pre-EuroBioc2023conference two-day workshops in Ghent, 18-19 September 2023 > - Introduction to genomic data analysis with R and Bioconductorhttps://bioconductor.github.io/2023-09-18-BiocIntro-EuroBioc/- Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductorhttps://bioconductor.github.io/2023-09-18-RNASeq-EuroBioc/

2023-07-28

Konstantinos Daniilidis (13:47:14): > @Konstantinos Daniilidis has joined the channel

2023-08-02

Beth Cimini (08:20:34): > @Beth Cimini has joined the channel

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2023-08-03

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2023-08-04

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2023-08-10

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2023-08-16

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2023-08-17

Maria Doyle (15:25:31): > New paper out this week on grand challenges in bioinformatics education and traininghttps://www.nature.com/articles/s41587-023-01891-9 - Attachment (Nature): Grand challenges in bioinformatics education and training > Nature Biotechnology - With the increasing need for bioinformatics expertise in the life sciences, a coordinated effort is needed to proactively and critically reflect on the challenges of…

2023-08-18

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2023-08-20

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2023-08-22

Leo Lahti (03:19:32) (in thread): > Is this something that could be made available for our October course in Norway?

Vince Carey (09:32:56) (in thread): > @Alex Mahmoudcan say … i think we need to get more systematic in terms of making requests, predicting load, and reporting on outcomes.

Alex Mahmoud (11:35:03) (in thread): > Tentative answer is yes, but would be great to get information on the number of workshops to be included and how many participants are expected

Leo Lahti (13:41:50) (in thread): > Currently we have one more workshop coming (4 days) but we expect run at least 2-3 more next year. The October course is currently expected to have about 28 participants but the numbers will become more exact during September.

Alex Mahmoud (15:31:03) (in thread): > At the scale of under 50 people and a single concurrent workshop per event, I think it should be doable by october

2023-08-23

Leo Lahti (08:30:53) (in thread): > The need would be to have the system up for 8 hours per day for 4 days.

2023-08-24

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2023-09-04

Anna Lewkowicz (16:51:11): > @Anna Lewkowicz has joined the channel

2023-09-06

Lisanna Paladin (07:19:24): > Of particular interest for people involved in training (organization):teacher:In occasion of the2nd Biohackathon Germany, a small group of people will work on a project that we believe might be of your interest as it is of ours: aTraining Management Platform. > If you are interested in joining, please consider that the event will be hybrid (on site registrations limited to 80 people) and that the registration deadline is on the 17th of November.:eyes:Looking forward to see you there! - Attachment (denbi.de): 2nd BioHackathon Germany > The ‘German Network for Bioinformatics Infrastructure – de.NBI’ is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data. - Attachment (denbi.de): Training Management Platform: Empowering Trainers and Trainees > The ‘German Network for Bioinformatics Infrastructure – de.NBI’ is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data.

Pariksheet Nanda (12:54:31): > Hello! I’m giving a 15 minute departmental presentation for microbiology & immunology grad students + postdocs trying to convince them to use Bioconductor instead of base R:face_palm:(at least one person attempted but found it “confusing”). Do any of you have some tried-and-tested materials I incorporate into mine? I’ve seen Michael Lawrence’s slides he shows at the Bioconductor conference of how GenomicRanges objects solve important errors that can arise from usingdata.frames and I also have Martin Morgan’s introductory R functions of explaining method dispatch when doing typical statistical analysis and how applying S4 classes aren’t all that different.

Pariksheet Nanda (13:21:00) (in thread): > Links: > 1. Michael Lawrence’s presentation (slide: Reality bites)https://www.bioconductor.org/help/course-materials/2017/BioC2017/Day1/Workshops/Ranges/Ranges.pdf > 2. Martin Morgan’s introductory functions (https://github.com/Bioconductor/BiocTrainer): > > > x <- rnorm(300) # Can explain optional arguments > df <- data.frame(x, y = x + rnorm(300)) # Related variables > plot(y ~ x, df) # plot is a generic. Dispatches to plot.formula. Symmetric to above y ~ x > fit <- lm(y ~ x, df) # Tells you coefficients but not statistical fit > anova(fit) > > class(fit) # emphasize this! > typeof(fit) > str(fit) # too complex > > fit$coefficients # this is bad! > coef(fit) # using API is better > > methods(class = "lm") # How do we learn about lm? > ?plot >

2023-09-07

Frederick Tan (09:28:18) (in thread): > Two ideas/resources > * State of the art methods –https://carpentries-incubator.github.io/bioc-project/02-introduction-to-bioconductor.html#packages-interoperability > * Production quality classes –https://carpentries-incubator.github.io/bioc-intro/60-next-steps.html#summarizedexperiment

2023-09-08

Pariksheet Nanda (09:12:29) (in thread): > Access to state of the art methods is a great talking point. Talking about classes is harder to an audience that has little / no experience with them. Because you point to Carpentries material, even Greg Wilson mentioned that getting people in uses bait-and-switch (see his 2014 PyCon talk): tell people they’re learning git, but they’re really learning software engineering practices; tell people they’re learning R or python, but really they’re learning functions, etc. So it might be more useful to tie wanting to learn classes to a marketable skill that may well be exquisite ggplot visualization via the tidySummarizedExperiment package.

Frederick Tan (09:58:12) (in thread): > Emphasis can be on “production quality” in the sense that many many people have tested/reviewed these classes so there are likely fewer bugs (vs making your own in base R)

2023-09-11

Kozo Nishida (09:10:33): > I have set up bioc-intro translation system below,https://bioconductor.crowdin.com/bioc-intro(You can use DeepL translation assist in this project.)https://github.com/bioconductor-translations/bioc-intro-translationbut I cannot attend the bioc-teaching meeting. If anyone has any thoughts or concerns, please let me know in this channel.

Jenny Drnevich (09:21:30) (in thread): > @Lucio Queiroz@Izabela Mamede:arrow_up:Have you started on the translation to Portuguese?

Laurent Gatto (09:22:30) (in thread): > I am happy to get a team of students/TAs to review the French translation.

Kozo Nishida (09:30:27) (in thread): > If anyone would prefer to set up Crowdin forhttps://github.com/carpentries-incubator/bioc-introinstead ofhttps://github.com/bioconductor-translations/bioc-intro-translation, please let me know. > > Also, if anyone wishes to become the manager ofhttps://bioconductor.crowdin.com/, please let me know.

Lucio Queiroz (09:34:17): > @Lucio Queiroz has joined the channel

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2023-09-13

Javier Carpinteyro Ponce (09:21:53) (in thread): > I’d be interested in contributing for an Spanish version:slightly_smiling_face:

2023-09-14

Kozo Nishida (02:36:47) (in thread): > @Javier Carpinteyro PonceThank you for the message. I have added Spanish tohttps://bioconductor.crowdin.com/bioc-intro. I would be happy if you could join in the translation. > You can use DeepL assistance for the translation. Feel free to give it a try.

Javier Carpinteyro Ponce (09:41:19) (in thread): > @Kozo NishidaI’d like to set up Crowdin but I am new to this. I wonder you could guide me through. Thank you:slightly_smiling_face:

2023-09-15

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2023-09-20

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2023-09-21

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2023-09-25

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2023-09-29

Lucio Queiroz (12:10:14) (in thread): > Hi@Jenny Drnevich, sorry for the really late reply. I just synced the Bioc Slack workspace to my devices. Previously, I had just jumped on it through the browser, so I missed your message.@Lucio Queiroz(myself),@Pedro Baldoni,@rodrigo arcoverde&@Izabela Mamedefinally got together to discuss the Portuguese language translation effort. > > We already signed on Crowdin and hope to start soon.

Lucio Queiroz (12:15:02): > Another question for@Kozo Nishida, so thebioc-intro-translationrepo is not being maintained as a fork of thebioc-intro?

2023-10-04

Izabela Mamede (08:12:31) (in thread): > First chapter of bioc-intro already translated also =D

Jenny Drnevich (08:27:06) (in thread): > Yay! Do you have a link for it? I have someone from Brazil in my workshop this semester and I’d like to have them look at it.

Laurent Gatto (08:58:24) (in thread): > https://bioconductor.crowdin.com/bioc-intro

2023-10-11

Kozo Nishida (03:25:26) (in thread): > @Javier Carpinteyro PonceSorry for the very late reply. > I would like to do that, but I’ve been very busy lately, so it might be a little longer before I can. > I appreciate your patience as it might take some time.

2023-10-15

Karthik Desingu (23:56:33): > @Karthik Desingu has joined the channel

2023-10-17

Javier Carpinteyro Ponce (09:49:50) (in thread): > @Kozo NishidaNo worries. Busy over here as well :)

2023-10-24

Jenny Drnevich (09:17:18): > Reposted from the Life Science Trainers Slack. Another opportunity to get free Carpentries Instructor Training for those in the Midwest US. Looks like they want to prioritize early-career, primary undergrad, minority-serving institution and/or tribally affiliated college, but are actively recruiting more applicants.https://www.linkedin.com/posts/mbdh_midwestbigdatainnovationhub-mbdh-carpentries-acti[…]229038088192-TR06?utm_source=share&utm_medium=member_desktop - Attachment (linkedin.com): Midwest Big Data Innovation Hub on LinkedIn: #midwestbigdatainnovationhub #mbdh #carpentries #datascience #scholarship… > :loudspeaker: The Midwest Big Data Innovation Hub (MBDH) is offering a scholarship to prepare you to teach data science! > > :arrow_right: This 4-day virtual training program will teach…

2023-10-30

Batool Almarzouq (03:43:10): > Hi Everyone:sparkles:W are very happy to introduce***** “Using the Ensembl genome browser and REST API to retrieve genome annotation data”*****, a one-of-a-kind event that will equip you with the skills to navigate the vast world of Ensembl and unlock its hidden treasures:books:Led by experts in the field, this workshop will guide you through every step of the process. Learn how to retrieve both small and large-scale datasets, equipping you with the tools for analysis and interpretation. The morning sessions will introduce you to the Ensembl genome browser and BioMart interfaces, providing a comprehensive understanding of their capabilities.You will also dive into the world of Ensembl REST API. Discover how to programmatically retrieve Ensembl data using Python and R. Harness the power of these programming languages to access and manipulate data effortlessly.This event is your gateway to a world of knowledge waiting to be explored. Don’t miss out on this extraordinary opportunity to transform your research. Join us at “Using the Ensembl genome browser and REST API to retrieve genome annotation data” and unlock the secrets of genomics like never before.Registration is complimentary for ISCB Members and nonmembers can participate for a fee that will include a free year of ISCB membership!:fire:Register today!For more information visit -https://www.iscb.org/iscbacademyWorkshop DetailsNovember 2, 2023 at 11:00 AM EDT - Part 1November 3, 2023 at 11:00 AM EDT - Part 2 - Attachment (iscb.org): ISCBacademy Tutorial Series - Using the Ensembl genome browser and REST API to retrieve genome annotation data - Registration > ISCB - International Society for Computational Biology - Attachment (iscb.org): ISCBacademy > ISCB - International Society for Computational Biology

2023-11-17

Priyanka (14:00:31): > @Priyanka has joined the channel

2023-11-29

Jenny Drnevich (14:56:26): > Interesting talk:https://www.youtube.com/watch?v=eGXBzewriOA. What about designing a workshop on learning how to prompt LLM for bioinformatic codes?! - Attachment (YouTube): Empirical evaluations of large language models for… - Stephen Piccolo - ISCBacademy Webinar

2023-12-14

Marc Elosua (15:40:04): > @Marc Elosua has joined the channel

2023-12-21

jim rothstein (00:50:20): > @jim rothstein has joined the channel

Maria Doyle (06:47:19): > https://genomic.social/@bioconductor/111614291273826845 - Attachment (genomic.social): Bioconductor (@bioconductor@genomic.social) > Attached: 1 image > > :mega: Join our Collaboration Session with @thecarpentries@hachyderm.io on December 29th from 4-5pm PST. > > We will showcase how to translate Bioconductor-Carpentries teaching materials using Crowdin, with machine translation support from DeepL, Google, and ChatGPT APIs. > > Participation details can be found in the community calendar at the bottom of https://carpentries.org/community/ > > #Bioconductor #TheCarpentries #Translation

2023-12-22

Maria Doyle (09:47:42): > :mortar_board:**** Seeking New Members for Bioconductor Carpentries Team**We’re inviting Bioconductor/R users interested in teaching and earning Carpentries certification to join our team. Check out the details and apply here:https://forms.gle/X12vSZoNc6Z4DHNL8

2023-12-28

Kozo Nishida (17:35:10): - Attachment: Attachment > Hi all, I will start a Carpentries collaboration session for translating > • https://carpentries-incubator.github.io/bioc-intro/ > • https://carpentries-incubator.github.io/bioc-rnaseq/ > • https://swcarpentry.github.io/git-novice/ > 1.5 hours from now. > You can sign up to attend on the Community Sessions Etherpad. > In the session, I will share how to use AI (DeepL / Google Translation / ChatGPT) to make translation easier. > https://hackmd.io/@joelnitta/SkCSC6ZNT

2024-01-11

Nilesh Kumar (12:00:54): > @Nilesh Kumar has joined the channel

2024-01-26

Ramon Massoni-Badosa (10:41:51): > Hi all! Could you please recommend a tutorial/resource to learn how to use GenomicRanges and all companion packages?

Ramon Massoni-Badosa (10:41:57): > thanks:slightly_smiling_face:

Lori Shepherd (10:48:26) (in thread): > Have you checked out the vignettes of the package? They are viewable under Documentation from the GenomicRanges package landing page:https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html

Ramon Massoni-Badosa (12:41:06) (in thread): > yes, and it’s great! But I was thinking of an online course or tutorial that includes exercises, live demos, etc.

Ramon Massoni-Badosa (12:41:15) (in thread): > something like the data carpentrieshttps://carpentries-incubator.github.io/bioc-intro/

Sean Davis (12:51:23): > A little off-topic, but here it is anyway. - Attachment: Attachment > May be of some modest interest to folks here–resources for using and guiding GenAI (like ChatGPT) in education: > > https://seandavi.github.io/campus-llm-kb/resources_education.html

Spencer Nystrom (12:59:56) (in thread): > Another package to look at (and Google around for) is plyranges, which extends tidy syntax to granges.https://sa-lee.github.io/plyranges/index.html(Related tidyomics book:https://tidyomics.github.io/tidy-ranges-tutorial/compute-overlaps.html) - Attachment (sa-lee.github.io): A fluent interface for manipulating GenomicRanges > A dplyr-like interface for interacting with the common Bioconductor > classes Ranges and GenomicRanges. By providing a grammatical > and consistent way of manipulating these classes their accessiblity for new > Bioconductor users is hopefully increased.

Ramon Massoni-Badosa (13:08:23) (in thread): > thank you!

Kasper D. Hansen (14:07:25) (in thread): > http://kasperdanielhansen.github.io/genbioconductor/

Kasper D. Hansen (14:07:51) (in thread): > This is old, but the stuff on GenomicsRanges is still very relevant. All the videos are on Youtube.

Ramon Massoni-Badosa (14:17:18) (in thread): > thank you sir

2024-02-06

Yanina Bellini Saibene (11:32:16): > @Yanina Bellini Saibene has joined the channel

2024-02-18

Sean Davis (11:08:00): > Always worth a repost. HT:@Vince Carey - File (PDF): williamsBicycle.pdf

2024-02-20

Maria Doyle (05:57:37): > :wave:Calling Bioinformaticians in India!:flag-in:Passionate about Bioconductor and teaching? Ready to share your expertise? > > Join our global Bioconductor Carpentries instructors team! Shape bioinformatics education in India and beyond.:rocket:With no applicants from India so far, we’re eager to support training in your region. Apply now:https://forms.gle/eMLYoKtUTKV2fMSz5Deadline: February 25th - File (PNG): Bioconductor Carpentries Team.png

2024-02-23

Chris Magnano (16:34:37): > @Chris Magnano has joined the channel

2024-03-01

Ye Meng (04:09:14): > @Ye Meng has joined the channel

2024-03-04

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2024-03-05

Pratibha Panwar (01:21:04): > @Pratibha Panwar has joined the channel

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Zaynab Aderonke Ogunnubi (04:00:13): > @Zaynab Aderonke Ogunnubi has joined the channel

2024-03-10

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2024-03-11

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2024-03-17

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2024-03-25

Rishi (09:16:53) (in thread): > Hi when will be the next round open again?

2024-03-26

Maria Doyle (06:52:03) (in thread): > Hi Rishi, at the moment, we don’t have funds allocated for future rounds. However, if a place becomes available—for instance, if someone we’ve offered a place to can’t accept—we may be able to accommodate. We encourage you to fill outour application formwith your details so we can consider you for any openings or if we secure additional funding. Thanks for your interest!

Sara m.morsy (16:09:26): > @Sara m.morsy has joined the channel

2024-03-27

Maria Doyle (05:00:01): > Hi everyone, > I’m sharing an opportunity from our friends at SciLifeLab and the Training Hub in Sweden, seeking a Scientific Training Officer focused on Open Science and FAIR principles. This role aligns closely with our community’s interests and comes through a collaboration with the ELIXIR Training Platform, a key supporter of our initiatives. Full details and application (by April 15):SciLifeLab Career Opportunity. This is an exceptional chance for those with experience in Open Science or Data Stewardship. We’re sharing this to highlight collaborative opportunities that directly benefit our community. Please share within your networks or contacttraininghub@scilifelab.sefor more.

Laurent Gatto (05:40:36) (in thread): > You could also advertise it in the#jobschannel, it might get more visibility

abhich (05:45:43): > @abhich has joined the channel

Frederick Tan (08:42:00): > Was the bioc-intro lesson based oncarpentries.org/blog/2024/03/dc-r-ecology-adoption? Looks like it’s now following the ggplot->dplyr->tidyr path of R4DS

Jenny Drnevich (10:02:23): > Coincidentally, I am in the middle of teaching the bioc-intro lesson. I only have 6 total hours, so I am omitting a lot. Today is the last day, and I have a note to myself to check on the time right after doing the select/filter part of dplyr and to skip to the ggplot section so they get to see it. I like the idea of moving ggplot to the beginning. I quickly looked through the new Ecology lesson, and the only thing that really bugs me is that their example data set clearly has 4 separate groupings of points, but they never discuss finding out what they are or show what what factor in the data set it relates to! Totally misses the scientific point…https://datacarpentry.org/R-ecology-lesson-alternative/visualizing-ggplot.html#changing-aesthetics

2024-03-28

Laura Symul (08:39:27): > @Laura Symul has joined the channel

2024-03-29

Laurent Gatto (08:26:59): > The bioc-intro is based on what I teach the undergrads in biomedical sciences, which is itself based on the original ecology lesson.

2024-04-04

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2024-04-12

Arnab Mukherjee (12:13:21): > @Arnab Mukherjee has joined the channel

2024-04-13

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2024-04-17

Maria Doyle (15:59:51): > ICYMI new handbook for trainers on how to improve the FAIRness and sustainability of bioinformatics training materials, released last month:https://elixir-europe-training.github.io/ELIXIR-TrP-FAIR-training-handbook/ - Attachment (elixir-europe-training.github.io): FAIR training handbook > Are you a developer of training material? Do you want to get more community involvement with your training material by making it Findable Accessible Interoperable and Reusable (FAIR)? Look no further, you are at the right (web)address!

2024-04-18

Philipp Sergeev (03:01:53): > @Philipp Sergeev has joined the channel

2024-04-26

Aedin Culhane (19:53:16): > NIH Grant for training in advanced data analyticshttps://grants.nih.gov/grants/guide/rfa-files/RFA-OD-24-012.html - Attachment (grants.nih.gov): RFA-OD-24-012: Predoctoral Training in Advanced Data Analytics for Behavioral and Social Sciences Research (BSSR) - Institutional Research Training Program [T32] > NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Predoctoral Training in Advanced Data Analytics for Behavioral and Social Sciences Research (BSSR) - Institutional Research Training Program [T32] RFA-OD-24-012. OBSSR

2024-04-29

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2024-05-03

Heshmat A. Borhani (04:17:56): > @Heshmat A. Borhani has joined the channel

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2024-05-05

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2024-05-07

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Carlo Pecoraro (12:17:45): > Course on Network Analysis in Systems Biology with R/Bioconductorhttps://www.physalia-courses.org/courses-workshops/network-in-systems-biology - Attachment (physalia-courses): Network Analysis in Systems Biology with R/Bioconductor > 3-6 June 2024 To foster international participation, this course will be held online

2024-05-09

Philippe Laffont (07:39:47): > @Philippe Laffont has joined the channel

2024-05-10

Lisanna Paladin (04:12:10): > :loudspeaker:Calling all learners!:star2:JoinBioNT‘s fifth workshop titled “Strategies for training and knowledge exchange with a consulting perspective’‘!:computer::spiral_calendar_pad:Save the Dates: June 25-26, 2024:alarm_clock:Workshop Schedule: 09:00 - 16:00:hourglass_flowing_sand:Registration Deadline: June 7, 2024 > > If you are interested in theories of learning, developing training materials, assessing training needs, and gaining insights into effective training delivery, consulting-like approaches, and teaching technical knowledge, consider joining our workshop. > We look forward to receiving your applications for this training workshop, which is based onThe Carpentriesmaterial and supported byELIXIRandDe.NBI:books::bulb:Visit our event webpage:point_down:to discover the program details, meet the organising team, and submit your application.:globe_with_meridians:https://www.cecam.org/workshop-details/1361#LearningOpportunityhashtag #BioinformaticsWorkshophashtag #DigitalLifeScienceshashtag #NetworkForTraininghashtag #ComputationalLifeSciences - Attachment (linkedin.com): The Carpentries | LinkedIn > The Carpentries | 2,014 followers on LinkedIn. We teach foundational coding and data science skills to researchers worldwide. | The Carpentries teach foundational coding, and data science skills to researchers worldwide. > > Posts written by our Executive Director, Dr Kari L. Jordan, and shared through this account over the coming months, will be signed " – Kari”. - Attachment (elixir-europe.org): ELIXIR > A distributed infrastructure for life-science information - Attachment (denbi.de): de.NBI – German Network for Bioinformatics Infrastructure > The ’German Network for Bioinformatics Infrastructure – de.NBI’ is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data.

Maria Doyle (08:01:17): > :trophy:Last Chance to Nominate for the Bioconductor Awards 2024!:trophy:Time is running out to recognise individuals who have made impactful contributions to our community. Don’t miss this opportunity to honour their hard work and achievements!:star2:Criteria: Significant contributions in one or more ways to the project:busts_in_silhouette:Selection: 4 awardees based on impact:alarm_clock:Deadline: 15th May 2024 > > Nominate Now:Nomination FormLearn More:Bioconductor Awards

2024-05-11

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2024-05-14

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2024-05-22

Maria Doyle (14:38:04): > :rocket:Boost Your Bioinformatics Skills! > Join us for theBioC2024**** Bioconductor Carpentries RNA-Seq Workshop**!:date:July 22-23, 2024:round_pushpin:Grand Rapids, MI:mag:Who: Biologists and researchers with some R experience:bulb:Why: Hands-on Bioconductor training, expert instructors, networking opportunities:point_right:Register hereFor more details, check out our posts onMastodonandLinkedIn. > Please share with your networks or anyone who might be interested!

2024-05-23

Lucio Queiroz (11:13:58) (in thread): > ~The Google Maps and OpenStreetMap links are pointing to Van Andel in the Netherlands.~Fixed!

Maria Doyle (11:48:36) (in thread): > Oh thank you! I will fix that

Maria Doyle (13:28:14) (in thread): > fixed now

2024-06-10

Harshitha (09:34:06): > @Harshitha has joined the channel

Frederick Tan (09:39:20): > @Charlotte Soneson@Maria Doyleet al. the next twobioc-teaching paper writing sessionsfall on/near US holidays: June 19th and July 3rd. What do you think about rescheduling both of these one day earlier to Tue June 18th and July 2nd?

Charlotte Soneson (09:42:11) (in thread): > July 2 works for me. June 18 I may be available (but June 17 would be better)

Frederick Tan (09:45:24) (in thread): > Additional rescheduling considerations from today’s meeting > * @Laurent Gattocan only make first part of Jun 18th but generally easier with Tue/Thu than Wed > * @Jenny Drnevichout Jul 2nd week (I’m out starting Jul 3rd) > * CSAMA Jun 23-28

Laurent Gatto (10:17:47) (in thread): > Monday 17 June, I could join the first 20 minutes.

Maria Doyle (12:01:53) (in thread): > Jun 17 I could do first hour, Jun 18 and Jul 2 I can do.

Jared Andrews (17:19:19): > TheKIDS24 BioHackathonsignup is now OPEN!:date:Event Date:September 4-6, 2024:round_pushpin:Location:St. Jude Children’s Research Hospital - Memphis, TN:computer:Participation:In-person and Virtual > Join us for three days of intensive coding full of innovation, collaboration, and fun! Whether you’re attending in person or joining us virtually, this is your chance to make a difference and showcase your skills. Don’t miss out on this incredible opportunity to be part of something impactful.Register now and secure your spot!Register HereIf you have any questions please emailbiohackathon@stjude.orgWe can’t wait to see you there!:rocket:I am involved in planning this event at St. Jude, and we’re looking for enthusiastic folks to take a look. Come help build something cool and useful, see what St. Jude is about, and learn some new skills! Feel free to post here or DM me with any questions. > > Students and trainees are very welcome, so if anyone in your group/institution may be interested, please pass it along! Limited travel awards will be available.

2024-06-11

Ziru Chen (04:36:12): > @Ziru Chen has joined the channel

2024-06-30

Clara Tejido (12:50:14): > @Clara Tejido has joined the channel

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2024-07-02

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2024-07-05

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Vanessa Gonzalez Ribao (05:44:58): > Hi Team:slightly_smiling_face:I am Vanessa, training coordinator at GHGA and bring today great news for bioinformatics enthusiasts! GHGA is excited to host Zuguang Gu’s Webinar on July 18 at 2pm CET. Dive into advanced data visualisation techniques with R & #Bioconductor packages like ComplexHeatmap & InteractiveComplexHeatmap. Head over to our site formore info and free registration

Vanessa Gonzalez Ribao (05:46:22): - File (PNG): 07_2024_Bio_data_vis_twitter.png

Margherita (12:28:45): > @Margherita has joined the channel

2024-07-10

Sean Davis (18:59:11): > Random question. I’m teaching a basic R course and students will be using windows machines, which I haven’t had to touch in years. I’m asking admins to install R and Rstudio. Are there other recommended packages (git, git-bash, etc.) that I should ask for?

Jared Andrews (19:45:12): > Rtools to install from source if needed

Axel (20:56:06): > @Axel has joined the channel

2024-07-11

Robert Castelo (05:00:29) (in thread): > My students on Windows laptops have successfully usedhttps://gitforwindows.orgin combination with RStudio, you can read more about this athttps://happygitwithr.com/install-git#install-git-windowsso, I’d recommend installing “Git for Windows”. - Attachment (gitforwindows.org): Git for Windows > We bring the awesome Git VCS to Windows - Attachment (happygitwithr.com): Chapter 6 Install Git | Happy Git and GitHub for the useR > You need Git, so you can use it at the command line and so RStudio can call it. If there’s any chance it’s installed already, verify that, rejoice, and skip this step. (But consider updating an…

Maria Doyle (05:43:05): > :rocket:Join us for the EuroBioC2024 Carpentries Workshops!:date:September 2-3, 2024:round_pushpin:Oxford, UKWorkshops: > 1. Intro to Genomic Data Analysis with R and Bioconductor (2 days) > 2. Analysis & Interpretation of Bulk RNA-Seq Data using Bioconductor (2 days) > 3. Intro to the Bioconductor Project (1 day on September 3rd) > :mag:Who: Biologists, bioinformaticians, and developers. Check the application forms for prerequisites.:bulb:Why: Hands-on training, expert instructors, and fantastic networking opportunities:point_right:Register hereFor more details, check out our posts onMastodonandLinkedIn. > Please share with your networks!

Sathish Kumar (06:07:48): > @Sathish Kumar has joined the channel

Hothri Moka (07:21:11): > @Hothri Moka has joined the channel

Jenny Drnevich (09:35:33) (in thread): > Our Carpentries-style Intro to Data Analysis with R & Bioconductor has platform-specific instructions for R and RStudio:https://carpentries-incubator.github.io/bioc-intro/. Are you going to be teaching them git as well? The Software Carpentries Intro to Git lesson also has platform-specific directions for install Git and getting an account on GitHub:https://swcarpentry.github.io/git-novice/

Jenny Drnevich (09:38:17) (in thread): > Looks like they also use Git for Windows. I don’t know how these instructions compare to what Robert posted, but there is also a video:https://carpentries.github.io/workshop-template/install_instructions/#shell

Jenny Drnevich (09:40:27) (in thread): > I might discourage this for a beginner R class, just so you don’t have to deal with questions during install about “it says there is a newer source version and do I want to build it?”

Jared Andrews (10:02:50) (in thread): > Fair point.

Sean Davis (12:42:10) (in thread): > I’m not planning on teaching Git, but I host materials on github and an easy way to get those into Rstudio is to create a project from the github repo.

Jenny Drnevich (12:58:23) (in thread): > Good idea!

2024-07-12

Laurent Gatto (07:43:53): > bioc-intro is failing because of S4Vectors. But what is surprising, is that it seem to be wanting to downgrade all packages: > > # Bioconductor --------------------------------------------------------------- > - Biobase [repo: Bioconductor 3.19 -> *; ver: 2.64.0 -> 2.60.0] > - BiocGenerics [repo: Bioconductor 3.19 -> *; ver: 0.50.0 -> 0.46.0] > ... > # CRAN ----------------------------------------------------------------------- > - backports [repo: RSPM -> CRAN; ver: 1.5.0 -> 1.4.1] > - broom [repo: RSPM -> CRAN; ver: 1.0.6 -> 1.0.5] > ... > # RSPM ----------------------------------------------------------------------- > - crayon [1.5.3 -> 1.5.2] > - fastmap [1.2.0 -> 1.1.1] > ... > # carpentries ---------------------------------------------------------------- > - ragg [repo: RSPM -> carpentries; ver: 1.3.2 -> 1.3.1] > > Any idea?

2024-07-14

Sudipta Hazra (18:18:44): > @Sudipta Hazra has joined the channel

2024-07-23

Shaurita (17:39:16): > @Shaurita has joined the channel

2024-07-26

Qiwen Octavia Huang (19:47:55): > @Qiwen Octavia Huang has joined the channel

2024-07-30

Rishi (02:47:44) (in thread): > Hi , I would like to have your attention to the new Bioconductor packagebroadSeqwhich is strongly inline with workshop 2. [Please also suggest if I should post this somewhere else] - Attachment (Bioconductor): broadSeq (development version) > This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.

Kevin Rue-Albrecht (08:04:33): > Anyone else somewhat frustrated with the new narrow columns in the ‘overview’ section of each Carpentries episode (e.g.https://carpentries-incubator.github.io/bioc-intro/23-starting-with-r.html) ? Anything we can/want to do about it?

Kevin Rue-Albrecht (08:05:01) (in thread): > In the questions column, there’s barely room for a couple of words per line

Robert Castelo (13:05:02) (in thread): > Yesss, I also find it frustrating, I’d say that maybe the columns are not narrow but the margins, especially in the Questions columns, are too large.

2024-07-31

Zahraa W Alsafwani (17:21:09): > @Zahraa W Alsafwani has joined the channel

daohuymanh (23:58:16): > @daohuymanh has joined the channel

2024-08-01

Kevin Rue-Albrecht (10:42:42): > I’m going nuts trying to remember how to add new input files. It seems to render properly locally, but for some reason the github action seems to be downloading the new input files but not detecting them at the time of import data from them:https://carpentries-incubator.github.io/bioc-project/09-summarizedexperiment.html#creating-a-summarizedexperiment-object

Kevin Rue-Albrecht (10:43:24): > local view: - File (PNG): image.png

Kevin Rue-Albrecht (13:01:09) (in thread): > Never mind. It seems that i needed to wait an unusual amount of timefor GitHub pages to update (even after the action telling me it had deployed the new version of the website)

2024-08-12

Frederick Tan (08:50:49) (in thread): > Perhaps it was designed for wide(r) screens? The column becomes wide(r) after collapsing the left hand table of contents

Kevin Rue-Albrecht (09:11:05) (in thread): > Good trick collapsing the table of contents!

Frederick Tan (09:14:10) (in thread): > Stopgap at least … keep pushing for web designs that are friendly for 1024 pixels wide as at minimum it helps during training events

2024-08-16

Monthly education reminder Aug 2024 (07:00:03): > Hi everyone, > > Just a quick reminder about the monthly Bioconductor community education meeting on Monday, 3-4pm CEST. > * Meeting Link****:****Join the meeting on Jitsi (all welcome!) > * Collaborative Google Doc with Agenda**** ****(feel free to add items) > * Education and Training Webpage(for reference) > Looking forward to seeing you there! > > Charlotte & Laurent

2024-08-19

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2024-08-20

Josefina Suils (08:36:19): > @Josefina Suils has joined the channel

2024-08-27

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2024-09-09

Monthly education reminder (03:00:08): > Hi everyone, > > Just a quick reminder about the monthly Bioconductor community education meeting on Monday, 3-4pm CEST. > * Meeting Link****:****Join the meeting on Jitsi (all welcome!) > * Collaborative Google Doc with Agenda**** ****(feel free to add items) > * Education and Training Webpage(for reference) > Looking forward to seeing you there! > > Charlotte & Laurent - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge - 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.

Kozo Nishida (04:13:32): - Attachment: Attachment > I have built a Japanese version of bioc-intro website and made it available at https://swcarpentry-ja.github.io/bioc-intro/10-data-organisation.html . > Most of the translations on this website are due to the use of the DeepL API in https://bioconductor.crowdin.com/. > (I will review and improve that machine-translation.) > > If anyone wants to publish your language website (as well as Japanese), please reply.

Ludwig Geistlinger (08:10:09): > Hi@Charlotte Soneson@Laurent Gattojust a heads up that we would like to provide an update re: the OSCA tutorial and discuss next steps in today’s edu meeting if possible. I added to the gdoc agenda. Thanks!

Charlotte Soneson (08:29:41): > Sounds good!

Wes W (10:40:01): > so from September to December I have standing CCI meetings now that the semester has started at 9am EST every monday. I don’t think I will be able to make future meetings this semester. Just wanted to let you know in case you thought I just abandoned them. > > good luck this semester everyone!

Andrew Ghazi (15:09:09): > @Andrew Ghazi has joined the channel

2024-09-10

Ludwig Geistlinger (14:09:45): > Hi<!channel>: > > As discussed in yesterday’s education meeting, we would like to open up our OSCA-based scRNA-seq module for feedback from the community and review by Bioconductor’s education committee (GitHub repo/rendered course page). Our goal is to collect and implement feedback over the course of the next month prior to proceeding with contributing the module to theCarpentries incubatorand the collection ofBioconductor teaching modules.A bit of context:This workshop is based on theOSCA tutorialthat Davide Risso, Dario Righelli, Marcel Ramos, and myself gave at the ISMB conference last year. The tutorial is a light version of theOSCA bookthat concentrates on essential aspects for getting started with the book (“The OSCA book in a day”). The tutorial is in large parts a faithful copy of the OSCA book, but also adds contents that are not (yet) covered in the OSCA book such as interoperability with other popular single-cell analysis ecosystems and accessing data from the Human Cell Atlas.How to provide feedback:We welcome feedback provided throughGitHub issues. Contributions via pull requests should be discussed viaGitHub issuesfirst.Next steps:Feedback provided by Oct 07, 2024, will be considered and incorporated where appropriate during a dedicated sprint session. If you would like to participate in the sprint, please provide your availabilityhere.

2024-09-11

Kozo Nishida (13:07:07): - Attachment: Attachment > https://bioconductor-translations.github.io/bioc-intro/ is French website (by Google Translate). > I’ll let you all know the details later.

2024-09-20

Camille Guillermin (09:29:25): > @Camille Guillermin has joined the channel

2024-09-24

Jasmine Baker (12:48:53): > @Jasmine Baker has joined the channel

2024-09-25

Maria Doyle (07:00:25): > :mortar_board:Exciting opportunity for Carpentries Instructors!We’re seeking instructors for the2025 Bioconductor African Coursesin Nairobi, Kenya and West Africa. Teach R/Bioconductor or RNA-seq analysis to foster local capacity and collaboration.:white_check_mark:**** Carpentries certification required ****:school:**** One-week commitment ****:luggage:**** Travel & accommodation coveredInterested? Complete ourexpression of interest formbyOct 21, 2024** - Attachment (Google Docs): Bioconductor African Courses 2025 - Instructor Expression of Interest > We are excited to announce the upcoming Bioconductor African Courses scheduled for 2025. The first course will take place in Nairobi, Kenya in March/April, with a second course planned for West Africa a few months later. These courses aim to build local capacity and foster a strong network of learners and instructors across Africa. > Course Structure: > Each weeklong course consists of two teaching modules and a BYO data day: > Monday & Tuesday: bioc-intro module (Introduction to genomic data analysis with R and Bioconductor) > Wednesday & Thursday: bioc-rnaseq module (Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor) > Friday: Bring your own (BYO) data day > What We’re Looking For: > We are seeking Carpentries-certified instructors to teach these modules. Each module will be taught by a pair of instructors—one international and one based in Africa. Additional local instructors may be included to provide more teaching opportunities. > Instructors will teach one module (either bioc-intro or bioc-rnaseq) but are expected to stay for the full week to assist as a helper in the other module and the final BYO data day. This fosters collaboration and community-building among participants and instructors. You can express interest in teaching either the Nairobi course, the West Africa course, or both. > Funding: > Thanks to funding from the Chan Zuckerberg Initiative (CZI), travel and accommodation expenses will be covered for instructors. For more details on this and other CZI-funded Bioconductor projects, please check out our blog post. > > How to Express Interest: > Please complete our expression of interest form by Monday, October 21st, 2024. The form will ask for your certification status, area of expertise, and preferred module and location. > We are considering the following dates for the Nairobi course: > March 24-28, 2025, or > March 31-April 4, 2025 > Dates for the West Africa course will be confirmed later. We aim to finalise the instructor line-up for Nairobi by the end of the year and will follow up regarding West Africa soon after. > Should you have any questions, feel free to reach out to us directly. > Thank you for your interest in contributing to this important initiative. We look forward to hearing from you! > Maria Doyle > Bioconductor Community Manager > Email: mailto:maria.doyle@ul.ie|maria.doyle@ul.ie

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2024-09-26

Candace Savonen (14:54:16): > @Candace Savonen has joined the channel

Candace Savonen (15:17:55): > I’m a data scientist with Jeff Leek and I’m currently working on preparing a grant proposal to make a set of biomedical educational modules and LLM chatbot using Swirl as a basis. > > Was wondering if anyone has any data or leanings on what are the biggest training needs when it comes to Bioconductor packages? Any topics in particular?

2024-09-27

Candace Savonen (08:52:07) (in thread): > Hi@Frederick TanAlways running into you.:wave:

Frederick Tan (08:53:31) (in thread): > Not often enough! Though back to preparing for our variant analysis lab today:sweat_smile:

Maria Doyle (11:42:38) (in thread): > Hi@Candace Savonen! feel free to join our next teaching meeting on October 14th, 3-4 pm CEST. We’ll be discussing teaching Bioconductor objects to biologists, which could align with your project. You’re also welcome to add your proposal as an item to the agenda if you’d like. Here’s theagenda link

Candace Savonen (11:49:10) (in thread): > Awesome! I’ll definitely plan on joining!

2024-10-03

Sean Davis (19:54:16) (in thread): > @Maria Doyleis there an invite for the teaching meetings that you could forward along to get it on my calendar (and perhaps others)?

Sean Davis (19:55:50) (in thread): > @Candace Savonen, thanks for including Bioconductor in your plans. Like@Maria Doyleand lots of others, if you want to chat separately, we can try to find a time.

2024-10-04

Monisa Hasnain (02:04:48): > @Monisa Hasnain has joined the channel

Maria Doyle (08:59:36) (in thread): > Hi Sean, if you join theBioconductor Teaching Google group, you’ll automatically receive the monthly meeting reminder. The event is also listed in the Bioconductor events calendar, and here’s theGoogle Calendar link.@Charlotte Soneson, do you think there’s a way to make the event easier to add to non-Google calendars, or should we explore other options like setting up.icsfiles for these meetings?

Charlotte Soneson (09:06:15) (in thread): > Good question - I don’t know what people typically use (I’m still a bit on the manual side:sweat_smile:). I’m open to suggestions - I kind of like that it’s part of the Bioconductor events calendar though, it makes it easy for people to find.

Candace Savonen (09:36:15) (in thread): > @Sean DavisThat would be great! Would love to get the Bioconductor Community’s opinions about this and hopefully we’ll get funding for this proposal and can create a nice seamless infrastructure for us to collaborate on this tool!

2024-10-05

Ebele Lynda Okolo (13:29:03): > @Ebele Lynda Okolo has joined the channel

2024-10-09

Carlo Pecoraro (11:50:47): > Hi <!channel>****!****We have only a few spots left for our upcomingSingle-cell RNA-seq analysis with R/Bioconductorcourse, happeningonline from 4-8 November. This is a fantastic opportunity for biologists and bioinformaticians to dive deep into scRNA-seq workflows, covering everything from data filtering to advanced cell cluster and temporal ordering analysis.:link:Course details and registration:https://www.physalia-courses.org/courses-workshops/course18/Key topics include: > * Data processing, QC, and normalization > * Batch effect correction, cell clustering, and annotation > * Pseudo-time inference and temporal differential expression > * Hands-on practicals using R/Bioconductor - Attachment (physalia-courses): single-cell RNA-seq analysis with R/Bioconductor > 4-8 November 2024 To foster international participation, this course will be held online

2024-10-10

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2024-10-11

Ji Hen Lau (01:36:31): > @Ji Hen Lau has joined the channel

2024-10-14

Monthly education reminder (03:00:22): > Hi everyone, > > Just a quick reminder about the monthly Bioconductor community education meeting on Monday, 3-4pm CEST. > * Meeting Link****:****Join the meeting on Jitsi (all welcome!) > * Collaborative Google Doc with Agenda**** ****(feel free to add items) > * Education and Training Webpage(for reference) > Looking forward to seeing you there! > > Charlotte & Laurent - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Frederick Tan (08:34:34): > Will miss today as heading out for a conference:disappointed:Agenda looks great and added a few notes (biocswirl and bioc-scrnaseq sprint). See you at the Nov 11th call if not earlier!

Charlotte Soneson (08:35:26) (in thread): > Enjoy the conference!

Frederick Tan (08:41:52) (in thread): > Thank you:slightly_smiling_face:

Maria Doyle (09:04:11): > I’m trying to join but jitsi is stuck for me on “Join meeting”

Charlotte Soneson (09:05:22) (in thread): > This one?https://meet.jit.si/BioconductorTeaching - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Maria Doyle (09:07:35) (in thread): > Yes that one, but I eventually got in:sweat_smile:

Janani Ravi (09:16:52) (in thread): > @Maria Doyleis this for carpentries instructors as well?

Maria Doyle (10:05:53) (in thread): > Yes, it’s for anyone interested in Bioconductor education and training.

Tim Triche (14:17:30): > @Tim Triche has joined the channel

2024-10-16

Zelal Özgür Durmuş (03:48:42): > @Zelal Özgür Durmuş has joined the channel

Wes W (19:38:30): > Hey all, I am going to submit a bioconductor workshop proposal for CYTO 2025 in Denver , would anyone be interested in submitting with me and / or join and helping make the workshop? potential for galaxy integration

Wes W (20:02:36) (in thread): > one thing CYTO Workshops have never done (or at least in the history of me attending them) is a hands on workshop, where people can follow along in real time on their own devices. Like we do with the Bioconductor Conference ones… > > I want to build a workshop using bioconductor packages (flowcore, opencyto, flowSOM, flowAI, etc) , that will start with a set of FCS files and show people how to open and bring in their data, clean it up, normalize it, and then do some basic gating and clustering

chengyi ma (21:17:56): > @chengyi ma has joined the channel

2024-10-17

Vince Carey (05:04:17) (in thread): > Sounds great.@Alex Mahmoudis on vacation but if you want to useworkshop.bioconductor.orgframework, Alex could respond next week. BTW is NIAID Immport a source of relevant public data for you?

Maria Doyle (06:03:23) (in thread): > Hey Wes, this sounds like a great idea! I was wondering if there might be some overlap with the workshop from Bioc2023 on the cytoverse packages (flowCore, opencyto, etc.). Could it be worth reaching out to Andrew or others from that team for any insights or potential connections?https://bioc2023.bioconductor.org/abstracts/paper79/

2024-10-18

Maria Doyle (09:50:22): > :mortar_board:Exciting opportunity in Brazil for Carpentries Instructors and Bioconductor Presenters!We’re seeking a Carpentries-certified instructor to represent Bioconductor at the2025 Brazilian Genetics Society Meeting in Belém do Pará, Brazil. Helpco-teach a Bioconductor workshopand potentially present asymposiaorroundtableto raise awareness of Bioconductor in the Latin American bioinformatics and genetics communities.:white_check_mark:Carpentries certification required for co-teaching the workshop:school:August 13-16, 2025 (pending proposal approval):luggage:Travel & accommodation covered for the workshop instructor (grant funding or employer support also encouraged):information_source:* Interested in solely presenting a symposia or roundtable on Bioconductor? You’re welcome to apply! Travel support is prioritized for the workshop instructor, but the conference covers food and accommodation for presenters.Interested? Complete theexpression of interest formbyOct 26, 2024*!

Tim Triche (09:51:30) (in thread): > Have you talked to Norbert @ CZI about this? I bet CZI Latin America / Ancestry Networks would love to support this

Maria Doyle (09:57:34) (in thread): > Thanks, Tim! I haven’t reached out to Norbert yet, but that’s a great idea.@Izabela Mamede, have you been in touch with him or CZI Latin America/Ancestry Networks about this? If not, I could reach out. Thanks for the suggestion!

Felipe ten Caten (11:08:30): > @Felipe ten Caten has joined the channel

Izabela Mamede (11:40:55) (in thread): > Hey@Maria DoyleI have not, I do not have any direct contact with them. If you could reach out would be great

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2024-10-20

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2024-10-28

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2024-10-30

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2024-11-02

skuba (13:42:41): > @skuba has joined the channel

2024-11-04

Aedin Culhane (05:41:16): > ISMB/ECCB 2025 > is now accepting tutorial proposals > > Submission deadline: Thursday, December 19, 2024https://www.iscb.org/ismbeccb2025/call-for-submissions/tutorials - Attachment (iscb.org): Tutorials > ISCB - International Society for Computational Biology

Jared Andrews (13:33:22): > Ready to turn your data science passion into a career advancing biomedical research? > > The St. Jude Graduate School of Biomedical Science’s new MS in Applied Biomedical Data Sciences blends advanced coursework with hands-on practicum experience at St. Jude Children’s Research Hospital in Memphis, TN. Enjoy a full scholarship, a monthly cash fellowship, subsidized housing options, and a one-of-a-kind opportunity to apply data skills in a real-world medical research setting. > > Applications due Dec 1, with classes beginning August 2025. For more info, visit:Applied Biomedical Data Sciences Master’s Program | St. Jude Graduate School. > > Learn more by attending our upcoming virtual session on Nov. 18th focusing on Careers in Biomedical Sciences. Event Registration:https://stjudegs.qualtrics.com/jfe/form/SV_7ULUTqqNe5IrO1E

2024-11-06

Jenny Drnevich (15:53:19): > Hi all, we can discuss more at our meeting on Monday but I wonder what should be the “recommended” way to use/modify our Carpentries lessons? For example, here at Illinois we are planning on an Intro to R workshop and we want to use some of the BioC materials but we don’t have time to do all. We also need to add in some location-specific things and would like to have it all in one nicegithub.io. There is forking the current repo, but as we don’t ever intend to push any changes back I don’t think this is best option. Other repos I’ve seen are set up a template that can be copied but I don’t know if that is possible with this. Suggestions?

Kozo Nishida (20:37:31) (in thread): > How about creating a GitHub organization for training committee and put repos there?

Kozo Nishida (20:40:47) (in thread): > By the way, I createdhttps://github.com/bioconductor-translationsfor translation purposes. If it would be convenient to rename it to bioconductor-training [and use it for the purpose], please let me know.

Kozo Nishida (20:47:16) (in thread): > Currently, a translation site (likehttps://swcarpentry-ja.github.io/bioc-intro/) requires one repository per language and cannot serve multiple language sites from a single repository. For this reason, I believe a new organization (separate fromhttps://github.com/bioconductor) may be necessary for education-and-training.

Janani Ravi (23:48:07) (in thread): > if it had to be part of the main bioconductor, we can have particular nomenclature (for repo names) along with repo, issue, etc templates + tags to easily find them from the many bioconductor repos.Or yes, an org might not be a bad idea either.

2024-11-07

Angelique Trusler (04:22:05): > @Angelique Trusler has joined the channel

Angelique Trusler (04:22:13): > The Carpentriesseeks up to six individuals to serve on our Board of Directors for a 3-year term beginning February 2025. Learn more andnominate yourself. I’m happy to answer questions as well. Thank you all for continuing to invest in our organisation! - Attachment (carpentries.org): The Carpentries > The Carpentries is a fiscally sponsored project of Community Initiatives, a registered 501(c)3 non-profit organisation based in California, USA. We are a global community teaching foundational computational and data science skills to researchers in academia, industry and government.

Vince Carey (04:39:58) (in thread): > Just my 2c – I see no problem with forking the repo and refraining from PRing back.

Vince Carey (04:40:30) (in thread): > I would just be explicit in the README about the divergence.

Frederick Tan (06:26:36) (in thread): > Great question@Jenny Drnevich! This comes up here as well every so often. Historically we’ve gone with a Google Doc that points to the master repo and and notes what to pay attention to. I suppose the first question is how different are you thinking?

Cecilia M (07:13:24): > @Cecilia M has joined the channel

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2024-11-08

Kozo Nishida (08:25:16): - Attachment: Attachment > This is the Google Slides I used in my BioCAsia talk today. > https://docs.google.com/presentation/d/1Fi7tuhGHh1xkl3zOs4Hf4vL6kSXj7A702R5UdVmTxHQ/edit?usp=sharing

Tim Triche (08:26:48) (in thread): > These are great!

Stevie Pederson (08:50:50) (in thread): > Great talk too Kozo!

Wes W (09:57:49): > How hard is it to setup Galaxy to run a workshop using bioconductor packages in an R studio environment with say… 60 attendees? so like everyone gets their own instance, like we did with the old Orchestra NCI server?

Wes W (09:58:41): > I really want to submit this hands on workshop proposal on Sunday, but I am worried I am over promising (workshop would be in May) , if people can’t come with their laptops and spool up their own follow along instance… Thanks in advance!

Tim Triche (09:58:43) (in thread): > Is@Sean Davisor@Alex Mahmoudin this channel?They’dknow:grin:

Alex Mahmoud (10:03:48) (in thread): > If you want to set up your own,I’dsayit’ssomewhat complicated cause you need kubernetes and Galaxy configuration knowledge. If you have that background and access to a kubenretes cluster, Id say it can be done fairly easily. But you could also just use the running instance atworkshop.Bioconductor.orgif you want?

Wes W (22:48:12) (in thread): > id very much prefer to use the workshop link , thank you!

2024-11-09

Janani Ravi (12:11:59) (in thread): > Verycool, Kozo!:raised_hands:

Alex Mahmoud (12:56:12) (in thread): > Is it a one day thing, a multi-day event, or a class? Let me know rough details when you can plz

2024-11-11

Monthly education reminder (03:00:19): > Hi everyone, > > Just a quick reminder about the monthly Bioconductor community education meeting on Monday, 3-4pm CEST. > * Meeting Link****:****Join the meeting on Jitsi (all welcome!) > * Collaborative Google Doc with Agenda**** ****(feel free to add items) > * Education and Training Webpage(for reference) > Looking forward to seeing you there! > > Charlotte & Laurent - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Janani Ravi (09:43:50): > Do you have the meeting notes? Thanks!

Jenny Drnevich (10:02:58) (in thread): > It’s here, at the very bottom:https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?tab=t.0#heading=h.bwvjcl95pjgh

2024-11-12

Alex Mahmoud (16:51:00) (in thread): > Also talked today to Galaxy folks about the idea of doing a Galaxy on Kubernetes training for the joint conference. I was thinking we could do a specific Bioconductor one talking about creating/wrapping workshops, and then a more general joint one togetherdeploying the infrastructure?And then maybe an extension at the end for managing the Bioconductor Workshop flavor with the extra tooling.No details discussed just putting it out there to gauge interest/thoughts on the idea

2024-11-13

Maria Doyle (08:02:36) (in thread): > This would be a nice addition to the Bioconductor community section on Zenodo (cc@Sean Davis)! You can share ithere.

Sean Davis (08:11:18) (in thread): > https://zenodo.org/communities/bioconductor/records?q=&l=list&p=1&s=10&sort=newest

2024-11-15

Chioma Onyido (03:10:17): > @Chioma Onyido has joined the channel

2024-11-22

Carlo Pecoraro (12:21:01): > Hi<!channel>, we just wanted to inform you that the registrations are now open for the 2nd edition of the Physalia Spatial Omics in R/Bioconductor course with@stefano mangiola& Luciano Martelotto. This course provides a comprehensive introduction to spatial omics technologies, including imaging and sequencing methodologies, experimental design considerations, and cutting-edge data analysis tools. > > Designed for biologists and researchers with a basic background in omics, this course emphasizes practical applications and introduces the ‘tidy’ data principles tailored to spatial omics.:date:When: 19-21 May 2025:round_pushpin:Where: Online:link:Learn more and register:https://www.physalia-courses.org/courses-workshops/spatial-omics-1/ - Attachment (physalia-courses): spatial Omics in R/Bioconductor > 19-21 May 2025 To foster international participation, this course will be held online

2024-11-23

Rachel Wise (01:04:19): > @Rachel Wise has joined the channel

2024-12-02

Yi Ren (03:38:41): > @Yi Ren has joined the channel

Deena Gendoo (04:49:11): > Hi Everyone! Can anyone recommend upcoming face-to-face workshops on spatial transcriptomics, taking place in 2025? Thanks!

Ludwig Geistlinger (12:02:44): > Hi@Charlotte Soneson@Laurent Gatto. The renamed OSCA module (now:bioc-scrnaseq) is now included in the carpentries incubatorhttps://github.com/carpentries-incubator/bioc-scrnaseq. What is the process for including the module on theBioc education page?

Alan O’C (18:01:59) (in thread): > Wow, great stuff!

2024-12-03

Laurent Gatto (02:48:28) (in thread): > A PR should do.

Frederick Tan (08:21:18) (in thread): > Would this be the right place to insert? > * https://github.com/Bioconductor/bioconductor-training/blob/c81586ce0da9d5d8c940522fcf27185f6ceec568/README.md?plain=1#L33 > cc:@Maria Doyle

Maria Doyle (09:51:12) (in thread): > That place looks like a good spot to insert

Ludwig Geistlinger (17:25:11) (in thread): > Thanks! Opened PR here:https://github.com/Bioconductor/bioconductor-training/pull/49 - Attachment: #49 Add bioc-scrnaseq module > This pull request adds the new bioc-scrnaseq module to the list of modules in the README.

2024-12-08

Md.tarikul Islam (20:36:58): > @Md.tarikul Islam has joined the channel

2024-12-09

Monthly education reminder (03:00:27): > Hi everyone, > > Just a quick reminder about the monthly Bioconductor community education meeting on Monday, 3-4pm CEST. > * Meeting Link****:****Join the meeting on Jitsi (all welcome!) > * Collaborative Google Doc with Agenda**** ****(feel free to add items) > * Education and Training Webpage(for reference) > Looking forward to seeing you there! > > Charlotte & Laurent - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

2024-12-11

Tim Triche (12:01:26) (in thread): > argh, missed this (dead tired after a 5K). apologies:disappointed:

2024-12-23

Ying Xu (22:03:01): > @Ying Xu has joined the channel

2024-12-28

Pascal-Onaho (07:55:01): > @Pascal-Onaho has joined the channel

Radwa Sharaf (14:43:03): > @Radwa Sharaf has joined the channel

2024-12-29

Yahya Jahun (04:01:36): > @Yahya Jahun has joined the channel

Andrew Su (12:22:04): > @Andrew Su has joined the channel

Andrew Su (12:35:50): > Hi folks, I’m preparing an introductory course on applied bioinformatics. The students mostly will be wet lab biologists, and this will be their first bioinformatics course. We will be using various bioconductor packages in our case studies. I’d also like to give a high-level overview of bioconductor. Is there a slide deck I can use/adapt? This “What is bioconductor?” video is pretty great (thanks@Lori Shepherd! I would love to have access to those slides if you’re open to sharing) and open to other suggestions as well. Thanks all! - Attachment (YouTube): What is Bioconductor?

Tim Triche (12:38:14): > When does the course start? > 1) this is an excellent discussion topic > 2)@Maria Doylemay also have ideas > 3)I’mnot sure when the next Jitsi meeting is but if it’s before your semester starts, this would be an awesome agenda item

Tim Triche (12:39:27): > One of the reasons I have been interested in WASM/webR is that it puts tools for “doing stuff” directly into students’ hands.But obviously the flip side is that this is worthless without the community that underpins BioC.

Tim Triche (12:44:37): > Nevertheless, if they’re useful, here are two that have seen some high mileage: > * https://trichelab.github.io/webR/mixtures/ > * https://trichelab.github.io/webR/germline/ > I’m working on a Poisson/multinomial deck but it’s pretty rough right now and I can’t make any promises that it will be polished in time. > * https://trichelab.github.io/slides/GammaPoisson/

Tim Triche (12:46:38): > The Bioconductor-centric webR demos would not be possible without@Alex Mahmoudwhich further illustrates why BioC is a community above a collection of software.(I know you are well aware of this as a package developer and maintainer!)

Lori Shepherd (12:54:42) (in thread): > I can look them up and share what I have if you like. Please PM an email I can share with as I think it’s a Google slide deck.

Andrew Su (13:04:34) (in thread): > The course starts the second week of January:grimacing:but I have a little flexibility in when I present this bioconductor overview

2025-01-01

Pariksheet Nanda (15:47:58): > @Pariksheet Nanda has joined the channel

2025-01-02

George Kitundu (00:52:20): > @George Kitundu has joined the channel

Najuma Najeem (11:01:07): > @Najuma Najeem has joined the channel

2025-01-03

Gloria Amor Arroyo (05:35:56): > @Gloria Amor Arroyo has joined the channel

2025-01-05

Muku Bhandari (06:55:04): > @Muku Bhandari has joined the channel

2025-01-13

Monthly education reminder (03:00:20): > Hi everyone, > > Just a quick reminder about the monthly Bioconductor community education meeting on Monday, 3-4pm CEST. > * Meeting Link****:****Join the meeting on Jitsi (all welcome!) > * Collaborative Google Doc with Agenda**** ****(feel free to add items) > * Education and Training Webpage(for reference) > Looking forward to seeing you there! > > Charlotte & Laurent - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Frederick Tan (06:22:40) (in thread): > Sorry, have a doctor appointment this morning and won’t be able to make it@Charlotte Soneson@Laurent Gatto

Laurent Gatto (06:30:58) (in thread): > Thank you for letting us know.

2025-01-14

neslihan oztas (10:33:41): > @neslihan oztas has joined the channel

Jenny Drnevich (16:42:24): > Re: our discussions about building learning pathways. Galaxy has this:https://training.galaxyproject.org/training-material/learning-pathways/ - Attachment (Galaxy Training Network): Learning Pathways > Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge as you go. We always recommend to follow the tutorials in the order they are listed in the pathway.

Tim Triche (16:52:04) (in thread): > These are great!

2025-01-17

Laurent Gatto (01:06:20): > https://carpentries.org/blog/2025/01/teaching-llms-report/ - Attachment (The Carpentries): Teaching LLM Assistants in Carpentries Workshops, part 1 > Generative AI “assistants” such as ChatGPT and GitHub Copilot, based on large language models (LLMs), have gained a lot of attention over recent years and are impacting how people learn about and practice coding and data science. Some members of The Carpentries community have reported observing learners using ChatGPT and similar tools to assist them in and after workshops. Others have reported on efforts to educate members of their local communities about the models behind these tools, their advantages and limitations, and how to judiciously approach their use.

Angelique Trusler (01:43:06) (in thread): > {Sharing from another workspace} > > A second post will follow next week, describing the next steps that The Carpentries Curriculum Team has planned following those discussions. For now, we want to draw your attention to the short series of related community discussions we will host in the coming months. The sessions are listed onthe community calendarandthe community sessions etherpad, and will take place as follows: > * Tuesday 28 January,12:00 UTCand21:00 UTC:LLMs for Data Science: The Ethics of Teaching LLMs in Carpentries Workshops > * Tuesday 25 February,12:00 UTCand21:00 UTC:LLMs for Data Science: Essential Knowledge and Common Misconceptions > * Tuesday 25 March,12:00 UTCand21:00 UTC:LLMs for Data Science: Case Studies to Inform Carpentries Curriculum - Attachment (The Carpentries): Community Events > There are many opportunities to join community meetings, subcommittees and debriefing sessions. Find links to them on this Etherpad, and subscribe to the Google calendar below or use this ics feed to watch all that is going on throughout our community. > Request an accommodation The Carpentries is committed to providing inclusive and accessible content that enables all individuals, including those with disabilities, to participate and engage fully. To request an accommodation for a Carpentries event, please visit our Diversity, Equity, and Inclusion Statement and fill out the accommodation request form provided. - Attachment (timeanddate.com): Event Time Announcer - Carpentries Community Discussion > Event Time Announcer shows time for Carpentries Community Discussion in locations all over the world. In UTC it happens on Tuesday, January 28, 2025 at 12:00:00 noon. - Attachment (timeanddate.com): Event Time Announcer - Carpentries Community Discussion > Event Time Announcer shows time for Carpentries Community Discussion in locations all over the world. In UTC it happens on Tuesday, January 28, 2025 at 9:00:00 pm.

2025-01-31

Bastien CHASSAGNOL (17:10:44): > @Bastien CHASSAGNOL has joined the channel

2025-02-03

Chris Thomas (17:25:31): > @Chris Thomas has joined the channel

2025-02-10

Monthly education reminder (03:00:13): > Hi everyone, > > Just a quick reminder about the monthly Bioconductor community education meeting on Monday, 3-4pm CEST. > * Meeting Link****:****Join the meeting on Jitsi (all welcome!) > * Collaborative Google Doc with Agenda**** ****(feel free to add items) > * Education and Training Webpage(for reference) > Looking forward to seeing you there! > > Charlotte & Laurent - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Fabricio Almeida-Silva (07:52:05) (in thread): > Hi all. > Sorry, but I’m teaching a Master’s course today at UGent. I don’t think I will finish my lecture before the meeting ends, so I will most likely not join today.

Frederick Tan (09:02:25) (in thread): > Unfortunately in a similar boat here (though not at UGent:slightly_smiling_face:)

2025-02-11

Juliana Kentomahun Mautin (11:49:08): > @Juliana Kentomahun Mautin has joined the channel

2025-02-12

Carlo Pecoraro (07:17:08): > We still have a few seats available for our upcoming online course:Gene Set Enrichment Analysis in R/Bioconductor, in March (3-6).Course website: https://www.physalia-courses.org/courses-workshops/gse-in-r/**** ****In this course, we will teach the use of popular GSEA tools, both online-based and those implemented as R packages. We will give a detailed introduction to a variety of GSEA analysis methods, including overrepresentation analysis, univariate methods, and multivariate methods, as well as extensions of GSEA analysis, such as network-based GSEA and single-sample GSEA. Finally, you will also learn the downstream processing of GSEA results, including efficiently visualizing the massive GSEA results, clustering, and simplifying GSEA results via various methods. > We will also cover some other topics that are tightly related to GSEA analysis, such as multiple hypothesis testing. You will also learn to implement GSEA methods completely from scratch in R/Bioconductor. - Attachment (physalia-courses): Gene Set Enrichment Analysis in R/Bioconductor > 3-6 March 2025 To foster international participation, this course will be held online

2025-02-13

JP Flores (13:54:16): > @JP Flores has joined the channel

2025-02-14

Sarah (20:20:00): > @Sarah has joined the channel

2025-02-16

Frank Melo (18:58:28): > @Frank Melo has joined the channel

2025-02-18

Maria Doyle (04:40:34): > :mega:**** Seeking Carpentries-certified instructors for EuroBioC2025 ****:mortar_board::es:Hi everyone, > > We’re seeking Carpentries-certified instructors for Bioconductor Carpentry workshops that will be held before the EuroBioC2025 conference in Barcelona, Spain in September. Ideally, you’ll be attending EuroBioC2025 (September 17th-19th), but that’s not mandatory. We will provide funds to cover 2 nights’ accommodation. > > The Bioconductor Carpentry workshops we plan to run September 15th-16th are theRNA-Seq Analysis with Bioconductorand the newSingle-cell analysis with Bioconductor. > > If you’re available to teach, please let me know: > 1. Which workshop you’d be interested in teaching > 2. If you are able to self-fund your travel to/from Barcelona for the workshops. > **** *******Deadline: Friday, March 7th***If you need more time to figure out if you can, just let me know.

2025-02-21

Sean Davis (14:47:44): > Can someone do my homework and remind me where to find bioc carpentry train-the-trainer process?

Frederick Tan (14:52:39): > Are you looking fortraining.bioconductor.org/carpentry@Sean Davis?

Pariksheet Nanda (15:29:44): > Also if you’re looking for training material, Martin Morgan used this repository for running his “Train the Trainers” workshop at the Jackson Laboratoryhttps://github.com/Bioconductor/BiocTrainer

2025-02-26

Kevin Rue-Albrecht (05:55:25) (in thread): > * Happy to teach either workshop. It’d be my first time, so my preference would be as a helper rather than a lead, but I’m open to discussion. > * Self-funding the travel is possible. Flights are still reasonably affordable, accommodation seems to be the most expensive part.

Maria Doyle (06:15:59) (in thread): > Thanks Kevin. I’ve noted that.

2025-03-05

Karima Diafi (06:47:50): > @Karima Diafi has joined the channel

2025-03-06

Sean Davis (06:27:43): > Anyone have a TLDR version of “how to build and maintain an R package”? Looking for a basic hands-on that I can interactively present to a bioinformatics core/shared resource in 1-2 hours. There is stuff online, of course, but didn’t want to miss an opportunity to 1) surface stuff here and 2) find stuff that might be off the beaten google path….

Maria Doyle (06:42:07) (in thread): > Hi Sean, do you mean a Bioconductor package or a general R package? For general R, I think rOpenSci may have some resources from their Champions program (ping@Yanina Bellini Saibene)

Charlotte Soneson (06:43:47) (in thread): > I did something like this last year (in ~1.5h) for a group of Master students:https://csoneson.github.io/PackagingLecture2024/packaging-code.htmlStephanie Hicks has a nice lecture on the topic here:https://www.stephaniehicks.com/jhustatprogramming2024/lectures/09-r-pkg-dev/index.html

Yanina Bellini Saibene (06:45:58) (in thread): > Yes! we have these workshops: > * Package Development: the Mechanics (champions training):https://rpkgdev-mechanics-2024.netlify.app/ > * Package Development: Not Rocket Science (champions training):https://rpkgdev-rocket-2024.netlify.app/ > You can check all our workshops’ materials here:https://ropensci.org/training/We also have our Packages Developer and Peer Review Guide:https://devguide.ropensci.org(which is in English, Spanish and WIP Portuguese)

Janani Ravi (08:37:50) (in thread): > 1–1.5hR pkg devworkshop material presented by Maelle Salmon (rOpenSci) at R-Ladies East Lansing > * https://github.com/rladies-eastlansing/2021-rpkgdev > * Companion video

Pariksheet Nanda (19:26:23) (in thread): > I found that even before having a conversation on packages, I had to help bioinformatics postdocs and graduate students overcome their reticence and confusion about S4 objects and Bioconductor. Many in the department are R users but avoid using Bioconductor:sob:. So I just have 1 slide toward the end about packages and point them tor-pkgs.orgfor learning that topic on their own time. - File (PDF): PN_2024-04-19_bioconductor.pdf - File (Zip): PN_2024-04-19_bioconductor.zip

2025-03-07

Kevin Rue-Albrecht (12:42:42) (in thread): > Btw, for the purpose of travelarrangements and booking, when will instructors be selected? I might not come for those two days if I don’t teach (although maybe I could still participate in hackathons instead)

Maria Doyle (14:29:13) (in thread): > Within the next couple weeks, before end of March.

2025-03-10

Monthly education reminder (04:00:07): > Hi everyone, > > Just a quick reminder about the monthly Bioconductor community education meeting on Monday, 3-4pm CEST. > * Meeting Link****:****Join the meeting on Jitsi (all welcome!) > * Collaborative Google Doc with Agenda**** ****(feel free to add items) > * Education and Training Webpage(for reference) > Looking forward to seeing you there! > > Charlotte & Laurent - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Jenny Drnevich (12:06:47): > Updates from our meeting this morning that are time sensitive: > 1. @Robert Castelowould you please update the Arxiv paper with the version just re-submitted? > 2. Jenny indicated her interest in running a 1.5 hr training session for GBCC2025 on “How to re-use the Bioconductor Carpentry workshop materials for local workshops, including how to have it hosted on Bioconductor Workshop Galaxy”. This seems better than a talk on the paper. Abstracts for a talk are due Apr 1, so we would need to discuss on line. > 3. @Maria Doyledo we know if any of the 31 new Instructors are planning on going to GBCC2025 and want to help out? > 4. This all ties in with the re-design oftraining.bioconductor.organd moving the Carpentry workshop template totraining.bioconductor.org. > 5. How soon should we start widely advertising the BiocHow Tos? We need to get more - ask developers to help?

2025-03-11

Charlotte Soneson (01:49:47) (in thread): > Thanks Jenny! I will be at GBCC2025, happy to help out with the training session. And as far as I am concerned, I think we can probably start advertising the HowTos soon (I don’t think there are any technical hurdles to contribution remaining).

Robert Castelo (06:24:07) (in thread): > Hi, sure, I’ve assembled the files of the re-submitted and accepted version in a single PDF, which I’m attaching here. I’ve given it the formatting we more or less had in the arXiv version, inserting the figure, the table and the supplemental table in the spots where one would expect to find them. Please give a quick look and if you don’t have any suggestion, I’ll update the preprint. By the way, I will also be at GBCC2025 and can also help out with whatever you’re organizing. - File (PDF): Drnevich25preprint.pdf

Sanika Menkudale (07:11:31): > @Sanika Menkudale has joined the channel

Jenny Drnevich (09:48:28) (in thread): > Looks good to me! Thanks for putting all the figures in line. Is there a way to tag it as “In press, PLOS Computation Biology” or do we wait until we have a doi?

Robert Castelo (11:04:14) (in thread): > I’m afraid there’s no way to tag it as “in press”, but one can definitely link it to the final publication via the fields “Journal reference” and “Related DOI”, see for instancethis preprintof mine, which I updated on Oct 29th, 2014, while the final accepted publication inGeneticsappeared on September 29th, 2014. I could update now the preprint, and later the journal reference and corresponding DOI, once we get it.

Jenny Drnevich (11:05:34) (in thread): > I would go ahead and update the preprint now since we didn’t when we submitted the first revision. Thanks!

Robert Castelo (12:04:47) (in thread): > Okey, done: > > We have received your replacement of 2410.01351. Your temporary > submission identifier is: submit/6271495. > > You may update your replacement at:[https://arxiv.org/submit/6271495](https://arxiv.org/submit/6271495)Your replacement is scheduled to be announced at Wed, 12 Mar 2025 00:00:00 GMT. > The abstract will appear in the subsequent mailing as displayed below, > except that the submission identifier will be replaced by > the official arXiv identifier. Updates before Tue, 11 Mar 2025 18:00:00 GMT will > not delay announcement. > > The update will show up tomorrow Wednesday. In the last moment, I noticed we had removed the funding statements from the acknowledgements, because they go somewhere else in PLOS, and I’ve added them back, and also added page numbers. I’m attaching the final PDF I’ve submitted. When we get the final journal reference and DOI, I’ll update that info on the metadata of the preprint. - File (PDF): Drnevich25preprint.pdf

2025-03-12

Sisi Wang (19:42:05): > @Sisi Wang has joined the channel

2025-03-13

Mihai Todor (06:59:52): > @Mihai Todor has joined the channel

2025-03-14

kli klei (11:51:35): > @kli klei has joined the channel

2025-03-17

Jesulolufemi Adelanke (12:56:17): > @Jesulolufemi Adelanke has joined the channel

2025-03-18

Jennifer Slotnick (14:07:59): > @Jennifer Slotnick has joined the channel

2025-03-19

Sivaranjani Balachander (02:36:17): > @Sivaranjani Balachander has joined the channel

2025-03-24

Carlo Pecoraro (11:24:54): > We are excited to announce our upcomingonline course: “Epigenomics Data Analysis”, taking place fromApril 14-18. > > This course is designed forbiologistsandbioinformaticianswho want to develop practical skills in analyzingRNA-seq,ChIP-seq,ATAC-seq,MNase-seq, andHi-Cdata. Participants will work withreal-world datasetsand gainhands-on experienceusingcommand-line toolsandR/Bioconductor.Course website:https://www.physalia-courses.org/courses-workshops/course59b/ - Attachment (physalia-courses): Epigenomics Data analysis > Dates 14th-18th April 2025 To foster international participation, this course will be held online

Leo Lahti (18:41:31): > Brain, bacteria, and behaviour (PhD-level) summer course, The Netherlands, July 11-15 - also featuring R/Bioconductor & microbiome data science:https://www.radboudumc.nl/en/agenda/2025/july/07jul25-brain-bacteria-and-behaviour-summer-course - Attachment (radboudumc.nl): Brain, bacteria, and behaviour summer course - Understanding the gut brain axis > Looking for information about Brain, bacteria, and behaviour summer course? Read more about this Radboudumc agenda item

2025-03-25

Maria Doyle (04:11:31): > https://www.linkedin.com/feed/update/urn:li:activity:7310197726544060416 - Attachment (linkedin.com): #bioconductor #bioinformatics #rprogramming #datascience #carpentries… | Bioconductor > :mortar_board::earth_africa: Bioconductor Kenya Course Kickoff! :tada: > > We're excited to announce that our first Bioconductor course in Africa started yesterday in Nairobi! Day 1 was filled with learning and collaboration. Rachel Zozo, International Institute of Tropical Agriculture (IITA) Kenya Country Representative, gave the opening remarks, and Laurent Gatto from de Duve Institute, and Michael Landi from IITA taught the Bioconductor Carpentry Introduction to R and Bioconductor lesson. > > Later this week, sessions will be led by Fabricio Almeida-Silva from VIB, Laurah Ondari from IITA, and zedias Chikwambi from AIBST. The course organisation was led by Trushar Shah from IITA and Maria Doyle from University of Limerick, through a grant secured by Aedin Culhane and Maria Doyle. Thanks to other organisers who helped make this happen, Charlotte Soneson from Friedrich Miescher Institute for Biomedical Research and Umar Ahmad from Africa CDC. > > Thanks to Chan Zuckerberg Initiative and UL Global for their funding. > > #Bioconductor #Bioinformatics #RProgramming #DataScience #Carpentries #CZIScience #LearningTogether #Africa

Maria Doyle (04:12:07) (in thread): > @Jenny DrnevichI will ask them

2025-03-27

Jacqueline Murphy (05:41:43): > @Jacqueline Murphy has joined the channel

2025-04-14

Monthly education reminder (03:00:14): > Hi everyone, > > Just a quick reminder about the monthly Bioconductor community education meeting on Monday, 3-4pm CEST. > * Meeting Link****:****Join the meeting on Jitsi (all welcome!) > * Collaborative Google Doc with Agenda**** ****(feel free to add items) > * Education and Training Webpage(for reference) > Looking forward to seeing you there! > > Charlotte & Laurent - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Saad Farooq (07:51:59): > @Saad Farooq has joined the channel

2025-04-17

dhvani solanki (16:12:57): > @dhvani solanki has joined the channel

2025-04-24

Maria Doyle (14:02:30): > :mortar_board:New Publication! > > Our first paper on Bioconductor training from the Bioconductor Training Committee is now published in PLOS Computational Biology. We’re pleased to share our work with the community. > > Read here:https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012925Thank you to everyone involved for your contributions! - Attachment (journals.plos.org): Learning and teaching biological data science in the Bioconductor community > Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and best practices available within the Bioconductor project—an open-source software community focused on omics data analysis. This guide serves as a valuable reference for both learners and educators in the field.

Pariksheet Nanda (14:24:30) (in thread): > That’s cool! I didn’t know about the 31 Carpentry instructors trained. I agree that getting the Carpentries membership funded helps so much to bootstrap enough instructors to run workshops to then bring in potential new instructors from those workshop attendees and helpers.

2025-04-25

Aedin Culhane (03:32:18): > The OHDSI developers have a conference online today. Free to join if anyone is doing clinical or RWD.https://www.ohdsi.org/devcon2025/.

Aedin Culhane (03:32:22): > Agenda > 9:00 – 9:15am ET • Welcome & Introduction > • Paul Nagy, Johns Hopkins University > > 9:15 – 11:30am ET • OHDSI Projects Lightning Talks > • Stabilizing Gaia Core – Robert Miller, Miller Data Solutions > • CustomVocabularyBuilder – Jared Houghtaling, Tufts University > • CohortConstructor – Núria Mercadé-Besora, University of Oxford > • Updates on Strategus – Anthony Sena, Johnson & Johnson > • Experiences with SQLMesh/CICD integration with Databricks – Vishnu Chandrabalan, Lancashire Teaching Hospitals NHS Foundation Trust > • Updates from the Technical Advisory Board – Frank Defalco, Johnson & Johnson > > 11:30 – 12:30pm ET • Developer dialogue: Dev ops, DBT and, of course, LLMs > Moderator: Katy Sadowski, Boehringer Ingelheim > • Eduard Korchmar, EPAM Systems > • Egill Fridgeirsson, Erasmus MC > • Martin Lavallee, Boehringer Ingelheim > • Lawrence Adams, Artificial Intelligence Centre for Value Based Healthcare > > 12:30 – 1:00pm ET • Break > > 1:00 – 2:00pm ET • Sustainable Open-Source Ecosystems Panel > Moderator: Paul Nagy, Sean O’Reilly > • Data4Life – Peter Hoffmann > • The Hyve – Jan Blom/Wouter Franke > • Cognome – James Green