#outreachy

2022-03-18

Andres Wokaty (10:02:10): > @Andres Wokaty has joined the channel

Andres Wokaty (10:02:10): > set the channel description: For outreachy applicants to ask questions

2022-09-26

Peter Hickey (20:00:30): > @Peter Hickey has joined the channel

2022-09-27

Hervé Pagès (00:35:06): > @Hervé Pagès has joined the channel

Alex Mahmoud (12:41:57): > @Alex Mahmoud has joined the channel

2022-09-28

Haleema Sadia (15:54:24): > @Haleema Sadia has joined the channel

2022-10-05

Madelyn Carlson (11:03:48): > @Madelyn Carlson has joined the channel

Paul Villafuerte (11:04:02): > @Paul Villafuerte has joined the channel

2022-10-08

Phylis Atieno (13:04:46): > @Phylis Atieno has joined the channel

Phylis Atieno (13:05:53): > Hello everyone!

Phylis Atieno (13:09:16): > My name is Phyllis, an Outreachy applicant and I’m interested in working on the ‘Conversion of Sweave vignettes to R markdown’. Can’t wait to start contributing!@Andres Wokaty

Andres Wokaty (14:01:21): > Welcome Outreachy applicants! I’m Jen (or Wokaty). My pronouns are they/them. We’re super excited to have you learn about and contribute to Bioconductor. I’m the Bioconductor community organizer for Outreachy and also the mentor for the Conversion of Sweave vignettes to R Markdown project, which we also refer to as Sweave2rmd. We also have Bioconductor community volunteers whom we appreciate very much to help with questions. Please reach out if you have any questions!

Haleema Sadia (14:03:08) (in thread): > Thanks@Andres WokatySuper excited to be here!

2022-10-09

Phylis Atieno (02:59:08) (in thread): > Will surely reach out, thank you!

Chizi E (13:22:29): > @Chizi E has joined the channel

Chizi E (13:28:35) (in thread): > Thanks@Andres Wokaty. > Will be posting my queries here now

Chizi E (13:44:11): > I am working with the instructions linked on the Sweave2rmd github page (see below). > > I get the following error when I run “make info” and despite what I try, I can’t seem to address this issue:ERROR: ‘texi2any’ v5.1 or later needed but missing on your system.I have texi2any installed and a version check returns: (GNU texinfo) 6.5https://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Unix_002dalikes - Attachment (cran.r-project.org): R Installation and Administration > R Installation and Administration

Mariam Fayena (13:48:22): > @Mariam Fayena has joined the channel

Mariam Fayena (13:49:32) (in thread): > OK thanks

Haleema Sadia (17:29:33) (in thread): > Hi Chizi, > why are you doing “make info’? As per the installation instructions it is used to build r manuals from source.You can skip it if you dont absolutely need them

Frederick Tan (17:31:23): > @Frederick Tan has joined the channel

Dike Victoria Chiemela (17:53:41): > @Dike Victoria Chiemela has joined the channel

Haleema Sadia (20:53:47): > Hi@Andres Wokaty, > Do we need to open a PR for the first issue or adding a link to the repo would work?

Chizi E (21:04:15) (in thread): > Hi Haleema, my first time doing any compilation. And it seems that some of the steps before “make info” also had issues just as “make info” is throwing up errors. > > By troubleshooting the issue with “make file”, I get a chance to trouble shoot my whole compile process.

Chizi E (22:44:12) (in thread): > I think I will skip “make info” for now. I actually thought it was necessary to run “make info” successfully like the preceding processes

YuNan Guan (22:52:50): > @YuNan Guan has joined the channel

Haleema Sadia (23:06:17) (in thread): > Are you on linux based environment?

Chizi E (23:06:48) (in thread): > Yes Haleema! I’m on Linux (linux mint)

Haleema Sadia (23:17:19) (in thread): > After extracting from the tar file you have to : > 1. cd into the main directory > 2. Run the following: > > 1. ./configure > 2. make > 3. make check > if successful there will be a R shell script in the bin folder, you can try running it and see if it works.

Chizi E (23:28:26) (in thread): > Hi Haleema! I have the R shell script!! I can run R from that bin directory. May be it is sufficient to leave the compilation at this stage since R works

2022-10-10

Haleema Sadia (01:27:47) (in thread): > Yes. To work for the tasks the shell script seems to be sufficient.if need be you can build the manuals later. > also having the R studio will help.

Elendu Emmanuel (02:14:03): > @Elendu Emmanuel has joined the channel

Elendu Emmanuel (02:20:43): > Hi, I am Emmanuel an Outreachy internship applicant.

Elendu Emmanuel (02:24:43) (in thread): > Okay, thanks.

Elendu Emmanuel (02:55:58): > Hi@Haleema Sadiaplease how do I install R for windows system?

Halimat Chisom (03:28:50): > @Halimat Chisom has joined the channel

Halimat Chisom (03:29:48): > Hello everyone, > My name is Halimat, an Outreachy applicant. I’m applying to contribute to the ‘Conversion of Sweave vignettes to R markdown’ project. My pronouns are She/Her. > I’m looking forward to working with you. I just started setting up, so I don’t have any questions for now. > > Thank you

Halimat Chisom (03:30:11) (in thread): > Thank you

Chizi E (08:08:44): > Hola everyone!!! > > I’m getting an error while trying to install packages in my installation of R inside R-devel directory. > > I ran the following code: > > BiocManager::install(“bugsigdbr”) > and got the following error message: > > Error: Bioconductor does not yet build and check packages for R version 4.3; seehttps://bioconductor.org/install > did anyone else have a similar experience with their package installation?

Ani Chibuike Damian (10:09:43): > @Ani Chibuike Damian has joined the channel

Ani Chibuike Damian (10:12:28): > Hi everyone, I’m Ani Chibuike Damian, an applicant of the Outreachy program in my contribution stage. Looking forward to learn and contribute to the “Convert sweave vignettes to R markdown project”. My mentor is@Andres Wokaty. Really nice to be here. > My pronouns are He/him/his. No questions yet

Ani Chibuike Damian (10:15:04) (in thread): > Thank you so much.

Madelyn Carlson (10:17:25) (in thread): > GM! Happy to jump in here. Could you say a little more about where you are in the process? In general, once a PR is made on a new vignette (which will be ~ freshly~ .Rmd), other Sweave2Rmd volunteers and group members will review it before confirming. Around the approx. same time, the converted vignette should be hyperlinked in our project board to make it easy for other Sweave2Rmd members to locate it. Is that helpful? Not sure whether I’m completely speaking to your question.

Madelyn Carlson (10:19:07) (in thread): > Hi@Elendu Emmanuelhereare some instructions on installing R 4.2.1 for windows. In the page, you’ll see a link to R Windows FAQ for Windows-specific questions and a link at the top to download R. I hope that this is helpful!

Madelyn Carlson (10:19:31) (in thread): > Welcome, Halimat! Greet to meet you.

Madelyn Carlson (10:22:50) (in thread): > GM@Chizi E! Have you tried running these code chunks? First: > > if (!require("BiocManager", quietly = TRUE)) > install.packages("BiocManager") > BiocManager::install() > > then: > > if (!require("BiocManager", quietly = TRUE)) > install.packages("BiocManager") > > BiocManager::install("bugsigdbr") >

Madelyn Carlson (10:23:02) (in thread): > Let me know whether it still gives you error message

Madelyn Carlson (10:23:23) (in thread): > Great to meet you!

Ani Chibuike Damian (10:26:23) (in thread): > Thank you Madelyn

Madelyn Carlson (10:26:23): > Good morning! Welcome to all the Outreachy applicants, it’s wonderful to meet you. My name is Madelyn and I’ve been working with Jen on the Sweave2Rmd project for about 6-7 months. As y’all continue setting up and prepping for conversions, please let me know if you have any questions. Happy to help.

Ani Chibuike Damian (10:29:34) (in thread): > Surely, thank you.

Chizi E (12:15:22) (in thread): > Morning@Madelyn Carlson. I ran the code: > > if (!require("BiocManager", quietly = TRUE)){install.packages("BiocManager") } > > I got the result: > > Bioconductor does not yet build and check packages for R version 4.3; seehttps://bioconductor.org/install

Haleema Sadia (13:06:10) (in thread): > Hi, > So I saw two tasks on Github, first contribution task was not actually a vignette contribution but rather a standalone task which teaches how to use bioconductor packages and generate their rmd file. > In the task instructions it was written that we have to push code to Github and then comment link on the issue, which I did.

Haleema Sadia (13:08:51) (in thread): > Hi, > Thank you so much. > I am currently working on the sweave for biobase package and loading the whole project to run the chunks gives me an error. > Can I make the chunks work by linking it to the code any other way. (trying to understand how code chunks are actually running) > Also do I need to import everything in rmd file for them to actually work?

Haleema Sadia (13:10:36) (in thread): > Seems like bioconductor is not installed yet. > Do you get success after running this: > > if (!require("BiocManager", quietly = TRUE)) > install.packages("BiocManager") > BiocManager::install() >

Haleema Sadia (14:13:26) (in thread): > So I tried again.In R studio I installed th package and click on load All. > it runs successfully > but when I play a code chunk it gives not found.

Hervé Pagès (14:20:16) (in thread): > Hi@Elendu Emmanuel, please note that Windows is not recommended for the BSgenomeForge project:https://github.com/Bioconductor/BSgenomeForge. Do you have access to a Linux system? Linux is very easy to install. You can install it on a machine that has Windows already, on separate partitions, and configure the machine for dual boot. For example, if you install Ubuntu from a USB flash drive, the installation process will take care of all of this.

Hervé Pagès (14:23:28) (in thread): > Hi@Chizi E, Bioconductor does not support R devel yet. The currentdevelversion of Bioconductor (BioC 3.16) requires the latest Rrelease(R 4.2).

Haleema Sadia (14:30:14) (in thread): > Code chunks work now! > had to load the relevant parts manually.

Elendu Emmanuel (14:54:06) (in thread): > I don’t have access to a Linux system. I don’t know if Ubuntu CLI would do sir?

Hervé Pagès (15:00:28) (in thread): > Yes everything can be done at the command line in Linux if that’s what you are asking. FWIW I personally do all my development work at the command line on a laptop with Ubuntu 22.04.

Chizi E (15:04:08) (in thread): > Hi@Hervé Pagès, the error message that is displayed seems to show that the R-devel in question has R with version number 4.3

Hervé Pagès (15:22:56) (in thread): > Yes 4.3 is R devel. You need to install 4.2.

Madelyn Carlson (15:40:56) (in thread): > Thanks for that additional context. I should rephrase one of the things I wrote. When I said “once a PR is made on a new vignette…“ I meant the .Rmd version of the Bioconductor vignettes we’re working on, rather than a separate, new vignette contribution. > > To generate .Rmd file from the original .Rmw, you can usepandocto convert, see screenshot below. Once the file has been copied and updated to make the original .Rmw file, you’ll push your branch back to GitHub withgit push origin file-rmd. At that point, you can go togithub.comto create a pull request. You’ll be able to copy the link to the vignette you pushed to GitHub and can copy it, go to theProject Board, and paste it as a hyperlink on the vignette name that you converted. - File (PNG): Screen Shot 2022-10-10 at 3.40.42 PM.png

Madelyn Carlson (15:41:33) (in thread): > Please let me know if you have any follow-up Qs. I can’t tell how clear or confusing my message was, haha

Maria Doyle (17:30:01): > @Maria Doyle has joined the channel

Elendu Emmanuel (18:38:03) (in thread): > Thank you so much@Madelyn Carlson

Elendu Emmanuel (18:41:54) (in thread): > Thank you so much@Hervé Pagès. I think I will just install the Ubuntu CLI since you said everything needed can be done there as I have no access to a Linux system.

Halimat Chisom (18:47:09) (in thread): > @Chizi Ewere you able to move past this?

Hervé Pagès (19:18:03) (in thread): > I’m not sure what you mean by “installing the Ubuntu CLI”. I don’t know about using the Ubuntu CLI (Command Line Interface?) on a non-Ubuntu system. Maybe you’re thinking of running Ubuntu from a USB flash drive without actually installing Ubuntu on your machine? Unfortunately you won’t be able to do any R/Bioconductor development with a setup like that. > As I said, if you have enough disk space left on your machine, it’s possible to install Linux in addition to Windows, using a dual boot setup. This won’t alter your Windows installation at all. It will only reduce the amount of disk space available when you’re in a Windows session. The 2 installations will coexist on your hard drive, and each of them will own a piece of it.

Elendu Emmanuel (19:28:16) (in thread): > My laptop is not high spec laptop. That’s why I am skeptical about doing that. But I just installed Ubuntu on my virtual machine. Will that do? I am so sorry that I am asking all this questions@Hervé Pagès

Peter Hickey (20:03:19): > @Peter Hickey has left the channel

Hervé Pagès (20:43:38) (in thread): > Just to be clear, you don’t need a high spec laptop at all. Linux runs on all type of hardware, even low spec and/or old hardware. It actually runs better than Windows on this type of hardware. > I don’t know what your installation of Ubuntu on your virtual machine looks like. I suspect that running Ubuntu on top of a virtual machine that runs on Windows has more requirements in terms of specs than running Linuxnativelylike in the dual-boot configuration that I’m advising. Running Linuxnativelyis also likely to be more efficient and more stable. > BTW you also want to make sure that you are on a 64-bit system and that you install the 64-bit version of Ubuntu. Some 32-bit systems limit the amount of memory that can be used by a given process. For example, for 32-bit Windows, this limit is about 3GB per process. To forge a BSgenome data package, depending on the size of the genome, R will sometimes need to be able to allocate a little bit more than 3GB of memory, e.g. 4GB or 5GB. So make sure that your setup supports that. > I just updatedhttps://github.com/Bioconductor/BSgenomeForge/wiki/List-of-contribution-tasks-for-the-Outreachy-application-periodby adding: > * At least 6GB of RAM > to the list of system requirements. > Also make sure that the filesystem in your Linux setup uses Unix-style filepaths e.g./usr/bin,/home/<username>etc… > Thanks!

Chizi E (21:26:24) (in thread): > I was not able to move past this issue unfortunately

Elendu Emmanuel (23:58:58) (in thread): > Okay, I will install Ubuntu natively on the system and start the updated task. Thank you so much@Hervé Pagès.

2022-10-11

Chinwe (00:35:11): > @Chinwe has joined the channel

Chinwe (00:47:13): > Hello everyone, > My name is Chinwendu Nwazojie, you can call me Chinwe. I am applying as an outreachy intern to contribute to the ‘Conversion of Sweave vignettes to R markdown’ project. My pronouns are she/her/hers. > I’m looking meeting new friends and working with you.

Hervé Pagès (01:31:02) (in thread): > Sounds good! Let me know how it goes and if you need any help with this.

Elendu Emmanuel (03:59:34) (in thread): > Okay sir. Thank you so much@Hervé Pagès

Atuhurira Kirabo Kakopo (07:23:19): > @Atuhurira Kirabo Kakopo has joined the channel

Atuhurira Kirabo Kakopo (07:30:01): > Hello everyone. My name is Atuhurira Kirabo Kakopo, and my pronouns are she/her/hers. I am an Outreachy applicant, and I am very excited to learn from and contribute towards the Bioconductor community! Looking forward to the journey ahead!

Haleema Sadia (11:10:38) (in thread): > Thank you so much. This was really helpful. > I have created a PR for an Sweave vignette in biobase package. What should I do next? > > Also where should I paste the link. I cant edit anything on the project board in anyway.

Andres Wokaty (12:34:23) (in thread): > @Haleema SadiaI’ll update the project board.

Andres Wokaty (13:25:20): > set the channel description: For outreachy applicants to introduce themselves and ask questions. > > The two project repositories for the Dec 22 cohort are > * https://github.com/Bioconductor/BSgenomeForge > * https://github.com/Bioconductor/sweave2rmd

Andres Wokaty (13:29:54) (in thread): > Please use R 4.2. I’ve updated the instructions, which are much simpler on the issue athttps://github.com/Bioconductor/sweave2rmd/issues/31.

Andres Wokaty (14:02:08): > If you plan to apply for the Sweave2Rmd project, I’ve made a Doodle poll to see what would be a good time to do a short overview of the project:https://doodle.com/meeting/participate/id/egLmOXra. If you’d like to attend please answer the poll by Thursday 8am ET so that I can post the meeting information before Friday. Attendance is optional. - 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!

2022-10-12

Akwamfon Eventus (06:49:06): > @Akwamfon Eventus has joined the channel

Akwamfon Eventus (06:55:16): > Hi Everyone<!here>, > Hello Mentor@Andres WokatyI’m Akwamfon Eventus (Him/He), an applicant for the Dec22 Outreachy Open Source Internship. > I am applying to contribute on this project. I wish to contribute to the “sweave2rmd” project. > Great to be here.

Akwamfon Eventus (07:06:23) (in thread): > Hello@Madelyn Carlson, please can you give a quick list of what complete set up would be, I just got started and still trying to navigate.

Madelyn Carlson (11:18:59) (in thread): > Good morning@Akwamfon Eventus- absolutely.This pagedescribes the prep work needed once R and RStudio are good to go, e.g., installingdevtoolsandBiocManager. You may have more questions once you get to the steps labeled “Contribution Task” - if that’s the case, just give me a shout. Also,hereis a list of more detailed instructions. - Attachment (bioconductor.github.io): Contribute > Learn how to contribute to our project.

Haleema Sadia (12:09:42) (in thread): > Hi. > A warm welcome to you:slightly_smiling_face:

Ani Chibuike Damian (15:26:35) (in thread): > Welcome. Great to have you here

2022-10-13

Prisca Chidimma Maduka (07:54:04): > @Prisca Chidimma Maduka has joined the channel

Prisca Chidimma Maduka (08:09:31): > Hieveryone,mynameisPrisca,one oftheOutreachyapplicants. Iamexcited tobehere:dancer:.I’m looking forwardtolearningandcontributing.

Haleema Sadia (11:01:22) (in thread): > Hi Prisca, Welcome to the community!

Prisca Chidimma Maduka (11:09:33) (in thread): > Thankyou:dancer:@Haleema Sadia

Andres Wokaty (12:12:32): > Friday October 14 at 11:00 am - 11:30 am ET I’ll host an overview of Sweave2Rmd via Jitsi Meethttps://meet.jit.si/moderated/a957a5a386dd2fd24ed3d44d5c07f769d7cd16293f41eb2d423946ffe444adea. Attendance is optional. I’ll try to stick around a few minutes after the meeting to answer questions. - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Atuhurira Kirabo Kakopo (13:17:08) (in thread): > Hello Prisca, nice to meet you as well.

Hervé Pagès (13:57:19) (in thread): > Hi Prisca, welcome!

Prisca Chidimma Maduka (14:13:10) (in thread): > Thankyou@Atuhurira Kirabo Kakopo@Hervé Pagèswhatawarmwelcome:pleading_face:

Atuhurira Kirabo Kakopo (15:28:27): > Hello everyone. I’ve been trying to install the BSgenome.Hsapiens.UCSC.hg38 package, but my internet has been up and down all day and I keep getting an error indicating timeout (300 seconds) has been reached. After a bit of searching, I’ve found that I can increase this time limit in the?download.filefile and I’m kindly asking if anyone knows where it could be located on a PC? Alternatively, has anyone come across this problem and has any possible solutions? Many thanks!

Andres Wokaty (15:42:25) (in thread): > You might be able to increase the time limit withoptions(timeout = 600)or higher.

Andres Wokaty (15:54:11): > I wanted to mention thathttps://support.bioconductor.org/is a good resource for Bioconductor questions.

Atuhurira Kirabo Kakopo (16:09:02) (in thread): > Thank you a tonne! It worked perfectly

Prisca Chidimma Maduka (23:30:23) (in thread): > Thank you@Andres Wokaty,thisalsohelpedme.

2022-10-14

Hervé Pagès (00:11:58) (in thread): > Alternatively, you can put this in your.Renvironfile: > > R_DEFAULT_INTERNET_TIMEOUT=600 >

Chinwe (10:41:05) (in thread): > I am looking forward to this. In the next 20 mins

Andres Wokaty (11:03:40): > Just a reminder that the Sweave2Rmd Overview is starting now:https://meet.jit.si/moderated/a957a5a386dd2fd24ed3d44d5c07f769d7cd16293f41eb2d423946ffe444adea - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

2022-10-15

Prisca Chidimma Maduka (04:14:18): > I’m gettingthiserrorwhenIrunR CMD buildonatarball > > 1 Test Suite :GenomeInfoDb RUnit Tests - 21 test functions, 1 error, 0 failuresERROR in test_seqlevelsStyle_Seqinfo: Error in download.file(url, destfile, quiet = TRUE) :cannot open URL '[ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/315/GCA_000002315.2_Gallus_gallus-4.0/GCA_000002315.2_Gallus_gallus-4.0_assembly_report.txt'](ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/315/GCA_000002315.2_Gallus_gallus-4.0/GCA_000002315.2_Gallus_gallus-4.0_assembly_report.txt')Test files with failing teststest_seqlevelsStyle.Rtest_seqlevelsStyle_SeqinfoError in BiocGenerics:::testPackage("GenomeInfoDb") :unit tests failed for package GenomeInfoDb >

Hervé Pagès (14:57:36) (in thread): > GenomeInfoDbcontains an extensive set of unit tests that do a lot of queries to NCBI FTP site. Unfortunately, these tests sometimes fail due to connectivity issues with the site. Try to runR CMD checkwith--no-teststo skip the unit tests. It’s not ideal, but it’s ok in this particular situation.

Prisca Chidimma Maduka (15:04:53) (in thread): > Okay. Thanksa lot.

2022-10-17

Maria Fiorio (14:15:59): > @Maria Fiorio has joined the channel

Maria Fiorio (14:17:18) (in thread): > Thanks!!

Maria Fiorio (14:20:13) (in thread): > Do you have a recording of this meeting? I could not attend but I am super curious to learn more about the project

Andres Wokaty (14:22:09) (in thread): > No, but I can share the slides from the meeting:https://docs.google.com/presentation/d/11PX1CWperCET_oDMM43KSTIhwsuTtuqAO1kgY7Pq96w/edit#slide=id.g168379e359d_0_26. I also did a lightening talk at Bioc2022 about it. I’ll see if I can find that.

Andres Wokaty (14:28:59) (in thread): > I guess the lightening talks aren’t available. Sorry about that:confused:

2022-10-18

Elendu Emmanuel (00:04:16): > Hi, everyone please I need your help. I get this error: Error in getOctD(x, offset, len) : invalid octal digit when I run R CMD check on my file.

gunjan agarwal (00:30:49): > @gunjan agarwal has joined the channel

Prisca Chidimma Maduka (03:16:09) (in thread): > Didyourunitonthetar.gzfilegeneratedafterR CMD build

Elendu Emmanuel (03:46:18) (in thread): > R CMD build didn’t generate any file for me at all

Prisca Chidimma Maduka (03:48:31) (in thread): > I’mguessingyou’reintheGenomeInfoDbfolderright?

Elendu Emmanuel (03:51:40) (in thread): > I think so. I don’t really know. How do I confirm if I am there.

Elendu Emmanuel (03:53:42) (in thread): > I just cloned it then create my file inside and then insert the code and edit it then ran R CMD build

Prisca Chidimma Maduka (04:01:29) (in thread): > pwdshouldtellyouwhichdirectoryyou’rein.Ifit’sGenomeInfoDbthenyouneedtocd ..beforerunningtheR CMD buildThegoalistobeoutsideGenomeInfoDbfoldersoyouthatyoucanhaveaccesstoitbecauseyouneedtorunonthefolderitself.R CMD build GenomeInfoDb

Prisca Chidimma Maduka (04:14:58) (in thread): > ButyoudoknowthatR CMD buildandR CMD checkcomesafteradhocmanualtesting,right?@Hervé PagèsspecifiedallthestepsweneedtofollowoneachopenissueonGitHub.Maybeyoushouldcheck itoutagain.

Elendu Emmanuel (04:57:42) (in thread): > Okay, thank you. Sorry how do I do that ad hoc manual testing?

Elendu Emmanuel (05:32:36) (in thread): > Please how do I install a file I have worked on locally to carry out the test

Elendu Emmanuel (05:54:52) (in thread): > I tried to build the GenomeInfoDb. I just want to know if I am on track - File (JPEG): IMG_20221018_105116.jpg

Elendu Emmanuel (06:37:12) (in thread): > Please how long does it take to install the GenomeInfoDb after editing the file because mine is taking hours

Elendu Emmanuel (06:52:39) (in thread): > Please how long does it take to install the GenomeInfoDb because mine is taking hours

Prisca Chidimma Maduka (07:18:02) (in thread): > Minetookawhile.Not hours though

Elendu Emmanuel (07:42:03) (in thread): > Okay, maybe I am doing something wrong

Elendu Emmanuel (10:22:10) (in thread): > Hi, I have successfully installed the edited GenomeInfo locally and tested the registered_NCBI_assemblies(“Xenopus tropicalis”) functionality which returns the correct data. But when I try this function getChromInfoFromNCBI(“UCB_Xtro_10.0”), an error saying: Error in function (type, msg, asError = True) : could not retrieve from host:ftp.ncbi.nlm.nih.gov. please what could be the reason?

Atuhurira Kirabo Kakopo (11:21:02) (in thread): > Hi@Prisca Chidimma Madukafor clarity, in which location did you fork your GenomeInfoDb folder to? I’m having a bit of an issue with running the R CMD build command as well.

Atuhurira Kirabo Kakopo (11:21:28) (in thread): > @Elendu EmmanuelI hope you were able to resolve your issue!

Elendu Emmanuel (11:37:53) (in thread): > Yeah, somehow. I am just having this error: Error in function (type, msg, asError = True) : could not retrieve from host:ftp.ncbi.nlm.nih.govwhen I run this getChromInfoFromNCBI(“UCB_Xtro_10.0”)

Prisca Chidimma Maduka (11:59:25) (in thread): > I don’t think it really matters which folder, but for me, placed it on my desktop for easy access. What issues are having ?

Prisca Chidimma Maduka (12:00:24) (in thread): > @Elendu Emmanuelhaveyou tried running it again? It might be connection issues.

Elendu Emmanuel (12:05:29) (in thread): > No, I will try it later. My laptop is down now. Thank you so much

Atuhurira Kirabo Kakopo (12:09:24) (in thread): > > * checking for file 'GenomeInfoDb/DESCRIPTION' ... OK > * preparing 'GenomeInfoDb': > * checking DESCRIPTION meta-information ... OK > Warning in file(con, "r") : > cannot open file 'man': No such file or directory > ERROR > computing Rd index failed:cannot open the connection >

Atuhurira Kirabo Kakopo (12:10:14) (in thread): > I keep running into that error each time I run R CMD build GenomeInfoDb. I have my folder in the home directory

Prisca Chidimma Maduka (12:25:27) (in thread): > @Atuhurira Kirabo KakopoI’msorry,I am not sure what the issue is. Hope you installed all the required packages and their dependencies?

Iman Linje (18:34:12): > @Iman Linje has joined the channel

2022-10-19

Elendu Emmanuel (05:41:44) (in thread): > Good morning. Please what is the output of sessionInfo() suppose to be?

Atuhurira Kirabo Kakopo (05:55:57): > Hi all, I’ve been unable to successfully run R CMD build via terminal. This has been my output. Any insights would be helpful, thanks! - File (PNG): Screenshot from 2022-10-19 12-53-28.png

Atuhurira Kirabo Kakopo (07:52:14) (in thread): > Hi@Elendu Emmanuelthis is the output of my sessionInfo(). Is yours anything similar? - File (PNG): Screenshot from 2022-10-19 14-50-33.png

Andres Wokaty (09:50:11) (in thread): > It would be helpful if you show what’s in your GenomeInfoDb. This error suggests that it’s missing themandirectory.

Atuhurira Kirabo Kakopo (11:12:50) (in thread): > I was able to solve the issue by deleting the initial package and cloning it again. I’m not sure what changed- perhaps I was missing several crucial files- but it seemed to work! Thank you!

Elendu Emmanuel (16:41:22) (in thread): > Yes, it is

Elendu Emmanuel (16:41:38) (in thread): > Thank you

Elendu Emmanuel (16:56:03) (in thread): > I just tried building now and I got this error: Error in loadvignetteBuilder(pkgdir, True) : vignette builder ‘knitr’ not found. Please what could be the issue?

Varsha Verma (17:27:51): > @Varsha Verma has joined the channel

Hervé Pagès (17:28:08) (in thread): > Hi@Elendu EmmanuelIt looks like you don’t have theknitrpackage. Make sure you have all dependencies installed, including suggested packages (i.e. packages listed in theSuggestsfield), before you runR CMD build.

Elendu Emmanuel (18:59:56) (in thread): > Okay, thank you sir. I will install that and try again

2022-10-20

Heather Turner (03:09:51): > @Heather Turner has joined the channel

2022-10-27

Beryl Kanali (16:25:48): > @Beryl Kanali has joined the channel

2022-11-01

Andres Wokaty (09:26:40): > Outreachy applicants, > > As the contribution comes to a close, please record your contributions and shift your focus on your final application. On the final application, please answer the following community questions: > > * Why are you applying to this project? > * What do you hope to get out of your participation? > > We appreciate your interest and wish you the best.

Halimat Chisom (10:15:58) (in thread): > @Haleema Sadia

2022-11-02

Chinwe (04:22:36) (in thread): > Thank you

2022-11-04

Andres Wokaty (09:59:14): > <!here>Please remember to submit your final applications if you have not yet done so today. Thanks again for participating in the contribution period with Bioconductor!

2022-11-22

Phylis Atieno (13:54:34): > Congratulations@Beryl Kanalifor being selected as an intern for the Bioconductor Project:partying_face::partying_face::partying_face:

2022-11-23

Beryl Kanali (08:42:53): > Thank you@Phylis Atieno

2023-01-21

Taofeeqat (07:04:25): > @Taofeeqat has joined the channel

Hien (16:03:26): > @Hien has joined the channel

2023-01-22

Laurent Gatto (05:25:23): > @Laurent Gatto has joined the channel

Kim-Anh Lê Cao (21:20:03): > @Kim-Anh Lê Cao has joined the channel

2023-02-07

Maria Doyle (06:30:29): > Check out the new blog post:writing_hand:written by our two fantastic Outreachy interns,@Beryl Kanalifrom Kenya and@Atuhurira Kirabo Kakopofrom Uganda on their Outreachy experiencehttps://bioconductor.github.io/biocblog/posts/2023-01-22-OutreachyInternship/ - Attachment (bioconductor.github.io): Bioconductor community blog - Our experience as Outreachy interns with Bioconductor > Bioconductor participated in the Outreachy Internship program for the December 2022 cohort. Our interns share their experience working on their various projects and bioconductor in general.

Daniel Adediran (11:48:53): > @Daniel Adediran has joined the channel

2023-02-18

KritikaVerma (06:54:41): > @KritikaVerma has joined the channel

2023-02-19

KritikaVerma (11:29:44): > Hi > I am Kritika Verma. I am currently majoring in Computer Science, Mathematical Innovation and minoring in Computational Biology. I was interested in contributing and working with Bioconductor for Outreachy and an open source experience because I am quiet fascinated by bioinformatics. > Thank you

mahamtariq58 (12:16:31): > @mahamtariq58 has joined the channel

2023-03-06

Tuomas Borman (10:40:21): > @Tuomas Borman has joined the channel

Madelyn Carlson (10:55:00): > Welcome, Outreachy applicants!:tada:My name is Madelyn, pronouns she/her. We’re excited for the contribution period to begin and to meet y’all. I have been working with Jen and Paul on the Sweave2Rmd project for some time and am available to answer questions you have about Sweave2Rmd contribution tasks

Madelyn Carlson (10:55:01): > Here is the link to guidance for thefirst contribution taskand thesecond (optional) contribution task. Also,between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions.These sessions are optional - feel free to pop if it’s useful. Dates/times include: > * Wednesday, March 8, 11-11:45AM ET (Zoom link) > * Thursday, March 16, 10-10:45AM ET (Zoom link) > * Wednesday, March 22, 11-11:45AM ET (Zoom link) > * Thursday, March 30, 10-10:45AM ET (Zoom link) > Please let us know if these times do not work for you and we can adjust. & Again, welcome everyone! Happy that you’re here - Attachment: #62 Sweave2Rmd Knowledge Check - Attachment: #63 Replace a Sweave Vignette With an R Markdown Vignette

Zainab Ashimiyu-Abdusalam (12:30:53): > @Zainab Ashimiyu-Abdusalam has joined the channel

Reece (16:18:30): > @Reece has joined the channel

Reece (16:23:47): > Hi everyone I am Reece , an Outreachy applicant for the May cohort , and I am very excited to learn from and contribute towards the Bioconductor community! Looking forward to the journey ahead!:innocent:Interested in particularly the Convert Sweave Vignettes to RMarkdown project@Andres Wokaty@Paul Villafuerte@Tuomas Borman@Madelyn Carlson

Kayla Okereke (16:31:58): > @Kayla Okereke has joined the channel

khadijah (21:13:58): > @khadijah has joined the channel

khadijah (21:14:36): > Hi happy to be here,

khadijah (22:01:42): > 1. Hello mentors according to the article on how to contribute we are supposed to select a vignette on the project board, and set theStatustoIn Progress. Also, write your GitHub username underAssignedand setLast Modifiedto today. But i am unable to edit the project board

Andres Wokaty (23:10:45) (in thread): > I can do it for you. Can you make the comment about what vignette you would like to do in the issue itself so we can keep track there?

Vivian Ginikachukwu Ikeh (23:18:51): > @Vivian Ginikachukwu Ikeh has joined the channel

2023-03-07

Reece (00:15:32): > Heylo@Andres Wokaty@Madelyn Carlson@Paul VillafuerteWould like to know what time zones you are in for better communication time sync?

Aayushi Chauhan (01:42:32): > @Aayushi Chauhan has joined the channel

khadijah (02:05:09) (in thread): > Thank you ma here is it : genefilter/vignettes/howtogenefilter.Rnw

khadijah (02:05:59) (in thread): > I have also cloned and fork the repository , my github is Khadeeejah

Monalika Patnaik (02:37:38): > @Monalika Patnaik has joined the channel

Sonali Kumari (02:46:14): > @Sonali Kumari has joined the channel

Patricia Brianna (03:04:17): > @Patricia Brianna has joined the channel

Patricia Brianna (03:05:17): > wonderful to be here with everyone. let us make contributions together and change the world

Esther (03:15:06): > @Esther has joined the channel

Ameerah Kabir (03:35:00): > @Ameerah Kabir has joined the channel

Ameerah Kabir (03:35:46): > Hi Everyone! I am Ameerah Kabir, from Nigeria, a contributing intern from Outreachy internship. I can’t wait to make an impact. Thank youu.

Aayushi Singh (04:32:27): > @Aayushi Singh has joined the channel

Busayo Ojo (04:38:57): > @Busayo Ojo has joined the channel

Petrah (07:12:06): > @Petrah has joined the channel

Emmanuel Taiwo devbird007 (07:56:17): > @Emmanuel Taiwo devbird007 has joined the channel

Emmanuel Taiwo devbird007 (07:59:41) (in thread): > Hello@Andres WokatyI would like to work on: > genefilter/vignettes/howtogenefinder.Rnw > > Since I am unable to edit the Project Board myself.

khadijah (08:00:38) (in thread): > hi@Emmanuel Taiwo devbird007thats the same task i picked you can pick something else, there are lots of task on the board

Emmanuel Taiwo devbird007 (08:01:12) (in thread): > There’s a difference@khadijahgenefilter is different from mine which is genefinder.

Emmanuel Taiwo devbird007 (08:01:53) (in thread): > Really no need to be combative you know

Sreeyusha Vajinapally (08:17:59): > @Sreeyusha Vajinapally has joined the channel

khadijah (08:26:05) (in thread): > i was only pointing it out incase you dint see mine cuz you responded under the same thread and you even edited your message, i knew what i saw, nobody is combative, everybody is meant to work together

Emmanuel Taiwo devbird007 (08:29:54) (in thread): > I just edited my message now because I was having a problem with forking the repository and thought I would need to ask a question. But this isn’t worth fighting over. I think we should be more cooperative and focused on the project

Richard Dushime (08:40:00): > @Richard Dushime has joined the channel

Andres Wokaty (08:46:18) (in thread): > Please keep these requests on the the issue athttps://github.com/Bioconductor/sweave2rmd/issues/63so that they can be more easily managed. - Attachment: #63 Replace a Sweave Vignette With an R Markdown Vignette > Hello Outreachy applicants! > > Note: This task can be completed by multiple Outreachy applicants. Please choose this as your second (optional) contribution task to the Bioconductor Sweave2Rmd project as it builds upon the familiarity quiz in the Sweave2Rmd first contribution. > > Prep Work > > • Sweave2Rmd Knowledge Check > • Please read our contribution document, which gives a good overview of the project plus the general workflow. In particular, you will be performing the tasks from <https://bioconductor.github.io/sweave2rmd/articles/contribute.html#create-the-r-markdown–rmd-vignette-and-remove-the-sweave-vignette–rnw|Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw)>. > • Install pandoc > > Contribution Task > > Make a pull request replacing a Sweave vignette with an R Markdown vignette. > > 1. Select a vignette from our project board that is labeled ‘Easy’ or ‘Medium’, set to ‘Todo’ and are unassigned. > 2. Write a comment with the path of the vignette you’d like to do–e.g., BiocParallel/vignettes/Introduction_To_BiocParallel.Rnw to @Bioconductor/sweave2rmd. We will write your GitHub username as ‘Assigned’ and set ‘Last Modified’ to today. > 3. Perform the steps in <https://bioconductor.github.io/sweave2rmd/articles/contribute.html#create-the-r-markdown–rmd-vignette-and-remove-the-sweave-vignette–rnw|Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw)>. Note: You do not need to contact the maintainers to work on this set of vignettes as they have either been previously contacted OR they are maintained by the Bioconductor Core Team. > 4. Make sure that you request a review by writing @Bioconductor/sweave2rmd in a comment so that we can review your pull request. For example, @Bioconductor/sweave2rmd please review my contribution for Outreachy. > 5. If you receive any feedback requesting changes, please address them. > > Tip: You can find the PDF you’ll be replacing by visiting the landing page for the package under Documents. You can look up the package at <https://bioconductor.org/packages/devel/BiocViews.html#___Software|Bioconductor Software Packages>.
> Tip: You can read how we <https://bioconductor.github.io/sweave2rmd/articles/contribute.html#review-a-pull-request|review PRs> in the contribution document. Use the checklist to assess if your PR will pass review. > > If your pull request is good, it will be merged into Bioconductor! > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/convert-sweave-vignettes-to-r-markdown/contributions/.

Sweta Kumari (08:57:37): > @Sweta Kumari has joined the channel

khadijah (09:02:31) (in thread): > @Andres Wokatyare you saying i should leave a comment under this issue with the vignette i am working on?

Andres Wokaty (09:03:43) (in thread): > Yes, please leave a comment in that issue. This way other applicants and other sweave2rmd team members can see it.

khadijah (09:04:47) (in thread): > noted ma, thank you

Aliyu Atiku Mustapha (09:12:26): > @Aliyu Atiku Mustapha has joined the channel

Aliyu Atiku Mustapha (09:14:03): > Hi all, I am Aliyu Mustapha from Nigeria, an intern from Outreachy here to contribute on any project involving R or RMarkdown. Will appreciate a little guidance on how to proceed. Thank you.

Violet Akpeh (09:14:05): > @Violet Akpeh has joined the channel

Violet Akpeh (09:16:17): > Hello Everyone, My name is Violet. I just got accepted into the contribution stage of Outreachy

Violet Akpeh (09:17:05): > I want to find out if I can pick any issue to work on or they are supposed to be assigned by the mentors

Barakat Dindi (09:19:15): > @Barakat Dindi has joined the channel

Madelyn Carlson (09:21:29) (in thread): > hi there - Eastern Time

Madelyn Carlson (09:23:20) (in thread): > Excited for you to be here! Please let us know if you have any questions about the Sweave2Rmd contribution tasks

Madelyn Carlson (09:24:36) (in thread): > Welcome, it’s great to meet you!:wave:

Madelyn Carlson (09:26:38) (in thread): > Welcome, Aliyu - great to meet you. You can find guidance on completing the first contribution taskhere. Once finished, you have the option of working on a (optional) second contribution,guidance here. Please let us know if you have questions! - Attachment: #62 Sweave2Rmd Knowledge Check - Attachment: #63 Replace a Sweave Vignette With an R Markdown Vignette

Madelyn Carlson (09:30:20) (in thread): > Welcome Violet, great to e-meet you. After completing the first contribution task (instructions in issue linked here), you may work on asecond (optional) contributionin which you select a vignette to convert from the project board and post comment onthis issueto claim it. We will respond to your comment on the issue and update the project board accordingly - Attachment: #62 Sweave2Rmd Knowledge Check - Attachment: #63 Replace a Sweave Vignette With an R Markdown Vignette

Madelyn Carlson (09:30:30) (in thread): > Please let us know if you have any questions

Madelyn Carlson (09:31:46) (in thread): > accidentally commented my answer to your question in your previous post. Please see thread to your post (above) for my response. Let me know if you have any questions!

Reece (09:33:50) (in thread): > Thank you

Sreeyusha Vajinapally (09:34:58): > Hello@Andres Wokaty@Paul Villafuerte@Tuomas Borman@Madelyn Carlson

Madelyn Carlson (09:37:51): > GM all - excited to meet all of you! For those of you who are interested in getting started on Sweave2Rmd contribution tasks, please start with the first contribution task (instructions here). Once completed, you have the option of then starting thesecond (optional) contribution taskwhere you claim a vignette from the project board and convert it. The first contribution task is designed as a ramp to the second task, which is why we ask that you work on them sequentially. Please let us know if you have questions:relaxed: - Attachment: #62 Sweave2Rmd Knowledge Check - Attachment: #63 Replace a Sweave Vignette With an R Markdown Vignette

Violet Akpeh (09:42:04) (in thread): > thank you

Sonali Kumari (10:29:56): > Thank you so much@Madelyn Carlsonon the way to complete the first contribution task .

Ameerah Kabir (10:34:57): > Hi@Madelyn CarlsonI am interested in the Microbiome Study Curation contribution project, I am yet to see information about it, I would love to know if it is still available?

Madelyn Carlson (10:37:16) (in thread): > Hi Ameerah, glad that you reached out. You can find more details about that project in the#bugsigdbSlack channel. Please let me know if you have any challenges finding/joining the channel. The two project leads are available there for any questions you may have

Ufuoma Ejite (10:45:36): > @Ufuoma Ejite has joined the channel

Ufuoma Ejite (10:47:14): > Hello everyone!:blush:I’m super-excited to be here. > I’m looking forward to contributing to the Microbiome Study Curation project

Madelyn Carlson (10:51:41) (in thread): > Amazing! Join the#bugsigdbSlack channel for more information about the Microbiome Study Curation project. The project leads there can answer any questions you may have about the contribution tasks

Maryam Gbemisola (10:59:37): > @Maryam Gbemisola has joined the channel

Evan Chinny (11:07:53): > @Evan Chinny has joined the channel

Evan Chinny (11:13:39): > Hi everyone, > I’m excited to be here! My name is Ella Jessica.

Shravani Nag (11:51:28): > @Shravani Nag has joined the channel

Ameerah Kabir (13:56:53) (in thread): > Perfect. Thank you so much.

Tuomas Borman (14:19:24): > Hello all, I’m Tuomas, one of the mentors. I live in Finland, the home land of santa claus (https://santaclausvillage.info/) Instead of making toys for children, I’m working in the miaverse team whose developing tools for microbiome analytics. > > Nice to have new contributors; I’m happy to help if you have any questions about the project (I try to answer as soon as possible but sometimes I’m little bit busy) - Attachment (Santa Claus Village Rovaniemi Finland): Santa Claus Village in Rovaniemi in Lapland Finland Arctic Circle > Santaclausvillage.info: Welcome to official web site of Santa Claus Village in Rovaniemi in Lapland Finland – Arctic Circle | home of Father Christmas / Joulupukki

Madelyn Carlson (14:49:27) (in thread): > Welcome Ella, great to e-meet you! Let us know if you have any questions about the Sweave2Rmd project. & You can find more information about the Microbiome Study Curation project on the#bugsigdbSlack channel

Ibizugbe Merit (15:14:22): > @Ibizugbe Merit has joined the channel

Ibizugbe Merit (15:15:28): > Hello everyone,so excited to be here.I’mMerit Ibizugbe..I’mopen to contributing and learning

Monalika Patnaik (15:24:42): > Hello everyone:wave:Myself Monalika, an outreachy applicant from Delhi, India. would love to make valuable contributions in the project and looking forward to assist and learn from other fellow developers:blush:

irem Kahveci (15:47:03): > @irem Kahveci has joined the channel

Caroline Shi (22:05:39): > @Caroline Shi has joined the channel

2023-03-08

Unyime William (01:15:03): > @Unyime William has joined the channel

MaryJones (01:31:43): > @MaryJones has joined the channel

Leo Lahti (02:07:23): > @Leo Lahti has joined the channel

Atrayee Samanta (02:24:27): > @Atrayee Samanta has joined the channel

Rukky (02:34:09): > @Rukky has joined the channel

Sonali Kumari (02:44:17): > Hello@Tuomas Bormani am getting this error while using this code > > pandoc -f latex -t markdown file.Rnw -o file.Rmd > # Replace file.Rnw and file.Rmd with the name of the vignette you're converting > > I have followed all the steps written in contribute file - File (PNG): 2023-03-08.png

Tuomas Borman (03:09:26) (in thread): > Hello!@Madelyn Carlsoncan probably answer better, but my best guess is that there is an extra space and line at the end of the file –> “unexpected end of the file”… and that arrow thingy there > > Remove line 554 and try again

Sonali Kumari (03:14:51) (in thread): > ohk thanks for the reply

Sonali Kumari (03:18:23) (in thread): > got the same error after removing line no 554 also@Madelyn Carlsonplease clarify if you know the reason

Palak Tahlyani (03:31:13): > @Palak Tahlyani has joined the channel

Palak Tahlyani (03:47:58): > Hey everyone, Great to be here.Starting with my first contribution to this project.

Reece (03:58:45) (in thread): > @Sonali Kumarihave you tried to > 1. Check that you have installed pandoc correctly and that it is included in your system’s PATH. You can do this by running “pandoc –version” in the terminal to confirm that it is installed and accessible > 2. Make sure that the input file (file.Rnw) exists in the specified directory and that the name is spelled correctly. Similarly, ensure that the output file (file.Rmd) does not already exist in the directory or that you have write permissions to overwrite it. > 3. also check that you a running the command in the top level directory /correct point

Sonali Kumari (04:04:02) (in thread): > ohk thanks

Treasure Okafor (05:34:16): > @Treasure Okafor has joined the channel

Ufuoma Ejite (05:38:39) (in thread): > Thank you@Madelyn Carlson:blush:

Sonali Kumari (07:05:31) (in thread): > @Madelyn Carlsonissue still not solved please guide me how to overcome and get ahead

Levi Waldron (08:33:37): > @Levi Waldron has joined the channel

Andres Wokaty (08:42:19) (in thread): > Usually when this happens, there’s a problematic chunk of code somewhere. One way to deal with this is to try removing increments of code blocks until running pandoc is successful. Then at least I’ve identified the problem part. Once you identify the problem code block, leave it out of the .Rnw, run pandoc, then add it back in manually to the .Rmd.

Reece (08:43:56) (in thread): > thanks@Andres Wokatythis is insightful for debugging:slightly_smiling_face:

Sonali Kumari (09:08:12) (in thread): > ohk@Andres Wokatythank you !

Andres Wokaty (09:12:06): > Hi, I’m Jen. My pronouns are they/them. I’m one of the coordinators for Bioconductor along with@Maria Doyle. > > Thanks, everyone for your interest and enthusiasm. I wanted to give a short breakdown of our projects, mentors, and related channels. > > * A few mentors and community members are on this channel to answer general questions about Bioconductor, Outreachy, R, etc. > * Microbiome Study Curation (aka bugsigdb) is mentored by@Fatima Zohraand@C. Mirzayi (please do not tag this account)on#bugsigdb* Convert Sweave Vignettes to R Markdown (aka sweave2rmd) is mentored by@Andres Wokatyand@Paul Villafuerteon#sweave2rmdand supported by@Madelyn Carlsonour wonderful teammate > * Optimize microbiome data science framework is mentored by@Tuomas Bormanon#miaverse

Fatima Zohra (09:12:14): > @Fatima Zohra has joined the channel

C. Mirzayi (please do not tag this account) (09:12:15): > @C. Mirzayi (please do not tag this account) has joined the channel

Madelyn Carlson (09:16:19) (in thread): > ^^ appreciate you@Andres Wokaty!

Madelyn Carlson (09:19:18): > As a reminder, we are hosting the Sweave2Rmd-Outreachy office hour at 11-11:45AM ET today (Zoom link). This will be time where we explain the project and answer questions about the contribution tasks. If you’re unable to make it, no worries - we have another office hour session next week on Thursday, March 16, 10-10:45AM ET (and sessions each week for the 2 weeks after) and I will try my best to remember to record the session today and post it on this channel. Talk soon!

Namusisi Sharon (09:58:08): > @Namusisi Sharon has joined the channel

Emmanuel Taiwo devbird007 (10:10:03) (in thread): > Thank you, looking forward to it

Shallie (10:33:34): > @Shallie has joined the channel

Job David (11:14:53): > @Job David has joined the channel

Job David (12:07:06): > Hello everyone, I am David from Nigeria, I look forward to contributing to the sweave2rmd project, please can anyone tell me how to get started on it??

Maria Doyle (12:36:49) (in thread): > I was going to suggest asking that in the#sweave2rmdchannel but I see you already did:slightly_smiling_face:

Job David (12:37:35) (in thread): > Yeah thanks:pray:

Fortune Nnamdi (15:02:17): > @Fortune Nnamdi has joined the channel

Patricia Brianna (15:20:46) (in thread): > thanks everyone, so how do i get started

Andres Wokaty (15:30:15) (in thread): > I think it depends on what project you’re interested in.

Madelyn Carlson (16:04:09) (in thread): > hi hi welcome, great to meet you! Our Sweave2RmdContribute articlecontains guidance on about the project and steps to contribute to it. If you’re interested in learning more about the contribution tasks -here is a linkto issues pg detailing instructions for the first contribution task and alink to the second one. Please let me know if you have any other questions! - Attachment (bioconductor.github.io): Contribute > Learn how to contribute to our project. - Attachment: #62 Sweave2Rmd Knowledge Check - Attachment: #63 Replace a Sweave Vignette With an R Markdown Vignette

Madelyn Carlson (16:10:59): > For those of you who couldn’t make it to our first office hour for the Sweave2Rmd project,here is a recording of our discussion****.****Feel free to check it out and hear the questions we discussed. You can also tune in to our next office hour session on Thursday March 16, 10-10:45AM ET (Zoom link). After that the following sessions include: > * Wednesday, March 22, 11-11:45AM ET (Zoom link) > * Thursday, March 30, 10-10:45AM ET (Zoom link) > Please let us know if these times do not work for you - we are happy to adjust.

OLADIRAN OLUWASHOLA (18:03:29): > @OLADIRAN OLUWASHOLA has joined the channel

2023-03-09

Emmanuel Taiwo devbird007 (03:17:29) (in thread): > Thank you for the recording.

Ukpai Bishop (03:19:58): > @Ukpai Bishop has joined the channel

khadijah (04:16:34): > good morning@Paul Villafuerte@Andres Wokatyi am experiencing this error in my terminal while trying to install the package, - File (PNG): Screenshot 2023-03-09 at 10.15.28.png

Tuomas Borman (04:21:23) (in thread): > Hi, it seems that you are in terminal “$” –> try to run the code in R session instead

rohitsatyam102 (04:21:26): > @rohitsatyam102 has joined the channel

Reece (04:26:11) (in thread): > it was a great session

irem Kahveci (04:26:12) (in thread): > I solved the same problem on Mac by downloading via R. Do you want to download the package for R, which is in a base like a server?

khadijah (04:27:18) (in thread): > How do I run it in the R session terminal

irem Kahveci (04:29:50) (in thread): > > if (!require("BiocManager", quietly = TRUE)) > install.packages("BiocManager") > BiocManager::install() > > I just tried again, it works

rohitsatyam102 (04:31:12): > Hello everyone. I am Rohit Satyam from India (soon to be PhD student at KAUST in fall 2023). I am an Outreachy applicant and I am looking forward to contribute to#sweave2rmdproject and if time allows to#miaverseas well.

khadijah (04:32:15) (in thread): > I should Cd out of this folder

khadijah (04:33:32) (in thread): > @irem KahveciI’ll try this and let you know if it works

khadijah (04:34:59) (in thread): - File (PNG): Screenshot 2023-03-09 at 10.34.23.png

khadijah (04:34:59) (in thread): > the command acted like it worked, then i tried to knit and i got this error

irem Kahveci (04:35:32) (in thread): > I see

irem Kahveci (04:36:04) (in thread): > ı will sent example

khadijah (04:36:18) (in thread): > thank you very much, i am expecting

irem Kahveci (04:38:25) (in thread): - File (PNG): Screenshot 2023-03-09 at 12.36.20.png

Fortune Nnamdi (05:10:46) (in thread): > You’re welcome:innocent:

khadijah (05:48:54) (in thread): > what country should i select

khadijah (05:49:00) (in thread): - File (PNG): Screenshot 2023-03-09 at 11.48.33.png

irem Kahveci (06:16:25) (in thread): > Maybethis sourcewill help you

Chioma Grace (06:29:00): > @Chioma Grace has joined the channel

K Nodia (08:05:04): > @K Nodia has joined the channel

Aditi Singh (09:14:14): > @Aditi Singh has joined the channel

Andres Wokaty (09:15:14) (in thread): > Although I can’t see all of the message, I am guessing that the country selection is about choosing a mirror for download. You should choose the mirror in the country closest to you for a shorter download time.

Madelyn Carlson (12:25:44): > FYI for those of you who hadn’t already seen, more vignettes were added to theproject boardfor the second contribution

Andres Wokaty (16:29:59) (in thread): > The error you’re having athttps://community-bioc.slack.com/archives/C037LN1HQDB/p1678354499256359?thread_ts=1678353394.784029&cid=C037LN1HQDBis because you don’t have the package Biobase installed. If your package is genefilter, you can try installing it withBiocManager::install("genefilter"). BiocManager will try to install any dependencies for the package you’re trying to install so it will try to install Biobase for you.

khadijah (21:27:45) (in thread): > thank you so much@Andres Wokatyi ran the command it worked, however i tried to knit and i got this error in my terminal. Knitting was successful tho - File (PNG): Screenshot 2023-03-10 at 03.26.43.png

Andres Wokaty (23:06:31) (in thread): > I’m glad it successfully knitted. It’s not clear where the error is coming from. When you’re ready to submit your PR, I would make a note of it in the comments so that your reviewer can see if they’re getting the same error. I would include the error message, how you got it, what steps you took to resolve it, etc.

Aguobi Amara (23:10:50): > @Aguobi Amara has joined the channel

2023-03-10

Busayo Samuel (she/her) (03:56:08): > @Busayo Samuel (she/her) has joined the channel

Dennis Ndubi (04:26:15): > @Dennis Ndubi has joined the channel

khadijah (05:34:03) (in thread): > thank you@Andres Wokatyi have made a pull requesthttps://github.com/Bioconductor/genefilter/pull/11. I would appreciate your feedback. - Attachment: #11 Bioconductor/sweave2rmd: Conversion of howtogenefilter.Rnw to Rmd > @Bioconductor/sweave2rmd
> My name is Khadijah an Outreachy applicant. I was assigned this issue on the project board, > > @jwokaty Kindly review my PR. > > HTML
> PDF

khadijah (05:34:58) (in thread): > can you assign this task to me , i want to challenge myself morehttps://github.com/orgs/Bioconductor/projects/2/views/6?pane=issue&itemId=22088069

sophy (08:54:43): > @sophy has joined the channel

Ukpai Bishop (11:48:36): > Hello everyone please is there a deadline for the first contribution task

Madelyn Carlson (11:49:24) (in thread): > Great question, no there is no deadline for the first contribution task as long as it is done within the contribution period

Ukpai Bishop (11:50:02) (in thread): > Ok thank you very much

khadijah (15:07:25) (in thread): > @Andres Wokaty

Andres Wokaty (15:14:37) (in thread): > Did you finish the genefilter vignette? If you finished it, please put a link to your PR inhttps://github.com/Bioconductor/sweave2rmd/issues/63so we can update the board. Everyone has to finish the review on their first PR before getting another assignment. Because no one has done a perfect PR, I am recommending that everyone review their PR using the checklist at the bottom of the contribution document. This may reduce the amount of work you need to do during the review. - Attachment: #63 Replace a Sweave Vignette With an R Markdown Vignette > Hello Outreachy applicants! > > Note: This task can be completed by multiple Outreachy applicants. Please choose this as your second (optional) contribution task to the Bioconductor Sweave2Rmd project as it builds upon the familiarity quiz in the Sweave2Rmd first contribution. > > Prep Work > > • Sweave2Rmd Knowledge Check > • Please read our contribution document, which gives a good overview of the project plus the general workflow. In particular, you will be performing the tasks from <https://bioconductor.github.io/sweave2rmd/articles/contribute.html#create-the-r-markdown–rmd-vignette-and-remove-the-sweave-vignette–rnw|Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw)>. > • Install pandoc > > Contribution Task > > Make a pull request replacing a Sweave vignette with an R Markdown vignette. > > 1. Select a vignette from our project board that is labeled ‘Easy’ or ‘Medium’, set to ‘Todo’ and are unassigned. (As a FYI, although there is no maximum # of vignettes you’re allowed to convert, project leads must review everyone’s first PR before we are able to assess any additional vignettes from anyone contributing to the project). > 2. Write a comment with the path of the vignette you’d like to do–e.g., BiocParallel/vignettes/Introduction_To_BiocParallel.Rnw. We will write your GitHub username as ‘Assigned’ and set ‘Last Modified’ to today. > 3. Perform the steps in <https://bioconductor.github.io/sweave2rmd/articles/contribute.html#create-the-r-markdown–rmd-vignette-and-remove-the-sweave-vignette–rnw|Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw)>. Note: You do not need to contact the maintainers to work on this set of vignettes as they have either been previously contacted OR they are maintained by the Bioconductor Core Team. > 4. Make sure that you request a review by writing @Bioconductor/sweave2rmd in a comment so that we can review your pull request. For example, @Bioconductor/sweave2rmd please review my contribution for Outreachy. > 5. Make a comment in this issue with a link to your PR. > 6. If you receive any feedback requesting changes, please address them. > > Tip: You can find the PDF you’ll be replacing by visiting the landing page for the package under Documents. You can look up the package at <https://bioconductor.org/packages/devel/BiocViews.html#___Software|Bioconductor Software Packages>.
> Tip: You can read how we <https://bioconductor.github.io/sweave2rmd/articles/contribute.html#review-a-pull-request|review PRs> in the contribution document. Use the checklist to assess if your PR will pass review. > > If your pull request is good, it will be merged into Bioconductor! > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/convert-sweave-vignettes-to-r-markdown/contributions/.

Madelyn Carlson (15:36:26): > FYI for those of you who completed the knowledge check quiz, I will be emailing you a copy of your completed form so that you can refer back to it / use for your final Outreachy application if you choose to submit application for our Sweave2Rmd project.

khadijah (15:42:13) (in thread): > okay thank you, i will review my pr and i have also dropped a comment under the issue

Ukpai Bishop (15:45:43): > Hi@Madelyn CarlsonI can’t complete my knowledge check quiz because there is no open issue in the project board

Madelyn Carlson (15:47:22) (in thread): > For the knowledge check quiz, you can select a vignette that has already been claimed in order to answer the YAML question (because you’re not actually making any changes to the vignette). You’ll just need to select a vignette that’s unclaimed by anyone else for the second contribution task

Ukpai Bishop (15:48:03) (in thread): > Ohh. I did not know about this

Madelyn Carlson (15:48:38) (in thread): > Let us know if you have any other questions!

Ukpai Bishop (15:49:50) (in thread): > Some of the vignette does not have a github repo url

Madelyn Carlson (15:50:55) (in thread): > you can locate the other vignettes by searching the package name in Github and then looking in the “vignettes” folder for the file with the correct name

Madelyn Carlson (15:51:07) (in thread): > The URLs are for vignettes with a PR

Ukpai Bishop (16:32:55) (in thread): > Ok thank you

Madelyn Carlson (17:50:51) (in thread): > Np!

2023-03-11

Muluh (02:00:42): > @Muluh has joined the channel

Muluh (02:03:47): > Hello, I am Daena. I am excited about working on this project “Convert Sweave Vignettes to R Markdown”. My pronouns are she/her.

Dennis Ndubi (02:09:12): > welcome@Muluhjoin the#sweave2rmdchannel and incase of any challenge or suggestion feel free to communicate it here.. the community is here for you

Hannah Honda (02:25:19): > @Hannah Honda has joined the channel

Hannah Honda (02:38:29): > Hi everyone! My name is Hannah, an Outreachy applicant for the May cohort and I am really excited to learn and contribute towards the Bioconductor community! I started looking through the Prep work and am looking through Microbiome Study Curation instructions on Github. I’m wondering if I’m misunderstanding the instructions, but the gist seems to be to watch the videos, read through the paper sections to gain understanding about the background, methods, and get acquainted with the study materials? and then start contributing by completing the qualtrics link? Did I miss something?

Busayo Ojo (04:51:56) (in thread): > Yes, you’re right

Busayo Ojo (04:53:11) (in thread): > Are you on the#bugsigdbchannel?

Ibizugbe Merit (06:51:16) (in thread): > You’rewelcome@Hannah Hondajoin the#bugsigdbchannel…You’dget a clear instruction there

Hannah Honda (06:53:03) (in thread): > I missed that channel. Thank you for the guidance!

Ibizugbe Merit (06:58:01) (in thread): > You’rewelcome@Hannah Honda

MaryJones (08:25:14): > @Andres Wokaty:

MaryJones (08:37:33): > @Andres Wokaty: Hello everyone ,I copied the codes as it is but yet I get this error in RStudio. Here is the screenshots and pandoc, rmarkdown and TinyTeX is installed , please any suggestions or is there anything I am missing ?,thank you all,:pray: - File (PNG): pandoc issue in Rstudio at 3.16.38 PM.png - File (PNG): pandoc issue 2 at 3.30.21 PM.png

Andres Wokaty (10:01:57) (in thread): > I am guessing that you are in the top directory of the package. The error says it can’t find it Chromband.Rnw. The .Rnw files should be in the vignettes directory. Correct the path to the file or go into the vignettes directory before running the command again.

MaryJones (10:19:17) (in thread): > @Andres Wokaty: Ok, I do as instructed , thank you all.:pray:

khadijah (11:34:47) (in thread): > hi@Andres Wokatythe project board has not been updated with my pull request

Ukpai Bishop (14:55:33): > Hello everyone, I tried to run the command below > > pandoc -f latex -t markdown Rsamtools-Overview.Rnw -o Rsamtools-Overview.Rmd > > In VScode, after forking and cloning the repository, I got this error message > > Error at "Rsamtools-Overview.Rnw" (line 554, column 2): > unexpected end of input > > Does anybody have a possible solution? Thank you.

2023-03-12

Andres Wokaty (01:10:31) (in thread): > Sometimes when we use pandoc, we get these vague ‘unexpected end of input’ messages. To troubleshoot these, we usually try remove a block at a time until we find the problem spot, which we omit, so we can run pandoc then we add back in the problem spot manually using R Markdown. Pandoc seems to have an issue with the#$at the end of line 537: > > slxMaq09 <- sub(".bai$", "", slxMaq09.bai) #$ > > I would remove#$then try running pandoc.#is the start of a comment in R so I don’t think you have to add anything back in.

Andres Wokaty (08:34:14) (in thread): > Did you request to work on this vignette inhttps://github.com/Bioconductor/sweave2rmd/issues/63? - Attachment: #63 Replace a Sweave Vignette With an R Markdown Vignette > Hello Outreachy applicants! > > Note: This task can be completed by multiple Outreachy applicants. Please choose this as your second (optional) contribution task to the Bioconductor Sweave2Rmd project as it builds upon the familiarity quiz in the Sweave2Rmd first contribution. > > Prep Work > > • Sweave2Rmd Knowledge Check > • Please read our contribution document, which gives a good overview of the project plus the general workflow. In particular, you will be performing the tasks from <https://bioconductor.github.io/sweave2rmd/articles/contribute.html#create-the-r-markdown–rmd-vignette-and-remove-the-sweave-vignette–rnw|Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw)>. > • Install pandoc > > Contribution Task > > Make a pull request replacing a Sweave vignette with an R Markdown vignette. > > 1. Select a vignette from our project board that is labeled ‘Easy’ or ‘Medium’, set to ‘Todo’ and are unassigned. (As a FYI, although there is no maximum # of vignettes you’re allowed to convert, project leads must review everyone’s first PR before we are able to assess any additional vignettes from anyone contributing to the project). > 2. Write a comment with the path of the vignette you’d like to do–e.g., BiocParallel/vignettes/Introduction_To_BiocParallel.Rnw. We will write your GitHub username as ‘Assigned’ and set ‘Last Modified’ to today. > 3. Perform the steps in <https://bioconductor.github.io/sweave2rmd/articles/contribute.html#create-the-r-markdown–rmd-vignette-and-remove-the-sweave-vignette–rnw|Create the R Markdown (.Rmd) vignette and Remove the Sweave vignette (.Rnw)>. Note: You do not need to contact the maintainers to work on this set of vignettes as they have either been previously contacted OR they are maintained by the Bioconductor Core Team. > 4. Make sure that you request a review by writing @Bioconductor/sweave2rmd in a comment so that we can review your pull request. For example, @Bioconductor/sweave2rmd please review my contribution for Outreachy. > 5. Make a comment in this issue with a link to your PR. > 6. If you receive any feedback requesting changes, please address them. > > Tip: You can find the PDF you’ll be replacing by visiting the landing page for the package under Documents. You can look up the package at <https://bioconductor.org/packages/devel/BiocViews.html#___Software|Bioconductor Software Packages>.
> Tip: You can read how we <https://bioconductor.github.io/sweave2rmd/articles/contribute.html#review-a-pull-request|review PRs> in the contribution document. Use the checklist to assess if your PR will pass review. > > If your pull request is good, it will be merged into Bioconductor! > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/convert-sweave-vignettes-to-r-markdown/contributions/.

Ukpai Bishop (08:36:58) (in thread): > It’s for my knowledge check. And beside somebody have made a request already

Andres Wokaty (08:37:37) (in thread): > Ok, fair enough.

khadijah (09:05:34): > @Andres Wokatythe project board has not been updated with my pr:pleading_face:

Andres Wokaty (09:06:19) (in thread): > Ishttps://github.com/Bioconductor/genefilter/pull/11your pr? - Attachment: #11 Bioconductor/sweave2rmd: Conversion of howtogenefilter.Rnw to Rmd > @Bioconductor/sweave2rmd
> My name is Khadijah an Outreachy applicant. I was assigned this issue on the project board, > > @jwokaty Kindly review my PR. > > HTML
> PDF

khadijah (09:09:07) (in thread): > Yes ma

Andres Wokaty (09:09:23) (in thread): > I updated the board yesterday

Taofeekat Olorunkosebi (20:56:46): > @Taofeekat Olorunkosebi has joined the channel

2023-03-13

Suwaibat Suleiman (03:59:41): > @Suwaibat Suleiman has joined the channel

Parul Chaddha (08:56:30): > @Parul Chaddha has joined the channel

Andres Wokaty (11:37:48): > Hi everyone, welcome to the second contribution week. Please remember to ask questions on the public project channels. Your questions might be answered quicker and you’re likely helping someone who might be afraid to ask. Thanks to everyone who’s answering questions! I know this can be a really stressful period for everyone, but let’s try to enjoy it ;)

2023-03-14

Emile-Daisy (08:08:59): > @Emile-Daisy has joined the channel

Elisheba Asiimwe Joanita (10:01:06): > @Elisheba Asiimwe Joanita has joined the channel

2023-03-15

Rishi Singh (08:46:52): > @Rishi Singh has joined the channel

Madelyn Carlson (10:49:22) (in thread): > In case you hadn’t already seen - Jen updated the project board with your PR,see here.

khadijah (11:54:46) (in thread): > Yes thank you@Madelyn Carlsonand I have also made changes to all her review . Waiting for more instructions

idubor itohan (18:40:13): > @idubor itohan has joined the channel

2023-03-16

Madelyn Carlson (09:53:11): > Hi all - as a reminder, we are hosting the Sweave2Rmd-Outreachy office hour today at 10-10:45AM ET (Zoom link), starting in ~10 minutes. This will be time where we explain the project and answer questions about the contribution tasks. If you’re unable to make it, no worries - we have another office hour session next week on Wednesday, March 22, 11-11:45AM ET. Talk soon!

Madelyn Carlson (10:20:56): > Thank you to folks on our office hours today pointing out that our office hours overlap with BugSigDB office hours. In case y’all are interested in attending both sessions, we’re switching the Sweave2Rmd office hour in 2 weeks from Thursday, March 30 to Wednesday, March 29 at 10-10:45AM ET. So here is the schedule for the next two weeks. > * Wednesday, March 22, 11-11:45AM ET (Zoom link) > * Wednesday, March 29, 10-10:45AM ET (Zoom link) > Hope to see you there.

Madelyn Carlson (14:22:59): > In case it’s helpful,here is a linkto the recording from our office hour session this morning.

Emmanuel Taiwo devbird007 (16:38:21) (in thread): > Thank you for this link, I couldn’t attend today because I thought it wasn’t until tomorrow haha

2023-03-17

Vivian Ginikachukwu Ikeh (02:09:00) (in thread): > Thank you@Madelyn Carlson

Madelyn Carlson (11:00:32) (in thread): > Absolutely!

2023-03-18

rohitsatyam102 (04:26:01): > Quick question, do we have to contribute to all three Bioconductor projects present in Outreachy to confirm our Outreachy Intern candidature ?

Busayo Ojo (04:34:46) (in thread): > No you don’t have to contribute to all three.

2023-03-19

Reece11 (12:46:58): > @Reece11 has joined the channel

2023-03-20

rohitsatyam102 (05:21:21) (in thread): > Thanks for clarifying

2023-03-21

Oluwabukola Bamigbade (05:56:01): > @Oluwabukola Bamigbade has joined the channel

Madelyn Carlson (10:00:00): > Hi all - as a reminder, we are hosting the Sweave2Rmd-Outreachy office hour tomorrow at 11-11:45AM ET (Zoom link). We answer questions about the project and contribution tasks. If you’re unable to make it, we have another office hour session next week on Wednesday, March 22, 10-10:45AM ET. Hope to see you there!

2023-03-22

Madelyn Carlson (10:00:03): > Friendly reminder that our Sweave2Rmd-Outreachy office hour starts soon. Feel free to join for the 11-11:45AM ET session,Zoom link here

Madelyn Carlson (11:47:24) (in thread): > Key points & notes from our office hours session today: > * If you’ve made one or multiple PRs, some merged and some unmerged, you may link to both in the final Outreachy application, if you choose to complete an application for the Sweave2Rmd project. Or, if you’ve made one PR that is unmerged, you should post a link to that in the application. > * In the final Outreachy application for the Sweave2Rmd project, you will be asked to complete community questions. Those two questions are (1) why are you applying to this project? and (2) What do you hope to get out of your participation?

Beekaz (13:15:37): > @Beekaz has joined the channel

2023-03-23

Trishna Patel (13:59:46): > @Trishna Patel has joined the channel

khadijah (14:56:06): > @Andres Wokatykindly check your dm

Andres Wokaty (15:01:03) (in thread): > I will review your PR later today or tomorrow at the latest.

2023-03-25

Lydia Edogiawerie (09:26:44): > @Lydia Edogiawerie has joined the channel

2023-03-26

Emmanuel Adamolekun (09:09:07): > @Emmanuel Adamolekun has joined the channel

2023-03-28

Madelyn Carlson (12:19:26): > As a reminder, we are hosting the Sweave2Rmd-Outreachy office hour tomorrow at 10-10:45AM ET (Zoom link). We answer questions about the project and contribution tasks. Hope to see you there!

2023-03-29

Madelyn Carlson (09:00:00): > Friendly reminder that our Sweave2Rmd-Outreachy office hour starts soon. Feel free to join for the 10-10:45AM ET session,Zoom link here

2023-03-30

Eineje Ameh (02:31:31): > @Eineje Ameh has joined the channel

Eineje Ameh (02:32:20): > Good morningI wouldlike to applyfor the micro biome projectas I am an Outreachy applicantplease can I get a guide on how to do so!?

Tuomas Borman (03:43:16) (in thread): > There are two microbiome projects “Microbiome Study Curation” (#bugsigdbchannel) and “Optimize microbiome data science framework” (#miaversechannel). > > > Fro the website, yoy can find information and tasks that you need to completehttps://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductorI am the mentor of miaverse project, so I can help you on that (just send message privately or to miaverse channel) - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

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2023-03-31

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2023-04-01

MaryJones (03:41:05): > @MaryJones has left the channel

2023-04-03

Andres Wokaty (12:08:50): > Thanks everyone for your participation!

2023-05-04

sophy (13:02:42): > @sophy has left the channel

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2023-05-09

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2023-06-16

Maria Doyle (04:40:02): > Hello<!channel>outreachy! We’re gathering feedback on theBioconductor.orgwebsite and would love to hear about your experiences as newcomers. Your input will help us make our site more user-friendly and impactful for future users. Thank you!:pray:Survey link:https://t.maze.co/169169456

Shivang Bhanushali (08:55:18): > @Shivang Bhanushali has joined the channel

2023-07-04

Richard Dushime (09:56:14): > :seedling:Join Open Seeds Cohort 8!:seedling:Calling all aspiring open science ambassadors and research enthusiasts! Applications for Open Seeds’ eighth cohort, OLS-8, are now open until July 7, 2023. Don’t miss this opportunity to upskill in open and reproducible research, receive mentoring, and work on your own projects. With 317 mentees and 208 projects already supported, it’s time to be part of this transformative experience. Visithttps://openlifesci.orgfor more details and be part of the open science movement!:earth_africa::microscope:#OpenSeeds #OLS-8 #OpenScience - Attachment (openlifesci.org): OLS | OLS > A mentoring & training program for Open Science ambassadors

2023-08-03

Andrés Arredondo Cruz (16:55:00): > @Andrés Arredondo Cruz has joined the channel

2023-08-04

goodnews sandy (06:34:24): > @goodnews sandy has joined the channel

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2023-09-15

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2023-10-03

Cynthia (12:15:26): > @Cynthia has joined the channel

Cynthia (12:15:59): > Hello! My name is Cynthia. An Outreachy Applicant. So glad to be here !:hugging_face:

Andres Wokaty (12:29:37) (in thread): > Welcome :)

Cynthia (12:57:06) (in thread): > Thank you Jennifer:relaxed:

2023-10-04

Ayowale Ojo (02:53:56): > @Ayowale Ojo has joined the channel

Ayowale Ojo (02:57:17): > Hello everyone I’m an outreachy applicant and glad to be here to make contributions to the Microbiome project

mahamtariq58 (03:29:00): > Hi everyone, my name is Maham Tariq and I am an Outreachy applicant. I am excited to embark on a venture of open source.Looking forward to make meaningful contributions and collaborate effectively.

Maryam Gbemisola (03:50:24): > Hello everyone. My name is Maryam Gbemisola an Outreachy Applicant. Glad to contribute to this project

Maryam Gbemisola (03:50:52) (in thread): > Hello Cynthia

Maryam Gbemisola (03:51:14) (in thread): > Hello Ayowale

Chiagoziem David (04:20:41): > @Chiagoziem David has joined the channel

Chiagoziem David (04:22:48): > Hello everyone, my name is David Chiagoziem and I am an outreachy applicant. I’m so excited to be here and to embark on this journey. Let’s go:muscle::muscle::muscle:

Cynthia (04:41:05) (in thread): > Hi Maryam:relaxed:

Ayowale Ojo (05:19:27) (in thread): > Hi Maryam welcome

Fortune Nnamdi (07:57:21): > Hello everyone!I’mFortune Nnamdi. I am an Outreachy applicant andI’mreally excited to be here!

Chinwendu Enyinna (12:35:15): > @Chinwendu Enyinna has joined the channel

Chinwendu Enyinna (12:38:55): > Hi everyone, my name is Chinwendu. And I am an Outreachy applicant, excited to be here!

Andres Wokaty (12:47:20) (in thread): > Welcome, good to have you:slightly_smiling_face:

2023-10-05

Onyewuchi Esther Chikamso (03:41:28): > @Onyewuchi Esther Chikamso has joined the channel

Mildred Anashie (14:13:57): > @Mildred Anashie has joined the channel

Mildred Anashie (14:16:54): > Hello everyoneIam Mildred AnashieI’man Outreachy Applicant andI’mglad to be here, looking forward to making contributions

Andres Wokaty (14:26:30): > Welcome Outreachy applicants! Please join the#bugsigdbchannel for discussions related to the Microbiome Study Curation. Thank you for your interests and look forward to your contributions.

2023-10-06

Shriya Kamat Tarcar (17:53:30): > @Shriya Kamat Tarcar has joined the channel

2023-10-07

Greatman Ugorji (15:55:33): > @Greatman Ugorji has joined the channel

Clarissa Abidog (22:32:53): > @Clarissa Abidog has joined the channel

2023-10-10

claudia isabel reyes moreno (00:20:21): > @claudia isabel reyes moreno has joined the channel

claudia isabel reyes moreno (00:34:10): > Hello everyone, I am Claudia Reyes. I am an Outreachy applicant and Latino talent. I am very excited to be here. My purpose is to implement contributions that can make a difference and positively impact my project!:muscle:

2023-10-13

Francisca_Eze (12:23:29): > @Francisca_Eze has joined the channel

Francisca_Eze (12:26:15): > Hello everyone, My name is Francisca Eze, and I am from Nigeria. I am a budding data analyst with a curious mind and a willingness to learn. I am happy to contribute to this project.

Andres Wokaty (13:31:10) (in thread): > Welcome@Francisca_Eze. Be sure to join the project channel#bugsigdb.

2023-10-14

Francisca_Eze (07:28:37) (in thread): > thanks@Andres Wokaty

2023-10-16

saskia (18:33:26): > @saskia has joined the channel

saskia (18:33:43): > This looks like a really active channel! Would someone from your community be interested in joining the Code of Conduct Committee for the Bioconductor project. We also strive to have as much diverse representation of the community as we can, so please consider this. Applications are due on the 31st of October via this linkhttps://docs.google.com/forms/d/e/1FAIpQLSeTRs3m3-XNM7iGs0kyHfoaXNiwRVsgebmce10t0ieKfamaPg/viewform?usp=sf_link

2023-10-17

Anna Quaglieri (she/her) (02:03:52): > @Anna Quaglieri (she/her) has joined the channel

2023-10-18

PATIENCE ONAH (11:57:16): > @PATIENCE ONAH has joined the channel

PATIENCE ONAH (12:10:48): > Hello, I’m Patience Onah, an Outreachy Applicant. I am excited to be here. Look forward to making a meaningful contribution to Microbiome Study Curation project.

2023-10-23

Doreen Wanyama (13:57:36): > @Doreen Wanyama has joined the channel

Doreen Wanyama (13:59:22): > Good day everyone! My name is Doreen Wanyama an Outreachy applicant. I am glad to be here and I hope to make positive impact to this community

2023-10-24

Michael (10:30:29): > @Michael has joined the channel

2023-10-25

Yusuf Mabel (10:28:14): > @Yusuf Mabel has joined the channel

2024-01-18

Ukwueze Pascaline Nnenna (09:33:19): > @Ukwueze Pascaline Nnenna has joined the channel

2024-02-21

Maria Doyle (11:31:13): > :writing_hand:New Bioconductor blog post by our current Outreachy interns! Check out their journey and the great work they’ve been doing:https://blog.bioconductor.org/posts/2024-01-31-OutreachyInternshipJourney/Thanks@Chioma Onyido,@Esther Afuape, and@Peace Sandy:star2:If you’re inspired by their work and would like to mentor for the May-August intake, remember the deadline to submit a project is**** this Friday, Feb. 23 2024, at 4 pm UTC**. Learn more and submit your proposal here:https://www.outreachy.org/communities/cfp/bioconductor/.

2024-02-26

Hervé Pagès (11:25:01): > @Hervé Pagès has left the channel

2024-02-27

leila yesufu (17:31:35): > @leila yesufu has joined the channel

Bukola Agbabiaka (17:33:22): > @Bukola Agbabiaka has joined the channel

2024-02-28

taofeeqah bakare (18:29:01): > @taofeeqah bakare has joined the channel

2024-03-04

Isi Irabor (11:15:32): > @Isi Irabor has joined the channel

Melodee Okigbo (11:54:12): > @Melodee Okigbo has joined the channel

Victoria (Burah) Poromon (12:09:39): > @Victoria (Burah) Poromon has joined the channel

Chioma Onyido (12:15:29): > @Chioma Onyido has joined the channel

Chinedu Ihedioha (12:17:03): > @Chinedu Ihedioha has joined the channel

Fausat Olasubomi Abiola (12:28:21): > @Fausat Olasubomi Abiola has joined the channel

Naomi Ibe (13:00:27): > @Naomi Ibe has joined the channel

Adedoja Isaac (13:02:30): > @Adedoja Isaac has joined the channel

Sneha Singh (13:06:33): > @Sneha Singh has joined the channel

Juliet Ogbu (14:07:06): > @Juliet Ogbu has joined the channel

Oluwaseyifunmi Taiwo (14:23:41): > @Oluwaseyifunmi Taiwo has joined the channel

Bolanle Wahab (15:04:56): > @Bolanle Wahab has joined the channel

Bolanle Wahab (15:13:58): > Hello!:rocket:I’m excited to join this vibrant community where ideas flow freely. I’m Bolanle, an Outreachy Applicant, looking forward to connecting, learning, and sharing with all of you amazing people on the BioConductor project. Let’s make this space one filled with positivity, growth, and meaningful interactions. Cheers to new beginnings and awesome connections!

Svetlana Ugarcina Perovic (15:26:28): > @Svetlana Ugarcina Perovic has joined the channel

Melodee Okigbo (16:21:13) (in thread): > Hi@Bolanle Wahab, same here, can’t wait!

Okache Johnpaul (16:25:04): > @Okache Johnpaul has joined the channel

Oluwatosin Adesola (16:36:47): > @Oluwatosin Adesola has joined the channel

Oluwatosin Adesola (16:37:05): > Hello Everyone, > > I am Tosin Olatunji, an Outreachy applicant, and I am very excited to contribute to Fedora’s Project. > > I’m really looking forward to working with the team also, and cannot wait to do awesome work together. > > P.S, you can call me Bella as well. > Thanks!

Okache Johnpaul (16:58:48): > Hey Everyone! My name is Johnpaul, I’m a part of Outreachy’s May cohort and I look forward to contributing to the Microbiome Study, and working with you all.

Ruth Bamgbose (17:35:18): > @Ruth Bamgbose has joined the channel

Leenaa Al-Amin (17:36:31): > @Leenaa Al-Amin has joined the channel

Alex Eze (20:17:31): > @Alex Eze has joined the channel

Faith Ifeoluwa Alexander (21:21:03): > @Faith Ifeoluwa Alexander has joined the channel

Faith Ifeoluwa Alexander (21:24:46): > Hello everyone. I am an Outreachy applicant and you can call me Faith. It’s so great to be here and I look forward to working with amazing minds here and contributing to the BioConductor Project. Let’s roll up our sleeves and get started!

Amal Hirole (22:17:27): > @Amal Hirole has joined the channel

Amal Hirole (22:20:26): > Hello everyone, my name is Amal and I am from Canada. I am an Outreachy applicant for the May 2024 cohort. I look forward to making meaningful contributions to the Microbiome project.

Manisha Nair (23:13:08): > @Manisha Nair has joined the channel

Manisha Nair (23:22:32): > Hello everyone, I’m Manisha Nair, a fourth year college student from India. I’m an Outreachy applicant eager to contribute to Bioconductor project. Looking forward to make meaningful contributions and learning new skills.

2024-03-05

Nanlop Blessing Dafwat (00:51:45): > @Nanlop Blessing Dafwat has joined the channel

Nanlop Blessing Dafwat (00:54:05): > Hi everyone, I’m Nanlop from Nigeria. It is a pleasure to be here, I’m an outreachy applicant excited to contribute to the Bioconductor project. Looking forward to learning and contributing to this project.

Vamika Mendiratta (02:09:48): > @Vamika Mendiratta has joined the channel

Chinedu Ihedioha (03:54:14): > Hi everyone, I am Chinedu, an Outreachy Applicant from Nigeria. Super excited to be here, looking forward to learn and contribute.

Zaynab Aderonke Ogunnubi (03:59:57): > @Zaynab Aderonke Ogunnubi has joined the channel

Peace Daniel (04:20:50): > @Peace Daniel has joined the channel

Amanda Adoyi (05:15:27): > @Amanda Adoyi has joined the channel

Sandra Dindi (05:36:38): > @Sandra Dindi has joined the channel

Valentina Buoro (05:39:13): > @Valentina Buoro has joined the channel

Sandra Dindi (05:41:06): > Hi. I’m Sandra , an Outreachy Applicant from Kenya. Looking forward to contribute to this project.

Valentina Buoro (05:55:48): > Hello everyone, I’m Valentina, am outreachy applicant from Nigeria. I’m looking forward to collaborating and contributing to Bioconductor

Mildred Anashie (05:56:41) (in thread): > Hi Valentina > > Please join#bugsigdbchannel to get started

Aliyu Atiku Mustapha (05:57:19): > Hello everyone, my name is Aliyu from Lagos, Nigeria. I am an Outreachy intern applicant, I’m looking forward to contribute to the Bioconductor project.

Muqtadirat Yussuff (06:38:55): > @Muqtadirat Yussuff has joined the channel

Muqtadirat Yussuff (06:39:47): > Hi everyone, I’m Muqtadirat, a fellow outreachy applicant and I’m looking forward to learning and making great contributions

Ima-obong (Aimah) (07:41:11): > @Ima-obong (Aimah) has joined the channel

Ima-obong (Aimah) (07:42:40): > Hi everyone, I am Ima-obong Enyie, an Outreachy intern applicant, and I’m looking forward to contribute to the Bioconductor project.

Semilore Atolagbe (08:01:07): > @Semilore Atolagbe has joined the channel

Adenike Oladimeji-Kasumu (08:11:56): > @Adenike Oladimeji-Kasumu has joined the channel

Adenike Oladimeji-Kasumu (08:12:47): > Hello Everyone:hugging_face:I am Adenike, a 2024 Outreachy Applicant. I look forward to learning and most importantly, making contributions on the Bioconductor project with you all.

Amarachi Lewachi (08:51:32): > @Amarachi Lewachi has joined the channel

Emem Eduoku (09:04:47): > @Emem Eduoku has joined the channel

Onyeahialam Gracious (09:33:23): > @Onyeahialam Gracious has joined the channel

Onyeahialam Gracious (09:49:04): > Hi everyone, I am Gracious and I’m excited to be here to share my contributions and learn with you all.

Sneha Singh (09:53:03): > Hello, I wanted to know that what should I write for slack username? The name that is displayed over here or actual username which I can find on my account settings.

Bolarinwa Abosede Julianah (09:58:31): > @Bolarinwa Abosede Julianah has joined the channel

Bolarinwa Abosede Julianah (10:00:14): > Hello everyone.I’m Julianah.An outreachy applicant.I’m so excited to be here andI’mlooking forward to contributing to the project

Andres Wokaty (10:10:38) (in thread): > If this is for a contribution task, this is a good question. I recommend asking on#bugsigdbso that others may benefit.

Shreya Badchariya (10:13:25): > @Shreya Badchariya has joined the channel

Sneha Singh (10:14:48) (in thread): > Alright!

Eleni Liapi (10:42:12): > @Eleni Liapi has joined the channel

Amarachi Lewachi (14:03:08): > Hi everyone. My name is Amarachi a 2024 outreachy applicant. I look forward to contributing towards this project alongside you all.

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

Blessing Ene Anyebe (14:23:19): > @Blessing Ene Anyebe has joined the channel

Latifat (14:23:55): > Hello everyone. My name is Latifat, a 2024 Outreachy Applicant. I look forward to contributing to this project.

Rodney Ighalo (14:28:25): > @Rodney Ighalo has joined the channel

Idiat Alli (16:35:16): > @Idiat Alli has joined the channel

Chiemelie Carita Ndibe (16:37:58): > @Chiemelie Carita Ndibe has joined the channel

Chiemelie Carita Ndibe (16:40:21): > hello team, I am excited to be here and hope this learning process is fun too.

Chioma Agu (16:55:22): > @Chioma Agu has joined the channel

Ayomide Solarin (17:05:26): > @Ayomide Solarin has joined the channel

Ayomide Solarin (17:09:03): > Hello everyone, hope we are all doing great? I am Ayomide. I am an applicant for the May internship. I look forward to learning and contributing

Benedicta Imelda (17:51:33): > @Benedicta Imelda has joined the channel

Benedicta Imelda (17:52:06): > Hi everyone, I am happy to be here

Blessing Ene Anyebe (18:00:13): > Hello everyone, my name is Blessing. > It is lovely to be here. It has been great learning and studying how Microbiomes work. The Microbiomes curation project is invested in capturing patterns of microbial signatures and focuses on the easy use of microbial data aggregation, standardization, analysis, knowledge synthesis, etc. > > I am excited about Bugsigdb and seeing that it reminds me of the beautiful secondary school days of learning about plant and animal cells including DNA.:sweat_smile:I look forward to exploring Microbiomes, contributing, and adding value to the community as well. > > Cheers guys, it’s great to be here!:orange_heart:

Ibukun Hassan (18:02:44): > @Ibukun Hassan has joined the channel

Chioma Agu (18:15:17): > Hello Everyone > > my name is Chioma Agu and I am excited to join this community as an Outreachy applicant for the may 2024 cohort > > I look forward to contributing, connecting and collaborating with you all

Blessing Laweh (20:29:27): > @Blessing Laweh has joined the channel

Blessing Laweh (20:32:34) (in thread): > Omg! same here lols. I haven’t done Biology in a long time and this is making me nostalgic. Can’t wait to get started. Nice too meet you namesake:wink:

Shedrack Sunday (20:33:28): > @Shedrack Sunday has joined the channel

Blessing Laweh (20:36:19) (in thread): > Also, if you don’t mind helping me out, I’ve opened and read all he links on git about this project…I’m still confused one something. Which one exactly is the project? (Sorry, it’s my first time contributing to open source)

Shedrack Sunday (20:38:56): > Hello great minds!! > > My name is Shedrack Bamidele Sunday. I’m excited to be a contributor for the May 2024 Cohort of the outreachy internship. I look forward to collaborating with the mentors and you all on the Microbiome project to bring more life to the review much needed for this amazing open science work.:clap:

2024-03-06

Blessing Ene Anyebe (01:14:26) (in thread): > Hey Blessing, it’s lovely to meet you as well! I relate to feeling nostalgic as well.:joy:Check this article to get a soft landing:sweat_smile:https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps,don’thesitate to reach out! Good luck as well Blessing.:orange_heart: - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta…

Siva (01:25:45): > @Siva has joined the channel

Siva (01:30:06): > Hello<!channel>. I’m Siva, and I’m thrilled to be here as an Outreachy applicant. I’m genuinely excited about the opportunity to contribute to the project and make a meaningful impact.

Blessing Laweh (01:34:44) (in thread): > Thanks for your help Blessing, I really appreciate

Blessing Ene Anyebe (02:50:41) (in thread): > You’rewelcome:orange_heart:

Benedicta Imelda (03:07:10): > Hello guys, I am a bit confused about how to begin, can some one help me through.

Mildred Anashie (03:07:58) (in thread): > Please join#bugsigdbchannel

Benedicta Imelda (03:08:16) (in thread): > Yes I am on the channel

Benedicta Imelda (03:08:44) (in thread): > Will they assign project to me or something

Benedicta Imelda (03:09:14) (in thread): > Everything looks new and Strang to me

Mildred Anashie (03:09:15) (in thread): > Let me drop a message for you on the channel on how to begin

Benedicta Imelda (03:09:31) (in thread): > Thank you

Ufomba Justina (03:11:19): > @Ufomba Justina has joined the channel

Ufomba Justina (03:12:32): > Hi good morning guys my name is Ufomba Justina just joined the community please how do I get started please?

Sneha Singh (03:18:15) (in thread): > Welcome:smile:

Sneha Singh (03:20:03) (in thread): > Welcome:smile:you can refer to thishttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Bolarinwa Abosede Julianah (03:42:49) (in thread): > Welcome@Shedrack Sunday

Shedrack Sunday (04:31:29) (in thread): > Thank you:blush:

Emmanuel Doreen (05:06:13): > @Emmanuel Doreen has joined the channel

Dolapo Mosuro (05:33:09): > @Dolapo Mosuro has joined the channel

Faith Ifeoluwa Alexander (06:01:47): > Pls, I need help. I have watched the videos attached to the welcome message but I don’t seem to get an headway. I was more confused after watching the videos. Pls, can someone help me out?

Mildred Anashie (06:03:22) (in thread): > Hi FaithI’llshare a link on#bugsigdbfor you to follow

Mildred Anashie (06:03:31) (in thread): > It should help you

Nancywrites (06:06:44): > @Nancywrites has joined the channel

Mojisayo Awolesi (06:22:29): > @Mojisayo Awolesi has joined the channel

Mojisayo Awolesi (06:24:35): > Hello everyone, I’m Mojisayo, an Outreachy applicant from Nigeria, I’m excited about making impactful contributions.

Iman Ngwepe-Ntshibida (06:33:38): > @Iman Ngwepe-Ntshibida has joined the channel

Faith Omolara Adegoke (07:40:11): > @Faith Omolara Adegoke has joined the channel

Grace Paul (08:28:04): > @Grace Paul has joined the channel

Melodee Okigbo (08:31:42) (in thread): > Hi@Faith Ifeoluwa Alexander, have you made headway now?

Grace Paul (08:32:58): > Hello Everyone, I’m Grace, an outreachy applicant and i am super excited to be here and looking forward to making valuable contributions and learning along the way. Nice to meet everyone here.

Blessing Ene Anyebe (08:34:43) (in thread): > Hello@Grace Paul, you’re welcome check this article to get a soft landing:sweat_smile:https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well. - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta… - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Blessing Ene Anyebe (08:36:23) (in thread): > Hello@Mojisayo Awolesi, check this article to get startedhttps://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well.:orange_heart:also join the#bugsigdbproject channel - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Faith Omolara Adegoke (08:39:45): > Hello everyone. I am Faith, an Outreachy applicant. Nice to meet everyone here.

Blessing Ene Anyebe (08:40:21) (in thread): > Nice to meet you too@Faith Omolara Adegoke:orange_heart:

Faith Ifeoluwa Alexander (09:08:06) (in thread): > I am on it now@Melodee Okigbo. Thank you so much.

Esther Nelson (09:18:32): > @Esther Nelson has joined the channel

Blessing Anumba (09:44:08): > @Blessing Anumba has joined the channel

Blessing Anumba (09:48:40): > Good day everyone. My name is Blessing Anumba, a May 2024 applicant. I am very happy to join this wonderful team to contribute and learn on this project. So, I would like to ask, where can I get the first task to work on? Thanks guys.

Blessing Ene Anyebe (09:52:36) (in thread): > Hello@Blessing Anumba, you’re welcome check this article to get a soft landing:sweat_smile:https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well Blessing.:orange_heart:also join the#bugsigdbchannel - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta…

Blessing Anumba (09:56:26) (in thread): > Thank you so much for your help. I really appreciate it. I will not hesitate to reach out when necessary. How do I get across to the mentor here?

Blessing Ene Anyebe (09:59:24) (in thread): > These are the mentors@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido

Blessing Ene Anyebe (10:00:49) (in thread): > You’rewelcome Blessing:orange_heart:

Ibukun Hassan (10:43:56): > Hello everyone > GoodafternoonI’mreally confused > Been through all since morning but stilldon’tknow what to do. > > Idon’tmind if anyone could kindly explain better?:pray:

Esther Nelson (10:51:25) (in thread): > Hi@Ibukun Hassan, welcome:hugging_face:. It’s great to have you. Don’t worry too much, it’s all fine and cool if you follow the following procedures: > > Join the#bugsigdbchannel and you can also go through this to get started. > > Follow this,https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699, to begin your first contribution. > > One of our mentors@Chioma Onyidowrote an amazing blog on getting started and what’s to be expected from us during this stage,https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/. It’s gold if you ask me. > > These should be enough to get you started. Oh, and once you’ve made your first contribution, don’t forget to record it. Great to connect with you.

Elsie Dickson (10:52:04): > @Elsie Dickson has joined the channel

Anju Maurya (12:00:21): > @Anju Maurya has joined the channel

Mojisayo Awolesi (12:14:20) (in thread): > Thank you Blessing

Temitayo Ogidan (12:19:44): > @Temitayo Ogidan has joined the channel

Temitayo Ogidan (12:22:04): > Hello everyone,I’mTemitayo from Nigeria an outreachy applicant. Nice to meet you all.I’mexcited to make meaningful contributions alongside everyone here:hugging_face:

Joan C. Chukwuemeka (12:30:17): > @Joan C. Chukwuemeka has joined the channel

Adejoke Ogunyinka (12:30:58): > @Adejoke Ogunyinka has joined the channel

Joan C. Chukwuemeka (12:31:42) (in thread): > Welcome@Temitayo Ogidando join#bugsigdbchannel

Afnan Asif (12:34:05): > @Afnan Asif has joined the channel

Blessing Ene Anyebe (12:59:31) (in thread): > Hello@Temitayo OgidanYou are welcome! Check this article to get startedhttps://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well.:orange_heart:also join the#bugsigdbproject channel as@Joan C. Chukwuemekasuggested. Cheers - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta…

EBERE ADEKOGBE (13:04:33): > @EBERE ADEKOGBE has joined the channel

Aleru Divine (13:13:26): > @Aleru Divine has joined the channel

Anshika Arora (13:39:57): > @Anshika Arora has joined the channel

Millicent Adzepa (14:18:40): > @Millicent Adzepa has joined the channel

Millicent Adzepa (14:20:22): > Hello everyone, I am Millicent from Ghana , an Outreachy Applicant. I am excited to contribute and also learn from everyone.

Aditi Bhadoriya (14:23:43): > @Aditi Bhadoriya has joined the channel

Nikhil Mane (14:30:19): > @Nikhil Mane has joined the channel

Blessing Ene Anyebe (14:31:13) (in thread): > Hello@Millicent Adzepa, you’re welcome check this article to get a soft landing:sweat_smile:https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well.You should also join the#bugsigdbchannel. - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta… - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Millicent Adzepa (14:33:16) (in thread): > thank you very much, this is helpful

Blessing Ene Anyebe (14:34:15) (in thread): > You’rewelcome!:orange_heart:

idiaru Angela (14:34:45): > @idiaru Angela has joined the channel

idiaru Angela (14:41:08): > Hello everyone, I’m ISI from Nigeria and an outreachy applicant. it is my pleasure to meet you all. i look foward to learning and contributing with everyone here.

Blessing Ene Anyebe (14:42:30) (in thread): > Hello@idiaru Angela, you’re welcome check this article to get a soft landing.https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well.You should also join this channel#bugsigdb - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Oluwatoyosi Victoria Olanrewaju (14:51:46): > @Oluwatoyosi Victoria Olanrewaju has joined the channel

idiaru Angela (14:57:26) (in thread): > Thank you so much Blessing

Devashri (15:12:41): > @Devashri has joined the channel

Blessing Ene Anyebe (15:25:12) (in thread): > You’revery much welcome Angela

NWAKAEGO VINCENT (16:11:05): > @NWAKAEGO VINCENT has joined the channel

Osayuki Raymond Okhuarobo (16:28:25): > @Osayuki Raymond Okhuarobo has joined the channel

Osayuki Raymond Okhuarobo (16:30:19): > Hello everyone! > > My name is Osayuki Raymond from Nigeria, I’m an outreachy applicant and I’m looking forward to contributing to the Bioconductor community.

Blessing Ene Anyebe (16:55:09) (in thread): > Hello@Osayuki Raymond Okhuaroboyou’re welcome to the community. Check this article to get a soft landing.https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well. You should also join this channel#bugsigdb - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta… - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

idiaru Angela (17:03:02) (in thread): > hi Osayuki

2024-03-07

ADAEZE SIMON (02:01:32): > @ADAEZE SIMON has joined the channel

Ifenna Muonagolum (04:00:17): > @Ifenna Muonagolum has joined the channel

Hamidat Mohammed (04:42:42): > @Hamidat Mohammed has joined the channel

Serah Gituto (06:15:16): > @Serah Gituto has joined the channel

Serah Gituto (06:19:39): > Hello ,My name is Serah ,I am an Outreachy applicant and I look forward to contributing to the team.

Mildred Anashie (06:21:27): > Hi@Serah Gitutoplease join#bugsigdbto get started

Aleru Divine (06:21:45) (in thread): > Hi@Serah Gituto, welcome:hugging_face:Please join the#bugsigdbchannel, there are resources there and it is where everyone communicates, including the mentors and fellow contributors.You can go through this to get started.https://github.com/waldronlab/BugSigDBcuration/issues/94Ask me anything, I’m here to help.:hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Blessing Ene Anyebe (06:22:10) (in thread): > Hello@Serah Gituto, you’re welcome to the community, check this article to get a soft landing.https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well. You should also join this channel#bugsigdb - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta… - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Mehak Sharma (07:22:34): > @Mehak Sharma has joined the channel

Mehak Sharma (07:24:02): > Hey everyone! I’m Mehak, an Outreachy applicant and a machine learning enthusiast from India. Looking forward to actively contribute to this project:)

idiaru Angela (07:24:50) (in thread): > Hi Mehak. It is nice to meet you please join#bugsigdbto get started and check out the pinned messages for more information.

idiaru Angela (07:28:48) (in thread): > @Mehak Sharmayou’re welcome to the community, check this article to get a soft landing.https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94Please reach out if you have more questions#bugsigdb - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta… - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Osayuki Raymond Okhuarobo (07:45:28) (in thread): > Thank you@Blessing Ene Anyebe

Osayuki Raymond Okhuarobo (07:46:26) (in thread): > Hello@idiaru Angela

Blessing Ene Anyebe (08:02:45) (in thread): > You are welcome!

Iman Ngwepe-Ntshibida (08:39:54): > Hi, team. Some help please. How do we record our first contribution on Outreachy as after doing the survey there is no URL to use. Your help will be appreciated ?

Isoken Ibizugbe (08:43:56): > @Isoken Ibizugbe has joined the channel

Melodee Okigbo (08:45:26) (in thread): > Hi@Iman Ngwepe-NtshibidaIpastedthe link to the survey. > > I assumesince it’s asks for your details at the beginning I’m sure it records******your******response.

Isoken Ibizugbe (08:47:01): > Hi everyone, My name is Isoken an animal environmental biologist and a software engineering student. I am excited to contribute to this project.

Iman Ngwepe-Ntshibida (08:47:54) (in thread): > @Melodee Okigbohey Melodee, the link seem to direct to a new unfilled survey…:see_no_evil:is it ok to put it ?

Melodee Okigbo (08:52:14) (in thread): > It should be

Melodee Okigbo (08:54:29) (in thread): > The actual responses to survey are saved on Qualtrics XM with your details

Praise Agbetuyi (09:00:02): > @Praise Agbetuyi has joined the channel

NWAKAEGO VINCENT (09:01:47): > Hello everyone, My name is Nwakaego vincent from Nigeria I’m glad to be here.

Harshita Srivastava (10:26:42): > @Harshita Srivastava has joined the channel

Harshita Srivastava (10:27:45): > Hello everyone, myself Harshita from India . I am looking forward to working with mentors and fellow contributors . Thank you!!

wizdom Chris (11:46:39): > @wizdom Chris has joined the channel

wizdom Chris (11:47:33): > Hello I’m wisdom Chris , I’m glad to be here.

Joan C. Chukwuemeka (12:56:11): > Welcome@wizdom Chris, please do join#bugsigdbchannel for outreachy related discussions. I’m also available to help where I can.

idiaru Angela (13:16:16) (in thread): > Hi Harshita. It is nice to meet you please join#bugsigdbto get started and check out the pinned messages for more information.

Akinbode Mariam (13:17:19): > @Akinbode Mariam has joined the channel

Chris Awoke (14:07:55): > @Chris Awoke has joined the channel

fetlework gubena arage (14:47:30): > @fetlework gubena arage has joined the channel

Flourish Ralph (15:35:36): > @Flourish Ralph has joined the channel

2024-03-08

Derrick Nathan (02:12:21): > @Derrick Nathan has joined the channel

Glorious Katushabe (02:18:47): > @Glorious Katushabe has joined the channel

Glorious Katushabe (04:50:53): > My name is Glorious ,I am an Outreachy applicant and looking forward to contributing to the team.

idiaru Angela (05:02:09) (in thread): > Hello Glorious. Join#bugsigdbto get more information and look through the pinned messages to get started

EBERE ADEKOGBE (05:38:25) (in thread): > Hello Glorious, you are welcome!

Sidra Khan (07:30:21): > @Sidra Khan has joined the channel

Sidra Khan (07:37:50): > Hi everyone! My name is Sidra Khan from Pakistan. I’m outreachy applicant really looking forward to contributing to this project and learning from you all

Adenike Oladimeji-Kasumu (07:59:07) (in thread): > You are welcome@Sidra KhanDo well to join the#bugsigdbchannel to get started

Aishat Ijiyode (10:27:06): > @Aishat Ijiyode has joined the channel

Modinat Ganiyu (11:16:14): > @Modinat Ganiyu has joined the channel

Modinat Ganiyu (11:18:06): > Hello everyone. I’m an outreachy applicant. I’m excited to be here and I’m looking forward to learn alot and grow with you all

idiaru Angela (11:21:35) (in thread): > Hi Modinat. You’re welcome. Join#bugsigdbto get started if you haven’t and look through the pinned messages > The community is always ready to help if you have any more questions

sneha goel (12:52:37): > @sneha goel has joined the channel

Aishat Ijiyode (16:07:35): > Hello everyone, my name is Aishat. I’m an outreachy applicant, I am excited to contribute to this project and connect with you all

Omeyimi Longe (17:32:14): > @Omeyimi Longe has joined the channel

2024-03-09

Ima-obong (Aimah) (01:46:57): > Hello everyone it’s a new day and if you’re new here please joing the#bugsigdbchannel to begin your contributions

Joy Gold (01:53:40): > @Joy Gold has joined the channel

Jolade Okunlade (04:00:58): > @Jolade Okunlade has joined the channel

Modinat Ganiyu (04:17:54) (in thread): > Oh thank you@idiaru AngelaI appreciate

EBERE ADEKOGBE (05:10:54): > Welcome to everyone just joining, be sure to join the#bugsigdbchannel and yes I am also available to assist wherever possible.

Preethi grace Manthena (05:36:57): > @Preethi grace Manthena has joined the channel

Success Ologunsua (07:06:27): > @Success Ologunsua has joined the channel

Success Ologunsua (07:10:20): > Hi everyone, my name is Success and I am very interested in the Microbiome Study Curation project. As a microbiology graduate turned software developer, I’m excited about a project that combines these two fields and hope to make meaningful contributions.

Mildred Anashie (07:11:07) (in thread): > Hi success > Welcome, please join#bugsigdb

Success Ologunsua (07:11:39) (in thread): > Thank you! I’ll do that now

Navya Verma (08:24:34): > @Navya Verma has joined the channel

Navya Verma (08:25:37): > Hello, I am Navya Verma, an outreachy contributor, highly interested in microbiome, literature review and datasets analysis. Please guide me on how to start with the contributions.

idiaru Angela (08:32:51) (in thread): > Hi Navya, welcome! > Do well to join#bugsigdbas that’s where most community discussions happen. Check the pinned messages for information about how to get started > The community is always willing to help if you have any questions

Amaka Joyce (08:39:00): > @Amaka Joyce has joined the channel

Charity Mbabazi (09:25:43): > @Charity Mbabazi has joined the channel

Navya Verma (09:58:20) (in thread): > Okay, thank you.

Modinat Ganiyu (10:23:10): > @Navya Vermajoin#bugsigdbfirst. Then go through this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94Read through, click on the ‘Go to the first curation form’ to start your first task and your first contribution - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Dorcas Oladele (20:31:30): > @Dorcas Oladele has joined the channel

Dorcas Oladele (20:34:16): > Hi everyone, I’m Oladele Dorcas. As a human anatomy graduate, I am interested in the Microbiome Study curation project. I am excited to contribute meaningfully to this project

2024-03-10

ANUKRATI CHATURVEDI (01:58:04): > @ANUKRATI CHATURVEDI has joined the channel

Precious Orakwe (04:36:36): > @Precious Orakwe has joined the channel

Precious Orakwe (04:52:20): > Hello team, good morning to my fellow contributors and my mentors, my name is precious and am excited to contribute to this project, though am a newbie i i don’t know much about microbiome curation, please guide me through.

idiaru Angela (06:01:04) (in thread): > Hi Dorcas

Flourish Ralph (10:00:04) (in thread): > Hi Precious, kindly join#bugsigdbchannel so you can start contributing.Go through the pinned messages to see the next steps to take.

Bhavya Pandey (11:53:58): > @Bhavya Pandey has joined the channel

Bhavya Pandey (11:57:47): > Hello Everyone, I am Bhavya Pandey from India. I am an outreachy applicant and really interested in this project. I am looking forward to learn from you all and start contributing in this project !

Bukola Salawu (12:22:12): > @Bukola Salawu has joined the channel

Arnav Puri (14:23:44): > @Arnav Puri has joined the channel

Peace Daniel (15:25:30) (in thread): > Hello, welcome. Could you join this channel#bugsigdb

Taiye Michaels (21:20:09): > @Taiye Michaels has joined the channel

Taiye Michaels (21:30:19): > Hello everyone, my name is Taiye Michaels from Nigeria and I am looking forward to contributing to the Project Microbiome Study Curation > I am new to FOSS and will be happy to collaborate with you all on this journey. Any form of guidance/support will be immensely appreciated. Thank You

2024-03-11

Isoken Ibizugbe (05:31:28) (in thread): > You are welcome. Start off from herehttps://github.com/waldronlab/BugSigDBcuration/issues/94. This has all the information you need to get started with your contribution. > Also join the#bugsigdbchannel, so you can ask for help when needed. You can also tag me - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

NWAKAEGO VINCENT (06:32:41): > i have made my first and second contribution on the biconductor project , do i record the contribution together ?

idiaru Angela (06:35:32) (in thread): > Both contributions should be recorded using their various links on the outreachy website

NWAKAEGO VINCENT (06:38:01) (in thread): > thank you@idiaru Angela@Scholastica Urua

Aleru Divine (06:38:13) (in thread): > @NWAKAEGO VINCENTRecord each separately as they require different start and merge dates and different contribution URLs > > Record all contributions separately

Kelechi Madubuko (06:45:00): > @Kelechi Madubuko has joined the channel

Kelechi Madubuko (06:51:07): > Hello everyone.. I’m Kelechi Madubuko. I’m interested in contributing to the microbiome project. It’s nice to be here and i hope to connect with other contributors around the world

Scholastica Urua (06:56:54): > @Scholastica Urua has joined the channel

idiaru Angela (07:05:13) (in thread): > Hi@Kelechi Madubukowelcome! Join#bugsigdbto get started and check the pinned messages for information about how to get started

Kelechi Madubuko (07:15:02) (in thread): > Thank you@idiaru Angelaalready joined the#bugsigdbchannel. Let me hit the ground running right away

NWAKAEGO VINCENT (08:48:58) (in thread): > you are welcome@Kelechi Madubuko

Blessing Ene Anyebe (09:47:43) (in thread): > Hi@NWAKAEGO VINCENTI hopeyou’rein the#bugsigdbchannel? You should join that as well > > Good luck with your contribution too:orange_heart:

Millicent Adzepa (11:02:30): > hello everyone, I am Millicent, glad to be here

idiaru Angela (11:35:22) (in thread): > Hi@Millicent Adzepawelcome! Join#bugsigdbto get started and check the pinned messages for information about how to get started

Lawrence Franklin Chukwudalu (11:51:21): > @Lawrence Franklin Chukwudalu has joined the channel

Linda Uchenwoke (14:26:33): > @Linda Uchenwoke has joined the channel

Sandeep Pillai (17:45:51): > @Sandeep Pillai has joined the channel

2024-03-12

Saasha Gupta (03:52:48): > @Saasha Gupta has joined the channel

2024-03-13

Glorious Katushabe (09:40:32): > Hello team, my study has 3 groups ( samples are categorized into three groups: no transplant group (NT) , lung transplant event-free group (EF) , and lung transplant chronic rejection group (CR) and I am finding hardships in identifying group 1. and results are in this form NT vs EF, NT vs CR and EF vs CR, The LEfSe analysis exhibited significant differences between groups. I tried to create each as an experiment but I am getting a comment that there is no difference from previous experiment. Should I combine CR and EF and name it Lung Transplant to form group 1. your guidance is highly appreciated.

Muqtadirat Yussuff (09:42:59) (in thread): > Hi, you should post this on#bugsigdband if the paper states significant difference in each group then that’s 3 experiments like you listed. > > Unless you provide a section that shows combining the group is plausible, I’ll just stick to three experiments

Mildred Anashie (09:44:19) (in thread): > Hi@Glorious Katushabefrom this what I can interpret is that your group 1 for the first experiment is EF, the second is CR and the third is CR

Bolanle Wahab (09:45:14) (in thread): > Hi@Glorious Katushabecan you send this on BugSigdb channel with a link to your article?

Aleru Divine (09:46:15) (in thread): > @Glorious Katushabeyou will need to create 3 experiments. > 1. NT(group 0/control group) vs EF(group1) > 2. NT(group 0/control group) vsCR(group1) > 3. EF(group 0)vsCR(group1because it is the high severity group) > can you post this on the#bugsigdbchannel, discussions and questions usually take place there.

Navya Verma (10:47:38): > Hello everyone > The Microbiome Study Curation project is currently placed in the closed project category on the Outreachy website. So I cannot contribute now ?

Glorious Katushabe (11:01:08) (in thread): > Thank you for comments, I was supposed to post #Bugsigdb. It was an error. let me go ahead and post for guidance

idiaru Angela (12:48:17) (in thread): > If you haven’t already recorded a contribution on the outreachy website then you can’t apply for this project anymore as stated by the mentors. But however you can still contribute:blush:.

MizOgelicious (14:16:26): > @MizOgelicious has joined the channel

2024-03-14

Adegboye Rukayat (00:08:31): > @Adegboye Rukayat has joined the channel

Adegboye Rukayat (00:11:13): > Hello fellow Outreachy applicants and Mentors. Nice joining you on this channel

2024-03-15

Peace Sandy (08:20:25): > @Peace Sandy has joined the channel

fetlework gubena arage (14:25:44): > Hello Everyone, I did my second contribution but I don’t know what to do about the Outreachy application. How am I going to send them the first one It was just like a questioner.

Mildred Anashie (14:28:50) (in thread): > Hello > > Please ask your questions regarding this project on the#bugsigdbchannel

Mildred Anashie (14:29:16) (in thread): > But to record your contribution you can use the link to the survey you filled

2024-03-17

Taiwo Akinlagun (06:21:37): > @Taiwo Akinlagun has joined the channel

Raihanat Adewuyi (20:42:32): > @Raihanat Adewuyi has joined the channel

2024-03-19

Nikita Sen (02:37:03): > @Nikita Sen has joined the channel

NWAKAEGO VINCENT (04:44:41): > Glad to have you here@Nikita Sen@Raihanat Adewuyi

Shambhavi Sinha (08:42:09): > @Shambhavi Sinha has joined the channel

EBERE ADEKOGBE (10:45:48): > Hi everyone nice joining you all on this channel

2024-03-20

NWAKAEGO VINCENT (05:26:33): > you are welcome@EBERE ADEKOGBE

2024-03-27

fetlework gubena arage (01:22:00): > Hello@Svetlana Ugarcina PerovicI hope you are doing well. I was trying to finalize my application for outreachy internship and it requires me to provide a timeline of the project I will be working on if I got accepted. It indicates I should work with my mentors about the timeline. What should I write?

Isoken Ibizugbe (01:49:29) (in thread): > Ask in the bugsigdb channel

abhich (05:45:40): > @abhich has joined the channel

Svetlana Ugarcina Perovic (06:09:02) (in thread): > Please go to#bugsigdbthere you have the answer.

Abiola Salako (09:38:35): > @Abiola Salako has joined the channel

2024-04-24

Izabela Mamede (08:21:12): > @Izabela Mamede has joined the channel

2024-05-03

Svetlana Ugarcina Perovic (11:30:10): > <!channel>If you were an outreachy applicant and contributed to any of the Bioconductor projects#BugSigDB#sweave2rmd#BSgenomeForge#miaverse, please help us in spreading the word about your amazing work. > > You can share your experience (anonymously) by filling in this short surveyhttps://forms.gle/brqH5M2uTYMKy23x7Thank you! - Attachment (Google Docs): Outreachy-Bioconductor survey > Dear Outreachy-Bioconductor contributor, > Thank you for participating in the Outreachy-Bioconductor program. In order to improve the experience for future contributors as well as to spread the word about your amazing contribution to the Bioconductor projects in the form of a conference talk and publication, we would appreciate you taking just a few minutes to complete an online survey about your experience. > > All survey responses are collected anonymously. If you have any questions, please contact us. > > Many thanks in advance and best wishes, > Bioconductor team > Email address: mailto:jennifer.wokaty@sph.cuny.edu|jennifer.wokaty@sph.cuny.edu

Adenike Oladimeji-Kasumu (11:32:38): > Noted@Svetlana Ugarcina Perovicwill do that.

Mildred Anashie (14:38:59) (in thread): > Okay@Svetlana Ugarcina PerovicWill get on it

2024-05-07

Sonali Kumari (11:39:36) (in thread): > Really great initiative I have filled it. Tagging@Atrayee Samantamy co-intern to fill the same.

Svetlana Ugarcina Perovic (12:05:12) (in thread): > Thank you@Sonali Kumari!!!

2024-05-09

Atrayee Samanta (02:46:35) (in thread): > Thank you for tagging me, i have filled in the survey@Svetlana Ugarcina Perovic@Sonali Kumari

Svetlana Ugarcina Perovic (03:07:23) (in thread): > Thank you@Atrayee Samanta!!

2024-05-15

Sunil Nahata (08:31:55): > @Sunil Nahata has joined the channel

2024-07-02

Diána Pejtsik (10:57:58): > @Diána Pejtsik has joined the channel

Constanza Perez (18:54:59): > @Constanza Perez has joined the channel

2024-07-14

Sudipta Hazra (18:20:52): > @Sudipta Hazra has joined the channel

2024-07-15

Erick Navarro (16:20:27): > @Erick Navarro has joined the channel

2024-08-04

Adeshile Oluwatosin (10:07:16): > @Adeshile Oluwatosin has joined the channel

2024-08-19

Rema Gesaka (09:37:32): > @Rema Gesaka has joined the channel

2024-08-21

Maria Doyle (14:35:54): > :writing_hand:New Bioconductor blog post on an Outreachy internship experience by@Scholastica Urua, mentored by@Svetlana Ugarcina Perovic, and supported by the#bugsigdbteam. Check it out here:https://blog.bioconductor.org/posts/2024-08-15-OutreachyInternshipExperience/ - Attachment (Bioconductor community blog): Outreachy May 2024 – Bioconductor community blog > Bioconductor participated in the Outreachy Internship program for the May 2024 cohort. In this post, our intern shares her journey, detailing her experience working on the Microbiome Study Curation project and Bioconductor in general.

2024-09-10

Alex Qin (03:46:39): > @Alex Qin has joined the channel

2024-10-01

Basirat Kareem (12:26:09): > @Basirat Kareem has joined the channel

Kate Rasheed (12:34:40): > @Kate Rasheed has joined the channel

Aleru Divine (12:54:34): > Hello everyone!:wave:My name is Divine Aleru, and I’m from Nigeria. I’m a biochemist with a strong interest in molecular toxicology, and I’m thrilled to be part of this community. > > This is my third time applying for the Outreachy internship (third time’s the charm, right?), and I’ve previously contributed to BugSigDB. I absolutely love contributing to BugSigDB and can’t wait to connect with fellow applicants. I’m super excited to work together and look forward to making meaningful contributions! > > Cheers and good luck to everyone!:sparkles::clinking_glasses:

Basirat Kareem (12:58:09): > Hello, my name is Basirat Kareem. I just got accepted into the initial application phase of the Outreachy program. I am from Lagos, Nigeria. I find this project interesting and I am really excited start contributing.

Chioma Peters (13:06:39): > @Chioma Peters has joined the channel

Chioma Onyido (13:07:05) (in thread): > Welcome Divine! Good to have you back!

Chioma Onyido (13:07:20) (in thread): > Welcome Basirat! Good to have you here!

Chris Awoke (13:07:30): > Hi, friends. My name is Chris Awoke from Nigeria. I was just accepted into the Outreachy contribution phase, and I’m excited to contribute to this project and assist my fellow participants as well.

Chris Awoke (13:09:43): > Glad to meet y’all@Chioma Onyido,@Chioma Peters,@Basirat Kareem@Aleru Divine

Chioma Onyido (13:10:19) (in thread): > You’rewelcome to Budsigdb Chris! Good to have you here!

Aleru Divine (13:10:29) (in thread): > Thank you@Chioma Onyido

Aleru Divine (13:10:58) (in thread): > Hi@Basirat Kareem:wave:welcome!

Aleru Divine (13:11:39) (in thread): > Hi,@Chris Awokewelcome

Basirat Kareem (13:12:57) (in thread): > Thank you:grin:@Chioma Onyido@Aleru Divine

Chris Awoke (13:17:41) (in thread): > Thank you,@Aleru Divineand@Chioma OnyidoIt’s nice meeting you guys.

Eseoghene Orhorho (13:20:52): > @Eseoghene Orhorho has joined the channel

Eseoghene Orhorho (13:23:39): > My name is Eseoghene Orhorho from Lagos, Nigeria. I’m excited to join the Bioconductor community as part of the Outreachy program. I have a background in Research with Computer Science and self-taught data science experience. I’m looking forward to contributing to open-source projects, learning from all of you, and collaborating to make a meaningful impact. I look forward to connecting and growing with this amazing community!

Adeshile Oluwatosin (13:24:30): > Hello everyone,My name is Adeshile Oluwatosin, and I’m from Nigeria. I’m thrilled to have been accepted into the contribution phase of Outreachy. With a background in biochemistry, I am eager to apply my skills, learn from this community, and make meaningful contributions. I look forward to collaborating and connecting with all of you!

Chioma Onyido (13:25:15) (in thread): > You’rewelcome to the bugsigdb community, Eseoghene! Good to have you here!

Chioma Onyido (13:25:34) (in thread): > You’rewelcome to the bugsigdb community Adeshile! Good to have you here!

Adeshile Oluwatosin (13:25:46) (in thread): > Thank you:blush:

Eseoghene Orhorho (13:26:08) (in thread): > Thank you@Chioma Onyido

Aleru Divine (13:26:27) (in thread): > Hello again@Adeshile Oluwatosin:hugging_face:

Adeshile Oluwatosin (13:26:58) (in thread): > Hi@Aleru Divine

Adeshile Oluwatosin (13:28:07) (in thread): > Welcome@Chris Awoke

Adeshile Oluwatosin (13:28:32) (in thread): > Welcome@Basirat Kareem

Chioma Peters (13:31:12): > Hello everyone, good evening. My name is Chioma Joy Peters. I’m thrilled to join this community as part of the outreachy program. I got certified as a product manager this year, and I’m a journalist (mass communication) by Education. This is my first time applying to the outreachy program. I don’t know what to expect or how this will go, but I’m open to learning and doing what it takes to enjoy this process, grow, and learn from all the seasoned professionals on the project I will work on and hopefully get an internship.

Eseoghene Orhorho (13:33:38) (in thread): > Welcome@Chioma Peters

Chioma Onyido (13:37:04) (in thread): > You’rewelcome to the community Chioma! Good to have you here!

Chioma Peters (13:38:46) (in thread): > Hello Namesake…

Chioma Peters (14:24:52) (in thread): > Thank You everyone

Precious Orakwe (14:47:31): > Hello, fam. > Good day our mentors@Svetlana Ugarcina Perovic@Chloe Mirzayi@Esther Afuape@Scholastica Urua@Chioma Onyido@Peace SandyMy name is Precious from Nigeria, I am an industrial chemist, and I am so glad to be accepted for the contribution phase again, this is my 4th time applying to Outreachy.:smiley:I am so happy to be in this community. I look forward to contributing, collaborating, and learning from this community

Chioma Onyido (14:54:49) (in thread): > Welcome back to the community Precious! Good to have you here again!

Chiamaka Johnfred (15:10:57): > @Chiamaka Johnfred has joined the channel

Paavni Goyal (15:17:37): > @Paavni Goyal has joined the channel

Precious Orakwe (15:18:03) (in thread): > Thank you, looking forward to learning under your mentorship

Chiamaka Johnfred (15:21:34): > Hello everyone, My name is Chiamaka from Lagos, Nigeria. I’m excited to join the Bioconductor community as part of the Outreachy program. I’m a new grad of Kinesiology and Sports science and a project manager. I am excitedly looking forward to contributing to the open-source projects, learning from the great minds here, and collaborating to make a meaningful impact. Looking forward to connecting and growing with this amazing community, thank you!

Druscilla Nakanwagi (15:27:06): > @Druscilla Nakanwagi has joined the channel

Druscilla Nakanwagi (15:27:34): > Hello everyone, my name is Druscilla from Uganda and I am happy to be a part of this project

Paavni Goyal (15:31:11): > Hello everyone, good evening. > > I hope you’re all doing great! My name is Pavani Goyal, and I’m joining from India. I’m really excited to collaborate with all of you and contribute to the project. I’m passionate about contributing to open source and am here to improve my skills while learning new ones. I look forward to gaining knowledge from this community and working alongside you all.

Mary Agekameh (15:34:03): > @Mary Agekameh has joined the channel

Balikis sulaimon (15:36:20): > @Balikis sulaimon has joined the channel

Martha Kisakye (15:40:54): > @Martha Kisakye has joined the channel

Mary Agekameh (15:44:33): > Hello everyone, good evening. > > I hope you’re all doing great? > I’m happy to join this community as part of the Outreachy Program. > > My name is Mary Agekameh from Nigeria. I’m a programs associate. This is my first time applying for the program so I don’t know how it will go but I’m opened to collaborating, learning and growing. Thank you!

Mildred Anashie (16:10:31): > Hello Everyone:wave:My name is Anashie, Mildred Andokie an outreachy applicant, and I’m from Nigeria.I’m a Microbiologist with interest in Public health and I’m excited to be here again:hugging_face:I look forward to contributing to the Bioconductor community and connecting/collaborating with everyone:clinking_glasses:

Klangi (16:16:34): > @Klangi has joined the channel

Klangi (16:19:10): > Hello everyone, I’m Klangi, this is my first time contributing, I’m excited to be here.

Aleru Divine (16:20:59) (in thread): > Hi@Klangi, welcome.:hugging_face:

Chinwendu Joy Enyidiegwu (16:22:33): > @Chinwendu Joy Enyidiegwu has joined the channel

Chinwendu Joy Enyidiegwu (16:22:35): > @Chinwendu Joy Enyidiegwu has left the channel

Chinwendu Joy Enyidiegwu (16:22:37): > @Chinwendu Joy Enyidiegwu has joined the channel

Ibizugbe Merit (16:26:46) (in thread): > Welcome@Klangi

Chinwendu Joy Enyidiegwu (16:34:48): > Hello Everyone, > My name is Chinwendu Joy, an Outreachy applicant and I’m happy to join the Bioconductor Community. > and I’m eager to learn from all of you and contribute to this project. thank you

Liliana Garmendia (16:47:18): > @Liliana Garmendia has joined the channel

Blessdamy (16:48:36): > @Blessdamy has joined the channel

Ibizugbe Merit (16:52:02) (in thread): > You’re welcome@Chinwendu Joy Enyidiegwu:hugging_face:

Adeshile Oluwatosin (16:57:04) (in thread): > Welcome@Chinwendu Joy Enyidiegwu:hugging_face:

Adeshile Oluwatosin (16:57:21) (in thread): > Welcome:hugging_face:@Klangi

adekemi balogun (16:58:03): > @adekemi balogun has joined the channel

Mildred Anashie (16:58:27) (in thread): > Welcome@Chinwendu Joy Enyidiegwu

Mildred Anashie (16:59:02) (in thread): > Hi@Klangi, Welcome:hugging_face:

Mildred Anashie (16:59:30) (in thread): > Also join the#bugsigdbChanel to get started

Blessdamy (17:22:05): > Hello everyone, and special greeting to all mentors,@Svetlana Ugarcina Perovic,@C. Mirzayi (please do not tag this account),@Peace Sandy,@Chioma Onyido,@Esther Afuape,@Scholastica Urua, > > My name is Blessing Ejogbamu, and I am glad to join the Bioconductor community to contribute to the “Microbiome Study Curation” project. I studied Plant Biology and Biotechnology with a major in Biotechnology, which fueled my passion for literature reviews, biological research, and curation. > > I’m particularly excited about how microbiome studies can inform health and environmental research, and I’m eager to contribute to the curation of these valuable datasets. I would love guidance on how I can begin contributing in a meaningful way. > > Looking forward to learning from this amazing community and making impactful contributions. > I’m excited to start this journey with everyone.

Igwe Maryann (17:22:40): > @Igwe Maryann has joined the channel

Eseoghene Orhorho (17:29:31) (in thread): > Hello Blessdamy, I look forward to collaborating with you too.

Eseoghene Orhorho (17:31:04) (in thread): > On the#bugsigdbchannel, there’s a pinned message by@Svetlana Ugarcina Perovic. It has the guidelines to get you started. I don’t know how to share it here, so I’ll forward it to you.

Eseoghene Orhorho (17:34:41) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Blessdamy (17:38:35) (in thread): > Thank you for your assistance Eseoghene, I will do well to go through it! > > Looking forward to learning and collaboration with you as well:innocent:

Chris Awoke (17:39:50) (in thread): > You’re welcome onboard@Eseoghene Orhorho

Chris Awoke (17:42:37) (in thread): > You’re welcome,@Mary AgekamehBe rest assured we’ll work together to make meaningful contribution to the Bioconductor projects.

Amrita Das (17:49:32): > @Amrita Das has joined the channel

Adeshile Oluwatosin (18:39:51) (in thread): > Welcome:hugging_face:@Mary Agekameh

Samuel Ogunleye (20:02:56): > @Samuel Ogunleye has joined the channel

Eniola Kolawole (20:10:25): > @Eniola Kolawole has joined the channel

BOLARINWA AISHAT (20:30:16): > @BOLARINWA AISHAT has joined the channel

Royyale C (20:54:13): > @Royyale C has joined the channel

Eniola Kolawole (21:05:31): > Good day everyone, > > My name is Eniola Kolawole, I am a graduate of Science Laboratory Technology and did my final project in the area of Environmental Chemistry where I dealt with public health and environmental problems as a result of improper waste management. I am glad to have this opportunity to apply my research skill, theoretical knowledge, and laboratory skill in making tangible contributions to the Microbiome Study Curation Project in the Bioconductor Community. I hope we will be able to work together to achieve a great result at the end. Nice to meet you all. > > To our mentors@Svetlana Ugarcina Perovic,@C. Mirzayi (please do not tag this account),@Peace Sandy,@Chioma Onyido,@Esther Afuapeand@Scholastica Urua. Thank you for starting this journey with us.

Mildred Anashie (21:10:23) (in thread): > Hi@Eniola KolawoleWelcome:hugging_face:Also join the#bugsigdbcommunity to get started

Eniola Kolawole (21:14:23) (in thread): > Thank you@Mildred Anashie:heart:

Janani Ravi (21:54:16): > @Janani Ravi has joined the channel

2024-10-02

Peace Sandy (02:42:11) (in thread): > Welcome@Precious Orakwe

Peace Sandy (02:42:34) (in thread): > Welcome

Eniola Kolawole (03:11:20) (in thread): > Thank you@Peace Sandy:heart_hands:

Arpita (04:20:45): > @Arpita has joined the channel

BOLARINWA AISHAT (04:43:36): > Good day everyone > > My name is Aishat Bolarinwa, I am a Pharmacist and a data scientist. I am interested in the Microbiome Study Curation Project. I am new to open source contributions but I’m optimistic that I’ll be able to acquire as much knowledge and make impactful contributions with the help of the community and mentors@C. Mirzayi (please do not tag this account)@Scholastica Urua@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther AfuapeThank you for having me.

Mildred Anashie (04:55:48) (in thread): > Hi@BOLARINWA AISHATWelcome:hugging_face:Please join#bugsigdb

Chris Awoke (04:58:53): > Hi,@BOLARINWA AISHAT. You’re welcome. Kindly join the#bugsigdbchannel to get started. > > You’ll see the pinned message by@Svetlana Ugarcina PerovicOr here’s it:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539You can thereafter, check this one by@Aleru Divine:point_right:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

James Efienemokwu (10:15:13): > @James Efienemokwu has joined the channel

Dorcas Samuel (11:35:55): > @Dorcas Samuel has joined the channel

Obuli Abraham (11:43:26): > @Obuli Abraham has joined the channel

James Efienemokwu (11:55:03): > Hello everyone, my name Is James Efienemokwu I am a full stack developer and technical writer with a background in bioinformatics and biochemistry. It is a pleasure to be part of the bioconductor community, I am very eager to learn and contribute to this awesome project, thank you.

Eniola Kolawole (12:00:40) (in thread): > You are welcome James. Check the pinned message in the#bugsigdbchannel to know where to start from.

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2024-10-03

Samted Uche (teddyCodex) (00:42:37): > @Samted Uche (teddyCodex) has joined the channel

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Himanshi Srestha (14:50:05): > Hi everyone :wave:****, I’m Himanshi Srestha , an Outreachy applicant!****I’m excited to contribute to BugSigDB by synthesizing human microbiome studies and analyzing microbial signatures linked to health outcomes. Looking forward to learning more about microbiome research and collaborating with all of you to enhance the BugSigDB database!

Adeshile Oluwatosin (15:27:59) (in thread): > Welcome:hugging_face:To get started, join #bugSigDB channel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Himanshi Srestha (16:56:27) (in thread): > Thank you so much@Adeshile Oluwatosin

Adeshile Oluwatosin (17:33:30) (in thread): > You are welcome

Joy (21:06:45): > @Joy has joined the channel

Joy (21:07:57): > Helloeveryone, > > My name is Joy, and I’m an Outreachy applicant for the December 2024 to March 2025 round. I’m excited to contribute to the MolEvolvR project and to collaborate with such a talented and diverse group! > > Looking forward to working with you all and learning from this experience!:blush:

Inimfon Ebong (21:13:38): > @Inimfon Ebong has joined the channel

Teresia (23:05:20): > @Teresia has joined the channel

2024-10-04

Monisa Hasnain (02:04:54): > @Monisa Hasnain has joined the channel

Princess Rehoboth Asuelimen (05:30:58): > @Princess Rehoboth Asuelimen has joined the channel

Princess Rehoboth Asuelimen (05:35:35): > Hello everyone, my name is Princess Asuelimen. Excited to be here. I’m looking forward to contributing and learning a lot on this platform.

Adeshile Oluwatosin (05:47:02) (in thread): > Welcome@Princess Rehoboth Asuelimen:hugging_face:Check out#bugsigdband#molevolvrJoin one of the channels and start contributing:blush:

Ameerat Bibire (08:00:46): > @Ameerat Bibire has joined the channel

Matthew Idungafa (08:54:16): > Welcome@Inimfon Ebongand@Ameerat Bibire, it’s nice to have you here, kindly go through pinned messages and feel free to ask questions if you are lost

Evan Chinny (10:03:51): > Hello.. I’m new here . Looking forward to contributing

Andres Wokaty (10:35:59): > set the channel description: Applicants can introduce themselves and ask questions. > Dec 24 projects > * Microbiome Study Curation > * Developing MolEvolvR for protein analysis: extending the web app, and creating a companion R package

Oluchi Nwankwo (12:57:39): > @Oluchi Nwankwo has joined the channel

Oluchi Nwankwo (13:00:04): > Hello everyone, my name is Oluchi Nwankwo. I’m happy to be here, and I look forward to contributing and learning a lot on this platform.

Adeshile Oluwatosin (13:49:15) (in thread): > Welcome@Oluchi Nwankwo:hugging_face:Check out#bugsigdband#molevolvrJoin one of the channels and start contributing:blush:

abdulwasiu maryam (13:52:11): > @abdulwasiu maryam has joined the channel

abdulwasiu maryam (13:54:52): > Hello everyone, I am Maryam, A microbiologist and a software developer. I would be glad to contribute to Microbiome Study Curation.

Shachi (14:09:47): > @Shachi has joined the channel

Shachi (14:18:46): > Hello everyone! I’m Shachi from India, excited to contribute to this project and learn alongside all of you.

Adeshile Oluwatosin (14:33:47) (in thread): > Welcome@Shachi:hugging_face:Check out#bugsigdband#molevolvrJoin one of them and start contributing

Adeshile Oluwatosin (14:34:35) (in thread): > Welcome@abdulwasiu maryam:hugging_face:To get started, join#bugsigdbchannel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the#bugsigdbchannel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Awa (14:59:24): > @Awa has joined the channel

Awa (15:00:40): > Hi, I am Awa, an outreachy applicant and I’m thrilled to contribute to the MolEvolvR project

Janani Ravi (15:08:55) (in thread): > Hi Awa, please join#molevolvrand introduce yourself there. Also go through the pinned posts and notes posted above, and see where you’d like to start contributing.

Erick Navarro (16:01:39): > @Erick Navarro has left the channel

Zara Adwan (16:43:38): > @Zara Adwan has joined the channel

Zara Adwan (16:45:44): > Hello everyone, I am Zara, a biomedical and data scientist. > I am excited to contribute to this project and learn with you guys!

Awa (16:48:14) (in thread): > Hi Zara, welcome. There are two projects. Which one are you interested in?

Zara Adwan (16:56:28) (in thread): > Bugsigdb

Awa (16:57:54) (in thread): > Join the#bugsigdbchannel and introduce yourself for instructions on how to begin contributing. You can also check the pinned messages there for directions.

Samuel Nnanna (17:27:54): > @Samuel Nnanna has joined the channel

Samuel Nnanna (17:29:00): > Hello Everyone, i am Samuel and I am Biochemistry and Microbiology Graduate. I’d really love to contribute to the project and I’m looking forward to the experience

Adeshile Oluwatosin (18:25:59) (in thread): > Welcome:hugging_face:@Samuel Nnanna

Janani Ravi (19:02:00) (in thread): > Welcome, Samuel! are you interested in#bugsigdbor#molevolvr? If you would like to generate case studies for a few microbial proteins, you’re most welcome to!

Rohit Gupta (22:48:02): > @Rohit Gupta has joined the channel

Rohit Gupta (22:53:15): > Hello Everyone! > > I am Rohit from India. Really excited to contribute to this project and learn with all of you. > I have decent understanding of Data Analysis, Software development and have basic understanding of Biochemistry. > Would love to contribute to#bugsigdb

2024-10-05

Samuel Nnanna (00:52:10) (in thread): > Thank you so much@Adeshile Oluwatosinand@Janani RaviI’minterested in#bugsigdbandI’mcurrently going through the prep work to fully understand the project and how to contribute, thanks to members of this project for the quick “getting started” tips.

Samuel Nnanna (00:54:24) (in thread): > Welcome Rohit:smirk::smirk:

Adeshile Oluwatosin (01:34:48) (in thread): > Here it is again for easy reach, > To get started, > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, i’m here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Adeshile Oluwatosin (01:39:05) (in thread): > Welcome:hugging_face:@Rohit GuptaTo get started, join#bugsigdbchannel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the#bugsigdbchannel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Rhoda Wambui (03:57:07): > @Rhoda Wambui has joined the channel

Rhoda Wambui (04:00:05): > Hello everyone I am Rhoda from Kenya and I am excited to contribute to this project .I also hope to learn from you guys.

Adeshile Oluwatosin (04:11:59) (in thread): > Welcome@Rhoda Wambui:hugging_face:

Adeshile Oluwatosin (04:12:27) (in thread): > Join either of the channels to get started#bugsigdb#molevolvr

Rohit Gupta (10:03:40) (in thread): > Thank you so much@Adeshile Oluwatosinand@Samuel Nnanna:melting_face::slightly_smiling_face:

Adeshile Oluwatosin (10:21:44) (in thread): > You are welcome

Ebele Lynda Okolo (13:28:52): > @Ebele Lynda Okolo has joined the channel

Ebele Lynda Okolo (13:48:23): > Hello everyone, > I am Ebele Okolo, an Outreachy contributor. I am a microbiologist and a software developer interested in gene and Viruses. I am excited to contribute to this project and will appreciate all the guidance and mentorship i can get. Thank you

Adeshile Oluwatosin (13:49:15) (in thread): > Welcome@Ebele Lynda Okolo:hugging_face:

Adeshile Oluwatosin (13:49:41) (in thread): > Check out#bugsigdband#molevolvrJoin one of the channels and start contributing

Mildred Anashie (16:14:43) (in thread): > Welcome@Ebele Lynda Okolo:hugging_face:

Khushal Sarode (18:06:46): > @Khushal Sarode has joined the channel

Ifeoma Okafor (20:56:21): > @Ifeoma Okafor has joined the channel

2024-10-06

Toluwalase Abigail (00:57:31): > @Toluwalase Abigail has joined the channel

Toluwalase Abigail (00:59:11): > Hello, everyone!I’m Toluwalase, and I’m excited to be an Outreachy applicant happy to contribute to theMicrobiome Study Curationproject. Looking forward to collaborate with everyone!:hugging_face:

Samuel Nnanna (01:30:03) (in thread): > Hello@Toluwalase Abigail. Welcome to the project. > Head on to the#bugsigdbchannel, there are alot of helpful tips on how to get started.

Oromidayo Owolabi (12:48:36): > @Oromidayo Owolabi has joined the channel

2024-10-07

jubril adeyi (07:59:44): > @jubril adeyi has joined the channel

jubril adeyi (08:02:48): > Hello, everyone!I’m Jubril, an Outreachy applicant and looking forward to contributing to theMicrobiome Study Curationproject.

BOLARINWA AISHAT (08:17:46) (in thread): > Welcome on board > > Kindly join#bugsigdband check out the pinned messages for directions > > Best wishes

Samuel Nnanna (08:22:37) (in thread): > Welcome@BOLARINWA AISHATHead on to the#bugsigdbthere’s a plethora of info to help you get started and ask questions, if you have any confusions.

Adeshile Oluwatosin (08:48:56) (in thread): > Welcome:hugging_face:@jubril adeyiTo get started, join#bugsigdbchannel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the#bugsigdbchannel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Axxhie (17:06:18): > @Axxhie has joined the channel

2024-10-08

Vaishali Rawat (06:15:07): > @Vaishali Rawat has joined the channel

2024-10-09

Swazi (17:13:19): > @Swazi has joined the channel

Swazi (17:13:43): > Hello, everyone! > I’m Swazi Nkosi, an Outreachy applicant, and I’m thrilled to be here! I’m looking forward to contributing, learning, and collaborating with you all throughout this journey. I can’t wait to get started and make the most of this amazing opportunity!

2024-10-10

Tasha Daije (02:59:00): > @Tasha Daije has joined the channel

Tasha Daije (03:02:43): > Hello everyone, > I’m Natasha Daije, an outreachy applicant and would like to contribute to the Microbiome Study Curation project. Looking forward to working with and learning from y’all

Aleru Divine (03:03:47) (in thread): > Welcome@Swazi:hugging_face:Please join#bugsigdband check the pinned messages to get started on contributing.

Aleru Divine (03:04:26) (in thread): > Welcome@Tasha Daije:hugging_face:Please join#bugsigdband check the pinned messages to get started on contributing.

Adeshile Oluwatosin (03:50:46) (in thread): > Welcome@Tasha Daije:hugging_face:

Adeshile Oluwatosin (03:51:35) (in thread): > To get started, join#bugsigdbchannel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the#bugsigdbchannel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Adeshile Oluwatosin (03:52:01) (in thread): > Welcome@Swazi:blush:

Tasha Daije (05:42:36) (in thread): > Thank you for guidance

Adeshile Oluwatosin (05:43:24) (in thread): > Welcome:thumbsup:

Mildred Anashie (07:15:15) (in thread): > Welcome@Tasha Daije

Richie (08:17:58): > @Richie has joined the channel

Richie (08:25:24): > Hello everyone. My name is Richie, I’m from Mombasa, Kenya. Looks like I have some catching up to do, but I’m looking forward to making contributions to the Microbiome Study Curation project and learning from you all. Thrilled to be here!

Mildred Anashie (08:26:03) (in thread): > Hi@RichieWelcome:hugging_face:

Mildred Anashie (08:26:28) (in thread): > Join#bugsigdbto get started and view the pinned post

Adeshile Oluwatosin (08:39:50) (in thread): > Welcome:hugging_face:@RichieTo get started, join#bugsigdbchannel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #but gsigdb channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Charles Ebong (18:02:10): > @Charles Ebong has joined the channel

2024-10-11

Matthew Idungafa (11:42:43): > welcome@Charles Ebong, trust you’re doing great today? It’s nice to have you here

2024-10-14

Tino (08:13:33): > @Tino has joined the channel

2024-10-15

vandana maddi (22:46:28): > @vandana maddi has joined the channel

2024-10-17

Andres Wokaty (09:53:03): > Outreachy applicants, thanks for all your hard work and enthusiasm! With less than 2 weeks to go, please make sure that you’re recording your contributions onoutreachy.orgfor the projects you’re applying to.

Mildred Anashie (10:06:36) (in thread): > Thank you@Andres Wokaty

Fanny (10:44:47): > @Fanny has joined the channel

Adeshile Oluwatosin (10:53:49) (in thread): > Noted@Andres Wokaty

2024-10-19

Immaculate Atim (08:18:00): > @Immaculate Atim has joined the channel

2024-10-21

Joy (11:01:26) (in thread): > Thank you@Andres Wokaty

2024-10-23

anusha_R (08:59:48): > @anusha_R has joined the channel

2024-10-24

Mercy Cherop (12:55:24): > @Mercy Cherop has joined the channel

2024-11-28

Dan (08:28:44): > @Dan has joined the channel

Awa (11:13:06): > Congratulations to all successful Outreachy applicantshttps://www.outreachy.org/alums/2024-12/ - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

2024-12-21

Ouma Ronald (10:30:08): > @Ouma Ronald has joined the channel

2024-12-28

Michael Hungbo (07:31:01): > @Michael Hungbo has joined the channel

Pascal-Onaho (07:56:02): > @Pascal-Onaho has joined the channel

Srushti (12:57:22): > @Srushti has joined the channel

2025-01-02

George Kitundu (00:52:48): > @George Kitundu has joined the channel

2025-01-11

Shahenda Soliman (22:18:46): > @Shahenda Soliman has joined the channel

Shahenda Soliman (22:25:03): > Hello everyone, > I’m here as a result of trying to know more about microbiome curation project by Outreachy internship, in order to know more and see if I can choose this project in the contribution phase of the internship after I will get hopefully accepted in the upcoming initial application, Am I in the right place:thinking_face:?

2025-01-13

Svetlana Ugarcina Perovic (02:34:37) (in thread): > Hello, please join#bugsigdbwhere we discuss Microbiome Study Curation project.

Shahenda Soliman (09:31:08) (in thread): > Alright thank you.

Chidera (14:53:24): > @Chidera has joined the channel

2025-01-14

neslihan oztas (10:29:16): > @neslihan oztas has joined the channel

2025-02-03

Chris Thomas (17:25:37): > @Chris Thomas has joined the channel

2025-02-06

Akriti (13:17:36): > @Akriti has joined the channel

2025-02-11

Juliana Kentomahun Mautin (11:36:16): > @Juliana Kentomahun Mautin has joined the channel

2025-02-13

Anushka Paharia (09:23:16): > @Anushka Paharia has joined the channel

2025-02-27

Maria Doyle (18:13:54): > :writing_hand:**** New Bioconductor blog post on mentoring in Outreachy!****Svetlana Ugarcina Perovic shares her experiences with the Microbiome Study Curation project and open science. Check it out here:https://blog.bioconductor.org/posts/2025-02-26-outreachy-mentoring/Interested in mentoring? Submit a project byMarch 7, 2025, 4 PM UTC atOutreachy. > Thanks@Svetlana Ugarcina Perovic! - Attachment (Bioconductor community blog): Open Science Mentoring: My Journey with Outreachy Mentees – Bioconductor community blog > A blog for the Bioconductor community!

2025-02-28

Saloni Sharma (05:10:21): > @Saloni Sharma has joined the channel

2025-03-12

Sanika Menkudale (04:49:22): > @Sanika Menkudale has joined the channel

Sanika Menkudale (05:02:50): > Hello, I am Sanika Menkudale,looking forward to contribute in Outreachy internship cohort.how Can I know more about microbiome curation project? Thank you!

Svetlana Ugarcina Perovic (05:04:57) (in thread): > Hi Sanika, please join#bugsigdbchannel and feel free to ask questions there related to the Microbiome Study Curation project. Thanks!

2025-03-16

RITU VERMA (10:26:56): > @RITU VERMA has joined the channel

2025-03-17

Eseoghene Cynthia Princewill-Ukot (12:27:33): > @Eseoghene Cynthia Princewill-Ukot has joined the channel

progress olaoye (12:29:41): > @progress olaoye has joined the channel

progress olaoye (12:33:08): > Hello everyone, my name is Progress Olaoye Mylo, I usually go by Progress or Mylo. I’m glad to be a part of this team, and I look forward to making meaningful contributions!

Svetlana Ugarcina Perovic (12:40:37) (in thread): > Hello, please join#bugsigdbchannel and feel free to ask questions there related to the Microbiome Study Curation project. Thanks!

progress olaoye (12:41:26) (in thread): > Thanks Svetlana!

Daberechi Okorie (12:55:03): > @Daberechi Okorie has joined the channel

Precious Chijioke (12:56:05): > @Precious Chijioke has joined the channel

Jesulolufemi Adelanke (12:56:43): > @Jesulolufemi Adelanke has joined the channel

Shade Akinremi (12:56:56): > @Shade Akinremi has joined the channel

Jesulolufemi Adelanke (12:57:58): > Hello everyone, > My name is Jesulolufemi Adelanke. I’m really excited to be here and contribute to this project. > Looking forward to interacting with everyone. Nice to meet y’all.

Daberechi Okorie (12:58:40): > Hi everyone, > > My name is Daberechi, I’m an Outreachy applicant excited about the Microbiome project. > > I’m particularly drawn to this project’s impact on reproducible research and would love the opportunity to collaborate and learn with everyone. Looking forward to contributing!

Precious Chijioke (12:59:05): > Hello everyone, my name is Precious Chijioke. I’m excited to be part of this community, and I look forward to making meaningful and amazing contributions.

Svetlana Ugarcina Perovic (13:00:02): > Hello@Jesulolufemi Adelanke@Daberechi Okorie@Precious Chijiokeplease join#bugsigdbchannel and feel free to ask questions there related to the Microbiome Study Curation project. Thanks!

Daberechi Okorie (13:00:21) (in thread): > Thank you! joined!

Shade Akinremi (13:01:06): > Hello everyone, I am Shade Akinremi. I look forward to making meaningful contributions, collaborating with the team, and learning from everyone involved.

Svetlana Ugarcina Perovic (13:01:26) (in thread): > Hello, please join#bugsigdbchannel and feel free to ask questions there related to the Microbiome Study Curation project. Thanks!

Shahenda Soliman (13:20:07): > congratulations to the accepted applicants.

Eniola Kolawole (13:33:00): > Hi everyone > Good day to all the mentors in the house > I’m Eniola Kolawole > > Good to be here again. A lot happened the last time, from spoilt devices to no power supply. Hope to make this one count by being able to contribute massively, receive much help and as well help others. Thank you

Eseoghene Cynthia Princewill-Ukot (13:33:31): > Hello everyone! I’m Princewill-Ukot Eseoghene Cynthia but you can call me Ese. I’m from Nigeria. I’m happy to be here!

Anne-Marie Sharp (13:37:08): > @Anne-Marie Sharp has joined the channel

Anne-Marie Sharp (13:39:26): > Hello everyone, I’m Anne-Marie Sharp. Super excited to be part of this community. And looking forward to learning and collaborating

Yvette Odionye (13:43:52): > @Yvette Odionye has joined the channel

Yvette Odionye (13:46:40): > Hello everyone! > My name is Yvette Odionye, and I’m thrilled to be part of this Outreachy contribution round and I’m excited to contribute to this project and collaborate with all of you. > I am looking forward to learning, growing, and working together as a team. > Let’s make this a great experience together!:muscle:

Adeshile Oluwatosin (13:50:58) (in thread): > Welcome:tulip:@Yvette OdionyeKindly join#bugsigdbchannel

Juliana Kentomahun Mautin (14:22:20) (in thread): > You are welcome@Svetlana Ugarcina Perovic. Join#bugsigdbchannel to introduce yourself and ask your question

Emily Chima (14:22:43): > @Emily Chima has joined the channel

Juliana Kentomahun Mautin (14:23:45) (in thread): > You are welcome@Anne-Marie Sharp. Please join#bugsigdbto introduce yourself and ask your question relating to micro biome signature

Juliana Kentomahun Mautin (14:24:40) (in thread): > Welcome@Eseoghene Cynthia Princewill-Ukot. Join#bugsigdbto introduce yourself and ask questions relating Microbiome curation.

Utibe Ita (14:52:12): > @Utibe Ita has joined the channel

Igber Nicholas (15:25:16): > @Igber Nicholas has joined the channel

Igber Nicholas (15:42:24): > Hi everyone, I’m Nicholas Igber, a software developer with an undergraduate degree in biochemistry. I haven’t been in academia for a while, lol I’ve spent most of my time digging into codebases however I’m here now and ready to give it my best shot. I like to ask questions, some of which may sound dumb but it helps me understand better. when I’m not coding, I pass time either watching football, reading books, or playing chess. I’m super excited to be here and I’m willing to help however I can.

Eseoghene Cynthia Princewill-Ukot (16:17:05) (in thread): > Welcome onboard@Igber Nicholas

Igber Nicholas (16:17:48) (in thread): > thank you@Eseoghene Cynthia Princewill-Ukot

Halima Momoh (16:39:38): > @Halima Momoh has joined the channel

Lois Omonaiye (16:49:03): > @Lois Omonaiye has joined the channel

Halima Momoh (16:55:27): > Hey everyone!:wave:I’m Momoh Halima Abdullahi, super excited to be part of theMicrobiome Study Curationproject!:rocket:With a background in Chemical Engineering and a passion for UI/UX and problem-solving, I’m here to learn, collaborate, and make meaningful contributions. Can’t wait to dive into the world of microbiome data with this amazing community.

Lois Omonaiye (16:55:40): > Hello everyone! I’m Lois Omonaiye. I’m excited to contribute meaningfully, collaborate with the team, and learn from each of you. Looking forward to this journey together!

Adeshile Oluwatosin (17:10:45) (in thread): > Welcome:tulip:@Halima MomohKindly join#bugsigdbchannel

Juliana Kentomahun Mautin (17:19:14) (in thread): > Welcome@Lois Omonaiye. Kindly Join#bugsigdbchannel and feel free to ask any questions relating to micro biome curation

Juliana Kentomahun Mautin (17:20:41) (in thread): > Welcome@Igber Nicholas. Please kindly Join#bugsigdb. Please feel free to ask questions relating to Microbiome curation study in the channel.

Divya Karlapudi (22:28:52): > @Divya Karlapudi has joined the channel

Fik (22:59:47): > @Fik has joined the channel

Fik (23:08:11): > Hello everyone! My name is Gideon, and I’m excited to be part of this Outreach contribution round. I look forward to learning, growing, and collaborating with you all. Let’s make this a great experience together!:muscle:

2025-03-18

Krisha Jada (00:02:52): > @Krisha Jada has joined the channel

Juliana Kentomahun Mautin (00:41:30) (in thread): > Hello@Fik, you are welcome:blush:. Please kindly join the#bugsigdbchannel to get started and ask any questions relating to Microbiome study curation.

Richard Akintola (01:02:35): > @Richard Akintola has joined the channel

NIDHI SINGH (01:07:46): > @NIDHI SINGH has joined the channel

Star Chukwunyerenwa (Ozi) (05:21:29): > @Star Chukwunyerenwa (Ozi) has joined the channel

chiamaka Uche (06:02:08): > @chiamaka Uche has joined the channel

Eseoghene Cynthia Princewill-Ukot (08:37:59): > Hello everyone. Can anyone guide me on how to submit my contribution to outreachy,?

Anne-Marie Sharp (08:40:28) (in thread): > Hello@Eseoghene Cynthia Princewill-Ukotgo to your Outreachy dashboard. And to the Bioconductor project, you will see an icon to record/add contribution. Then simply follow the guide there. You will have to paste the link for the quiz/mini curation page and describe the contribution you made. > You can as well edit the contribution

emmanuel adeitan (08:40:55): > @emmanuel adeitan has joined the channel

Eseoghene Cynthia Princewill-Ukot (08:41:58) (in thread): > :pray:

emmanuel adeitan (08:42:20): > Hi everyone! I’m Emmanuel Adeitan, excited to contribute to projects and collaborate with you all!

Eseoghene Cynthia Princewill-Ukot (09:17:36) (in thread): > @Anne-Marie SharpIs it the original link to the form?

Anne-Marie Sharp (09:19:39) (in thread): > @Eseoghene Cynthia Princewill-UkotYes, I used thishttps://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy First Task > BugSigDB Outreachy First Task

Eseoghene Cynthia Princewill-Ukot (09:20:56) (in thread): > Thanks. You are the best:slightly_smiling_face:

Anne-Marie Sharp (09:21:46) (in thread): > You’rewelcome.Glad to help

Adeshile Oluwatosin (10:04:27) (in thread): > Welcome@emmanuel adeitanKindly join#bugsigdbchannel

Eseoghene Cynthia Princewill-Ukot (10:30:31) (in thread): > Welcome@emmanuel adeitan

Marvellous Jayesimi (10:52:03): > @Marvellous Jayesimi has joined the channel

Kafayat Azeez-Fashola (10:56:31): > @Kafayat Azeez-Fashola has joined the channel

Kafayat Azeez-Fashola (10:58:47): > Hi everyone! > I am Kafayat Azeez-Fashola, a data analyst and researcher. I am excited to explore the world of Microbiome with you all. > > Would you kindly guide me on how to get started? I have joined the#bugsigdbchannel already. > Thank you.

Eseoghene Cynthia Princewill-Ukot (11:26:04) (in thread): > Welcome@Kafayat Azeez-Fashola

Eseoghene Cynthia Princewill-Ukot (11:31:10) (in thread): > Kindly follow the instructions in the#bugsigdbchannel and make your first contribution

Adebisi Adeyemi (11:59:01): > @Adebisi Adeyemi has joined the channel

Adebisi Adeyemi (12:00:42): > Hello everyone, I’m Adebisi Adeyemi. Looking forward to contributing and learning with you all

Adeshile Oluwatosin (14:18:23) (in thread): > Welcome:tulip:@Adebisi AdeyemiKindly join#bugsigdbchannel

Mariam Omiteru (15:20:36): > @Mariam Omiteru has joined the channel

Mariam Omiteru (15:21:32): > Hi everyone, I’m Mariam. Excited to collaborate, learn and contribute

Kibe Ume (20:38:01): > @Kibe Ume has joined the channel

Kibe Ume (20:40:31): > Hi everyone! > > Glad to be here contributing for the June 2025 outreachy internship cohort. Looking forward to learning with y’all.

Adeshile Oluwatosin (21:29:28) (in thread): > Welcome:tulip:@Kibe UmeKindly join#bugsigdbchannel

2025-03-19

Juliana Kentomahun Mautin (03:16:32) (in thread): > Hello@Mariam Omiteru. You are welcome to this community. Please kindly join the#bugsigdbchannel to introduce yourself and ask any question relating to Microbiome curation study.

Juliana Kentomahun Mautin (03:20:22) (in thread): > @Kafayat Azeez-FasholaKindly check out the message to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169?thread_ts=1742198168.683169&cid=C04RATV9VCY. > > You can also check out the post which provides insightful tips on how to start your first curation .https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609?thread_ts=1727830699.572609&cid=C04RATV9VCY - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Ifunanya Benita Obiaku (06:34:53): > @Ifunanya Benita Obiaku has joined the channel

Amaka (06:46:03): > @Amaka has joined the channel

Oriade Adeola (09:52:14): > @Oriade Adeola has joined the channel

Oriade Adeola (10:30:30): > Hi everyone! > I am Adeola Oriade, a Product Designer with a skill in user research and documentation. I am excited to be contributing as an outreachy applicant. > I would appreciate if anyone can you guide me on how to get started? Thank you.

Adeshile Oluwatosin (10:45:11) (in thread): > Welcome:tulip:@Oriade AdeolaKindly join#bugsigdbchannel

Oriade Adeola (10:49:03) (in thread): > Ok, Thank you.

Janani Ravi (12:23:47): > @Janani Ravi has left the channel

D-coder111 (16:24:17): > @D-coder111 has joined the channel

2025-03-20

Ayomide Olugbenga Ojo (06:34:26): > @Ayomide Olugbenga Ojo has joined the channel

Ayomide Olugbenga Ojo (06:38:58): > Hi Everyone. I’m Ayomide Olugbenga-Ojo from Nigeria, and I’m super excited to be here. > I have a data analytics, cloud computing, and IT support background. I’m passionate about open-source technology and eager to learn, collaborate, and contribute to this amazing community. > In my free time, I enjoy storytelling, exploring tech innovations, and helping more people—especially women—get into tech. Looking forward to working with you all!

Ayomide Olugbenga Ojo (06:41:31): > I would really appreciate it if i could be guided on how to get started? Thank you.

Mildred Anashie (06:45:39) (in thread): > Hi@Ayomide Olugbenga OjoWelcome:hugging_face:Join#bugsigdbto get started

Victoria (Burah) Poromon (06:53:08) (in thread): > Hi@Ayomide Olugbenga OjoI’ll tag you to the welcome material on the#bugsigdbchannel. It will help you get started

Ayomide Olugbenga Ojo (07:12:43) (in thread): > Thank you Mildred. I have joined as well.

Ayomide Olugbenga Ojo (07:13:13) (in thread): > Thank you so much Victoria. Seen already.

Victoria (Burah) Poromon (07:13:37) (in thread): > You’rewelcome!

Mariam Omiteru (07:29:47) (in thread): > oh, sorry I’m just seeing this. I’m in the channel already, thanks though

Chinenye Aroh (09:16:46): > @Chinenye Aroh has joined the channel

2025-03-21

Juliana Kentomahun Mautin (05:09:30) (in thread): > Welcome@Ayomide Olugbenga Ojo

Ayomide Olugbenga Ojo (09:19:47): > @Ayomide Olugbenga Ojo has left the channel

Joy (13:46:10): > Hi everyone I am Joy from Nigeria. I am glad to be part of this Outreachy contribution stage. I look forward to collaborating with you all.

Eseoghene Cynthia Princewill-Ukot (14:24:47) (in thread): > Welcome@Joy.

2025-03-22

Gonza Gertrude (00:48:51): > @Gonza Gertrude has joined the channel

2025-03-27

Ameenat Oloko (07:50:16): > @Ameenat Oloko has joined the channel

2025-03-29

Bridget Imarhia (13:12:51): > @Bridget Imarhia has joined the channel

2025-03-31

Bola (09:21:43): > @Bola has joined the channel

Bola (09:24:52): > Hallo everyone , I’m Bola… i’m glad to be here

Mildred Anashie (09:30:56) (in thread): > Hi@BolaWelcome…Please join#bugsigdbto get started

Adeshile Oluwatosin (11:23:40) (in thread): > Welcome:tulip:@Bola

2025-04-07

Bola (04:14:37): > @Montana-DHallo, this is Bola

2025-04-11

Antonia Beatriz Soler Riera (09:15:40): > @Antonia Beatriz Soler Riera has joined the channel

Antonia Beatriz Soler Riera (09:22:11): > Hello, my name is Antonia, I received a mail 2 days ago saying my initial application for the June 2025 Outreachy internship cohort was approved, and the deadline for a contribution is in 4 days, so I am reading about bugsigdb project and will try to do my best. Thank you for the opportunity.

Anne-Marie Sharp (09:24:18) (in thread): > Hello Antonia.You’rewelcome. Please join#bugsigdbchannel, we can all assist you there

Adeshile Oluwatosin (09:35:53) (in thread): > Welcome@Antonia Beatriz Soler RieraPlease join the stated channel

Gonza Gertrude (10:31:11): > @Gonza Gertrude has left the channel

2025-04-13

USLACKBOT (21:26:10): > This message was deleted.

2025-04-14

Andres Wokaty (10:12:20) (in thread): > Hi@Bola, I recommend asking on#bugsigdb

Joseph Okoye (17:31:54): > @Joseph Okoye has joined the channel