#community-advisory-board

2020-03-30

Matt Ritchie (07:48:28): > @Matt Ritchie has joined the channel

Aedin Culhane (07:51:43): > @Aedin Culhane has joined the channel

Leonardo Collado Torres (07:51:43): > @Leonardo Collado Torres has joined the channel

Kozo Nishida (07:51:43): > @Kozo Nishida has joined the channel

Johannes Rainer (07:51:43): > @Johannes Rainer has joined the channel

saskia (07:51:43): > @saskia has joined the channel

Lori Shepherd (07:51:43): > @Lori Shepherd has joined the channel

USLACKBOT (08:07:59): > This channel’s now shared betweencommunity-biocandyagoubali. It works just like any other channel, except better — because here, there are two teams working together.

Laurent Gatto (11:56:55): > @Laurent Gatto has joined the channel

Laurent Gatto (13:07:12): > @Laurent Gatto has left the channel

Laurent Gatto (13:07:24): > @Laurent Gatto has joined the channel

Benilton S Carvalho (13:45:30): > @Benilton S Carvalho has joined the channel

Susan Holmes (16:54:54): > @Susan Holmes has joined the channel

2020-03-31

Aedin Culhane (11:45:32): > Excited to see the CAB getting together:wink:

Susan Holmes (14:15:15): > :+1:

Charlotte Soneson (15:11:19): > @Charlotte Soneson has joined the channel

USLACKBOT (17:49:05): > @Matt Ritchiestopped sharing this channel withyagoubali. In the future, any messages sent here will only be seen by members ofcommunity-bioc.

Yagoub Ali Ibrahim Adam (23:12:32): > @Yagoub Ali Ibrahim Adam has joined the channel

2020-04-01

Matt Ritchie (07:43:02): > Yes, welcome everyone to the CAB (@Susan Holmes,@saskia,@Lori Shepherd,@Leonardo Collado Torres,@Yagoub Ali Ibrahim Adam,@Benilton S Carvalho,@Kozo Nishidaand@Johannes Rainerwith me and@Aedin Culhaneas co-chairs). We should organise a meeting very soon to make some plans for the future (there are quite a few different time zones to work around, but I’m sure we can sort something out). I think I have everyone’s twitter handles to use in a tweet introducing the new CAB to the world (except maybe@Yagoub Ali Ibrahim Adam- are you on twitter?)

Matt Ritchie (07:58:43): > Beyond that perhaps we can start with some e-introductions? I’ll start - my name is Matt and I’ve been using Bioconductor tools since the very beginning of the project. I’ve been really fortunate to train in a few different labs in Australia, the UK and US that have made really valuable contributions to Bioconductor over the years. In my lab today, we use a lot of different Bioconductor tools to perform gene expression analysis and from time to time we create new tools of our own to try an make our analysis lives easier. I’m passionate about raising the profile of Bioconductor in the Asia/Pacific region where I am based and have helped organise a number of BioCAsia events over that past 5 years. Am really looking forward to working with you all to further develop and expand the Bioconductor community to benefit researchers across the globe.@Johannes Rainerdo you want to go next?

Johannes Rainer (08:08:44): > Sure, first of all it’s an honour to be part of the CAB! My name is Johannes, I’m a (german speaking) Italian and have been using R/Bioconductor now for over 15 years (or more?). I worked a lot with gene expression and genomics data but now, since ~4 years I’m working mostly with mass spectrometry data, specifically metabolomics data. I’m maintainer of two Bioconductor packages,ensembldbandFamAggand am contributing to a variety of others includingAnnotationFilter,MSnbase,xcms,mzR,CAMERA. I love to do R coding, but also to analyze data - and just to be sure you have myrealtwitter handle: it’s jo_rainer, not jorainer:slightly_smiling_face:

Matt Ritchie (08:22:53): > Awesome - thanks@Johannes Rainerfor all that you do (and I hope you are doing well in Italy in these difficult times). Who’s next @Lori Shepherd?

Lori Shepherd (08:28:54): > Hi Everyone! Super excited to be apart of CAB! I’m Lori Shepherd. I’ve been programming in R/Bioconductor for ~14 years through the Biostatistics Department at the RPCCC in Buffalo. I’ve been apart of the Bioconductor Core Team for ~4-5 years. I manage the Single Package Builder, ExperimentHub, AnnotationHub, BiocFileCache, BiocCheck, Support Site, Website, AMIs, and help with the daily builders and dockers as well as general maintenance on Bioconductor infrastructure packages. I love helping out with conferences and workshops. Looking forward to working with everyone to advance the Bioconductor community forward!

Matt Ritchie (08:37:57): > Thanks for keeping the Bioconductor project running so smoothly@Lori Shepherd- great to have you on the CAB. That’s 3 e-introductions down, 7 to go - feel free to have your turn@Yagoub Ali Ibrahim Adam,@saskia,@Susan Holmes,@Benilton S Carvalho,@Kozo Nishida,@Leonardo Collado Torresand@Aedin Culhane

Yagoub Ali Ibrahim Adam (09:16:48) (in thread): > Hello,@Matt RitchieUnfortunately I do not use twitter. However, I will create an account soon.

Yagoub Ali Ibrahim Adam (09:26:00) (in thread): > Here it is Y_A_I_Adam.

Yagoub Ali Ibrahim Adam (09:49:19): > Hello all, It is my pleasure and honor to be a member of theBioconductorcommunity-advisory-board.My name is Yagoub from Sudan. Currently,**** ****I am a postdoctoral scholar at Covenant University, Nigeria. I earned my doctorate in Bioinformatics at the University of São Paulo, Brazil. I work mostly with statistical gnomic, GWAS data analysis, and RNA-seq data analysis. I use R for all my projects (even when I use other programming languages such as c++, I embed R codes).

Leonardo Collado Torres (14:40:23): > Hi everyone! > > It’s an honor to be a part of the BioC CAB:taxi:! Thank you for coming up with this idea and making it a reality Aedin and Matt (and others too). I’m also a bit afraid of how much work this will be, to be honest. However, I think that there are lots of potential benefits too. > > I was just promoted 2 weeks ago to Research Scientist at the Lieber Institute for Brain Development, in Baltimore Maryland USA:us:, inside the Johns Hopkins Medical Campus. The idea is that I could become a principal investigator down the roadhttp://lcolladotor.github.io/2020/03/16/research-scientist-an-academic-career-launch-pad/. It will also allow me to keep our LIBD R club up and runninghttps://twitter.com/LIBDrstats. I’m from Mexico:flag-mx:and started learning R thanks to James Bullard who was a PhD student with Sandrine Dudoit’s lab at UC Berkeley. The BioC:bioc:conference was how I actually learnedRand I entered a cycle of going to conferences, then teaching in Mexico which is how I would actually learn (I forgot James’ course 1 week after it:sweat_smile:) since 2008. I met Rafael Irizarry and Ingo Ruczinski through the BioC2010 conference who recruited me to my PhD program (2011-2016). I’ve been at LIBD working with Andrew Jaffe since I finished my PhD (images athttps://speakerdeck.com/lcolladotor/cdsbmexico). I use R daily (more base than tidyverse, but could learn more about it) and I mostly work with RNA-seq data and have made some tools through time for it:derfinder(regionReportalso),recountand nowspatialLIBD; I need to check my packages again, sorry Lori!:scream::innocent:). Though I’ve never writtenS4classes myself and there’s plenty of things I still ask about on bioc-devel, Twitter, etc. I like blogging as a way to share what I know but also to practice writing in English. I also like using Twitter for science (most of the time)https://twitter.com/fellgernon. Together with Alejandro Reyes (also on this Slack) and others we created the Community of Bioinformatics Software Developers (CDSB in Spanishhttps://twitter.com/CDSBMexico) in 2018 and are in theory organizing our 3rd workshop this summer in Mexico:flag-mx:(pending COVID-19 updates). We have a recent blog post about it athttps://www.r-consortium.org/blog/2020/03/18/cdsb-diversity-and-outreach-hotspot-in-mexico. Joselyn Chavez from CDSB (also on this Slack) will talk about her recent experience with her first BioC package submission in the next#developers-forum. > > I think that what I do for CDSB could be merged somewhat with my role at BioC’s CAB. A lot of what I’ve done at CDSB’s Slack and community is based on things I learned from rOpenSci unconf2018 and the work of Stefanie Butland. I also think that maybe some of the blog posts that are more like guides that I’ve written here and there (and will continue to do as part of my LIBD job) and those efforts could be merged with my CAB role. > > Anyway, I’m looking forward to meeting you all! > > Best, > Leo

Matt Ritchie (17:36:36) (in thread): > Fantastic - thank you!

Benilton S Carvalho (18:17:12): > Pleasure to be here… thanks everyone for the hard work. I joined the BioC (devel) community back when there were 80 packages in the devel branch. I had the opportunity to be in Rafael Irizarry’s team (back at Hopkins), joining Simon Tavaré’s group (Cambridge University) afterwards. Returned to Brazil in 2013 (UNICAMP), where I’ve been working on the implementation of Precision Medicine analytical framework at our Uinversity Hospital. In the past years, I’ve delivered several workshops on the use of Bioconductor… Hope to be able to contribute as expected.

saskia (20:16:51): > I am very excited to be part of BioC CAB. As an early career post-doc (albeit on my second one), I may not have as much experience as the rest of you. However, I do maintain two Bioconductor packages, RUVcorr (sorry Lori for not getting it fixed sooner:sweat_smile:) and schex. Like@Leonardo Collado Torres, I have never programmed anS4class either. But I am eager to learn. I helped with the organization of the last BioCAsia conference and had a blast. I have also been to two useR conference and of course I am a member of RLadies:purple_heart:. Anyway I am excited to get to know everyone and help out where I can.

Matt Ritchie (23:27:09): > Thanks@Yagoub Ali Ibrahim Adam,@Leonardo Collado Torres,@Benilton S Carvalhoand@saskiafor contributing so much already to Bioconductor. We hope to channel that experience and enthusiasm on the BioC CAB. That just leaves@Kozo Nishida,@Susan Holmesand@Aedin Culhaneto round out the e-introductions.

Matt Ritchie (23:30:41): > Also in an attempt to get people together for a call to discuss the next steps, see if any of the times next week or the week after suit people (seehttps://doodle.com/poll/gfmfctq3cn9wx7s2- hopefully the timezones convert to your local time and the times suggested are somewhat reasonable. No problem if not though, we can try a later date, as I know COVID-19 is significantly disrupting people’s ability to work at the moment). Thanks! - Attachment (doodle.com): Doodle: Bioconductor Community Advisory Board > 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!

Leonardo Collado Torres (23:47:09): > Using the location (or a nearby city) a few of you listed on your Twitter profiles, I came up withhttps://www.timeanddate.com/worldclock/meetingtime.html?iso=20200409&p1=419&p2=196&p3=152&p4=215&p5=742&p6=233&p7=671&p8=224for April 9th (dunno if some you are changing to DST between the 9th and the 17th which are the options Matt listed) and sadly there’s always at least one “red” (normal sleeping hours). Though hopefully I got one or more of your locations wrong and we have better options for all:stuck_out_tongue: - Attachment (timeanddate.com): The World Clock Meeting Planner - Results > Results from the Meeting Planner that finds a suitable time to call or meet with people from around the world.

2020-04-02

Matt Ritchie (01:02:39): > Thanks@Leonardo Collado Torres! Our local admin support (Fiona) ran our approx locations through the same tool so hopefully the few times suggested aren’t too unfriendly (we’re coming off DST this Sunday in Melbourne). Scheduling is a tough problem - sadly there isn’t a Bioconductor package to solve this for us:wink:

Susan Holmes (04:47:35): > Hello there, this is a rather difficult time to be taking on extra duties. As for everyone now, my circumstances are very different than normal. I usually work at Stanford as a Professor in the Statistics department where I have been using R since 1998 and Bioconductor since 2002. In particular I have taught courses on using Bioconductor and have now published a book with Wolfgang Huber onModern Statistics for Modern Biologywhich is highly dependent on hundreds of packages. My work today is in Microbial Ecology and Immunity and with my group we have published several packages:phyloseqanddada2being the most popular. My current situation, (stuck in southern Portugal without a good internet connection but teaching two online courses) makes this time more challenging for interactions, but I hope we manage to meet up soon. - Attachment (web.stanford.edu): Home | Modern Statistics for Modern Biology > Home | Modern Statistics for Modern Biology - Attachment (Bioconductor): phyloseq > phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. - Attachment (Bioconductor): dada2 > The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

Federico Marini (06:42:10): > @Federico Marini has joined the channel

Federico Marini (06:43:37): > From my side, as a candidate applicant: congratulations to you all for being selected for the Bioc CAB! > As communicated to@Matt Ritchie, I’ll give my best to help out in Community-related activities, just without the “CAB nametag” on my T-shirt:slightly_smiling_face:

Johannes Rainer (06:44:56): > Talking about t-shirt - do we want to have stickers/t-shirts for the CAB:thinking_face:

Federico Marini (06:53:44): > See why I wanted to be in as well:smile:

Federico Marini (06:54:07): > a sketch of a taxi (cab) with Bioc colours?

Matt Ritchie (06:57:31): > Am a big fan of the old hexsticker (the collection is growinghttps://github.com/Bioconductor/BiocStickers, but there’s always room for 1 more)!

Johannes Rainer (07:03:52): > :expressionless:my drawing board is in my office - this would have to wait until I’m allowed to leave home again. But I could give it a try once this is over.

Lluís Revilla (07:41:42): > @Lluís Revilla has joined the channel

2020-04-04

Kozo Nishida (03:50:15): > Hi everyone. > I’m Kozo Nishida from Japan. > I’m happy to be a member of CAB. > In Japan, Koki Tsuyuzaki and others are trying to increase their contributions to Bioc. > We also have a hackathon (called BioPackathon) for this purpose. > In the future, we hope to move that event online and increase the frequency of the event, and contribute more to Bioc. > I haven’t become an author of the Bioc package yet, but I will submit my packages for transomics visualization and MSEA(Metabolite Set Enrichment Analysis) soon.

2020-04-06

Matt Ritchie (19:03:58): > Thanks everyone for replying to the doodle poll. Let’s aim for this Thursday 9th April at 9-10pm Melb AU time for our first virtual meeting - a BlueJeans invite and agenda will follow

2020-04-07

Matt Ritchie (08:55:22): > A draft agenda for our first meeting is athttps://docs.google.com/document/d/1REBuSpTuG5k20-0clr1FBagMFFvXxmlHW5Jdtwnx9Y4/edit?usp=sharing. Feel free to edit with your own suggestions

2020-04-09

Kozo Nishida (05:22:01): > @Matt RitchieI created a scheduled workflow for CBA virtual meeting call. > Feel free to modify it. (or delete it if not needed.) - File (PNG): Screen Shot 2020-04-09 at 18.20.16.png

CAB meeting call (06:30:00): > The CBA virtual meeting will start soon.

Matt Ritchie (07:03:33): > Have others been able to join the call OK?

Johannes Rainer (07:03:50): > Yep, we’re in the meeting:slightly_smiling_face:

Kozo Nishida (07:03:53): > OK we are already in bluejean

Leonardo Collado Torres (07:04:11): > It took me two times to get my audio working

Leonardo Collado Torres (07:04:17): > but it works now ^^

Matt Ritchie (07:04:22): > Great - will see you there soon I hope!

Leonardo Collado Torres (07:05:20): > https://bluejeans.com/738948215

Matt Ritchie (08:11:48): > Thanks everyone for your time today!

Matt Ritchie (08:14:26): > Forgot to mention that@Laurent Gattohas been speaking to the Carpentries folk about the potential to develop some Bioconductor specific training material. Can you tell us more? Maybe some CAB members are interested in contributing

Laurent Gatto (09:27:09): > Hello! You will find some notes herehttps://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharingIn a nutshell, we would like to get some members of the Bioconductor community trained to develop/contribute to some Carpentries/Bioconductor material. The number of trainers that can be trained is limited by the number of places available in these Carpentries instructor trainings. If more people that can enrol in the may event are interested, I am happy to gather more names and try to coordinate. - File (Google Docs): bioc-teaching

Kozo Nishida (10:20:47) (in thread): > Thank you for the information. > Is it OK to share this Google Docs link with my local Bioc community? > (One of them works for Carpentries.)

Laurent Gatto (10:34:57): > I am not sure it would be productive to make it public, but I suppose it is good to share it with the wider Bioc community.

2020-04-17

Matt Ritchie (18:03:04): > Be sure to forward this message to your networks and encourage people you know to apply:https://support.bioconductor.org/p/130094/

Matt Ritchie (18:03:25): > or on twitter:https://twitter.com/Bioconductor/status/1251200958807322625 - Attachment (twitter): Attachment > Bioconductor is excited to announce an opportunity to recognize those making significant outstanding contributions to the Bioconductor community with the launch of Bioconductor Awards. See more information https://support.bioconductor.org/p/130094/ #Bioconductor #Bioc2020 #rstats @Bioconductor

2020-04-25

Chris Fields (20:43:35): > @Chris Fields has joined the channel

2020-04-29

Matt Ritchie (09:31:53): > I have a question for those on the CAB interested in social media. Would you prefer we start a separate twitter account ‘bioc_community’ or similar or would interested tweeters prefer to be added to the current ‘bioconductor’ account? Can you show your preference with a:new:for a new account,:bioc:to be added to the current one or:shrug:for don’t mind either way. Thanks!

Nitesh Turaga (14:05:09): > @Nitesh Turaga has joined the channel

2020-05-01

Matt Ritchie (09:26:13): > Forgot to ask in the above message who on the CAB would like to be added to the above twitter account. If you can respond with a thumbs up:thumbsup_all:, I’ll make sure it is set up. Thanks!

2020-05-05

Aedin Culhane (11:00:49): > Hi@Matt Ritchie. Our last meeting was 7am Thursday April 9th. That was the second Thursday of the month. Assuming our regular meetings will be the second Thursday of the month, our next call is 7am Thursday 14th ? Is is there a bluejeans set up for the call?@Lori ShepherdDo we have minutes from the last meeting to approve? Also if people have agenda items please add it to the google dochttps://docs.google.com/document/d/1REBuSpTuG5k20-0clr1FBagMFFvXxmlHW5Jdtwnx9Y4/edit#heading=h.7s9c2w3oy7lw

Aedin Culhane (11:01:12): > Also who is interested in potential to fund ideas that require financial support via a future Chan Zuckerberg Initiative (CZI) Essential Open Source Software for Science (EOSS) grant (next cycle is due to openmid June) for funding between $50K - $250K for 1 year. Websitehere - Attachment (Chan Zuckerberg Initiative): CZI Launches Funding Opportunity for Open Source Software > Funding supports software maintenance, growth, development and community engagement.

Aedin Culhane (11:02:29): > Finally, if you have an opinion/experience/suggestions on virtual conferences, Bioc2020 committee would be grateful of your input. Contribute onhttps://docs.google.com/document/d/12mBgGjQRsmbxj3g8Qi73k1fMAckJHxJbHtdMn7S4Jgc/edit#heading=h.bdmjdr21sbf3

Lori Shepherd (11:06:45): > The blue jeans call is repeating monthly on the second Thur – the link ishttps://bluejeans.com/738948215and is indeed scheduled for Thur May 14th at 7 am EST – since many were making notes in the agenda, we cleaned up that and I posted a copy in the minutes folder on the CAB google drive folder (also following how the TAB seemed to operate) that can be views for final approval - we can probably make these separate documents for future meetings to have a clean agenda vs notes/discussion –

Aedin Culhane (13:02:54): > Thanks Lori.

2020-05-13

Johannes Rainer (12:56:37): > One small note regarding the CAB on the Bioconductorwebpage: please rename “EURAC” to “Eurac Research” - in the recent rebranding we got renamed …:neutral_face:

Lori Shepherd (13:25:12): > I’ll update it now – should be corrected within the hour

2020-05-14

CAB meeting call (06:30:00): > The CBA virtual meeting will start soon.

Kozo Nishida (06:41:45) (in thread): > I just replaced “soon” to “in 30 minutes” (with the workflow builder). > From the next time the message will be updated. > Sorry.

Leonardo Collado Torres (08:03:10): > Lori, this advice from Yihui Xie helped me a lot with PRshttps://github.com/rstudio/blogdown/issues/269#issuecomment-370818782

Leonardo Collado Torres (08:03:40): > basically make a branch on your fork instead of working on themasterbranch of the fork

Lori Shepherd (08:37:11) (in thread): > yes thank you!

Leonardo Collado Torres (09:33:26) (in thread): > np ^^ > > Using a branch on a fork makes it easier to sync a fork with the origin repo later on and keep things cleaner

2020-05-15

Leonardo Collado Torres (16:26:51): > I made these 2 short 3 min videos (English and Spanish) for the BiocCheck-a-thonhttps://twitter.com/fellgernon/status/1261391485666131970?s=20I likely need to learn how to get the videos to play on twitter without having to open an external link. Anyway, it was what I could do quickly - Attachment (twitter): Attachment > Have you heard about the #BiocCheck-a-thon? In this video I invite you to join the @Bioconductor team & community > > Could be useful to meet :globe_with_meridians: > Learn about #git @github :100: > Contribute :female-construction-worker::skin-tone-5::male-construction-worker::skin-tone-5: > > #rstats :raised_hands::skin-tone-5: > > :video_camera: https://jh.zoom.us/rec/share/4ulVdZSr-FhJWbP0yWzYQIoHRd33aaa80HcZ_foMxUv618yVPJSczNHiYChngsgN?startTime=1589571461000 > :notebook_with_decorative_cover: https://docs.google.com/document/d/1fMWAidTRPZNszn8ak8LqfPyAtTclVCHdc8lgd_3n_nk/edit?usp=sharing > > https://twitter.com/Bioconductor/status/1258652866841063424?s=20 - Attachment (twitter): Attachment > #rstats / @Bioconductor Join us for ‘BiocCheck-a-thon’, a week-long virtual activity to improve BiocCheck and the consistency and quality of Bioconductor packages! See https://github.com/Bioconductor/BiocCheck/wiki for details; starting May 18.

2020-05-17

Matt Ritchie (07:02:28): > Awesome - thanks@Leonardo Collado Torres!

2020-05-18

Johannes Rainer (00:57:41): > Great@Leonardo Collado Torres! Videos are great, but the audio transcript of them are also fun, I especially like that the “Bioconductor community” is transcribed to “bike and lipstick community” or the “piracy check hackathon”:joy:

Leonardo Collado Torres (12:24:21) (in thread): > haha, that’s funny

2020-05-20

Lori Shepherd (13:14:11): > There is now a public google calendar to advertise Bioconductor related events, conference, meetings, forums, etc. It can be accessed at:https://calendar.google.com/calendar/b/1?cid=YWtlczFvZGVsbW9kcDAzODV1ZHB2NDhpY29AZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQRequests for events to be added to the calendar can be sent to:events@bioconductor.org - Attachment (accounts.google.com): Google Calendar > With Google’s free online calendar, it’s easy to keep track of life’s important events all in one place.

2020-05-22

Lori Shepherd (12:48:45): > We would like feedback on the BiocCheck-a-thon to make it better the next time around. Kayla created a google form for feedback if people could promote responseshttps://docs.google.com/forms/d/e/1FAIpQLSfBdBuTcawOAgm9CXfjRl-tzaKBWbIB7ilYCMku747qUJPBGQ/viewform

Matt Ritchie (19:57:45): > Thanks - just tweeted! (with the short URL for the form -http://shorturl.at/hzBIV). Hope it went well - Attachment (Google Docs): BiocCheck-a-thon Check In > A quick survey to get feedback about our first community hack-a-thon.

2020-05-26

Robert Ivánek (03:55:26): > @Robert Ivánek has joined the channel

2020-06-02

Lori Shepherd (08:49:25): > Hello all — Please get the word out to nominate for the bioconductor awards. I posted on the bioconductor twitter, facebook, support site, and slack but would be great to post on some of your personal pages too! thanks!

2020-06-05

Yagoub Ali Ibrahim Adam (11:49:58): > OK @lori , I will do it

2020-06-11

Leonardo Collado Torres (07:10:58): > So my suggestion was to embed the events Google calendar tohttp://bioconductor.org/help/events/More details athttps://support.google.com/calendar/answer/41207?hl=en - Attachment (support.google.com): Add a Google calendar to your website - Calendar Help > You can add an interactive version of your calendar to your website, and add buttons for your website visitors to save your calendar events. Embed a calendar on your website On a computer, o

Johannes Rainer (07:13:06): > and eventually also have a short description there how to propose events or get them added

Leonardo Collado Torres (07:15:52): > Yup, that would basically be the same description already under “Use” athttp://bioconductor.org/

Leonardo Collado Torres (07:17:43): > I can send a PR if you want Lori

Lori Shepherd (07:32:16): > Yes please. I really like PR

Leonardo Collado Torres (08:34:43): > Here you go@Lori Shepherd:smiley:https://github.com/Bioconductor/bioconductor.org/pull/58

Susan Holmes (08:42:19): > Education material for complete step by step courses:

Susan Holmes (08:42:23): > https://www.huber.embl.de/msmb/course_spring_2020/index.html

Susan Holmes (08:43:19): > This is an example based on our book, but we have other projects in the works, this is especially useful for people who don’t know what they don’t know so need to be guided through all the available material in a logical way.

2020-06-16

Dan Bunis (11:34:26): > @Dan Bunis has joined the channel

Leonardo Collado Torres (11:48:34): > Lori, I just updated my calendar PR athttps://github.com/Bioconductor/bioconductor.org/pull/58but well, I’m not sure why I can’t see the color codes you have added (maybe it’s only for those that are “invited” directly to it, instead of just those who follow the calendar). Anyway, I don’t fully understand it

Lori Shepherd (11:59:54): > Hmm…. Okay I’ll look at it but probably not until later in the week

Lluís Revilla (12:00:43): > On the discussion of April (I found it now and don’t see if on May you had something already) , there is a point about how to useBioconductor/Contributions. I made some analysis on the common pitfalls/problems of thesubmission processthat might be useful for building some more documentation/tutorial. I plan to follow up on some comments recieved on the#developers-forum - Attachment (B101nfo): Bioconductor submissions | B101nfo > Exploring the submission process to Bioconductor. What happens, how long does it take, what are the common problems and solutions for new contributors.

Laurent Gatto (12:49:35): - Attachment: Attachment > Hello - I just wanted to point out here that we have a new diversity-affirming section in the BiocStickers repo (https://github.com/Bioconductor/BiocStickers/blob/master/README.md) featuring rainbow and trans versions of our Bioconductor sticker. Credits to @Aaron Lun and @Dan Bunis. Thank you!

2020-06-17

Leonardo Collado Torres (15:53:04) (in thread): > the meeting minutes take a bit to be posted because we all review them

Leonardo Collado Torres (15:53:42) (in thread): > though hm… I thought that we had approved the May ones

2020-06-18

Aedin Culhane (23:01:03): > Hi. We have in-kind sponsorship from sticker mule at the Bioconductor conference. eRUM are putting all of their sticker order in one go, and then the committee is mailing them out. I wonder if we could promote diverse Bioc via this>

2020-06-19

Federico Marini (01:38:27): > Hi@Aedin Culhane, AFAIK you can get pretty much “anything” from them (stickermule), well, being reasonable. When I asked for 1000 stickers, the sponsorship guy just told me straight away: “”if you need more because you’re runnin out, let me know and we just send more”

Federico Marini (01:39:21): > i.e. : I don’t think you break the deal if you askalso for the same amount of the extra bioc-diversity sticker:wink:

Dan Bunis (02:02:20): > Would love to see the rainbow and trans flags sent out. That would be lovely!

Federico Marini (03:51:32): > if you folks need it, happy to setup a call with the stickermulers again:wink:

Aedin Culhane (18:36:05): > I submitted a sponsership request to them and they offered an in-kind $300 sponsorship. (I said we normally get about 300 people.. I don’t know whether the virtual meeting will attract a larger audience).

Aedin Culhane (18:36:57): > @Federico MariniOn the eRUM website, I was unsure how to order/buy sticker, I clieck on the stickermule logo, but it just directed to the generic website. How did it work

Federico Marini (18:44:52): > oh this is strange

Federico Marini (18:44:55): > ah, wait

Federico Marini (18:46:48): > We advertised today two things: 1, the Gform to get a sticker delivered by us (we as organizers will cover the expenses); > 2, on the sticker by stickermule there’s a special link to the 10stickers for 1 euro to order any hex-series (basically an appetizer)

Federico Marini (18:48:12): > If you want them to print all the stickers with your design, I would advise you to do it directly via the sponsor team from them. They can basically have their production unit send you the proof “as if you’d buy it”, and then you’ll have provided them with an address they can use for delivery, that was it

2020-06-22

Sean Davis (17:48:09): > @Sean Davis has joined the channel

2020-06-23

Johannes Rainer (06:10:44): > @Aedin Culhane, don’t know if you are aware of it, but@Levi Waldronasked me if I could make a new sticker for BioC2020 - since it’s going to be online only. I’m currently working on that and should have it ready within the next days.

2020-07-02

Sean Davis (10:16:32): > Just FYI,@Laurent Gattoposted this in#education-and-training. - Attachment: Attachment > For those interested in a Bioconductor curriculum, there is now a google group. We are also preparing a first discussion to get started with the planning. Details in the google group: https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharing

2020-07-23

Kevin Rue-Albrecht (11:16:06): > @Kevin Rue-Albrecht has joined the channel

Kevin Rue-Albrecht (11:20:12): > Does a slide like that require any kind of warning?:grimacing:https://isee.github.io/iSEEWorkshop2020Slides/#12 > > “This presentation contains slides that some viewers may find disturbing”.

Leonardo Collado Torres (12:26:27) (in thread): > hehe, I don’t think so, but we’ll see what others think

Johannes Rainer (13:00:50) (in thread): > Me neither - but to be on the safe side you could also add the warning - which is also funny:slightly_smiling_face:

2020-07-27

Leonardo Collado Torres (12:06:18): > I’m at the “meet the Bioc core team” session, in case someone else wants to live tweet about the birds of a feather session by Atul

Leonardo Collado Torres (18:05:36): > What do you think about the live tweets today? Tomorrow I won’t be around for the last 2 workshops in case someone else wants to tweet about them

Leonardo Collado Torres (18:05:51): > though I can pre-schedule some tweets if necessary

2020-07-28

Aedin Culhane (11:16:37) (in thread): > I think the “warning” might make it funnier, people will wonder whats coming next

Kevin Rue-Albrecht (11:17:10) (in thread): > it’s in there now

Aedin Culhane (11:17:22) (in thread): > Probably leave the warning to the slide before though (in case it puts people off watching the talk)

Kevin Rue-Albrecht (11:18:36) (in thread): > It’s a bit weird with the flow, I thought I hit a middle ground with thishttps://isee.github.io/iSEEWorkshop2020Slides/#2

Kevin Rue-Albrecht (11:19:15) (in thread): > I also noticed after the fact that there is some ‘violence’ here:https://isee.github.io/iSEEWorkshop2020Slides/#9:grimacing:

Leonardo Collado Torres (15:21:10): > I’m going to go rest after the contributed talks session, I did schedule 1 tweet for each of the next 2 workshops, but please feel free to take over live tweeting! I’ve spent most of my day tweeting from BioC, CDSB and my account:stuck_out_tongue:

2020-07-29

Qian Liu (08:22:50): > @Qian Liu has joined the channel

Mike Smith (08:28:40): > @Mike Smith has joined the channel

Daniela Cassol (09:42:49): > @Daniela Cassol has joined the channel

Davide Risso (10:59:51): > @Davide Risso has joined the channel

2020-07-30

Anabella (13:17:23): > @Anabella has joined the channel

2020-08-02

Sean Davis (14:43:00): > FYI:https://www.cscce.org/ - Attachment (CSCCE): Center for Scientific Collaboration and Community Engagement - CSCCE > The Center for Scientific Collaboration and Community Engagement (CSCCE) is a research and training center to support and study scientific community engagement.

2020-08-11

Leonardo Collado Torres (15:56:15) (in thread): > I joined their Slack in 2020 but I haven’t had time to look around much for info. But if anyone wants to join, I can probably help you in that process

Leonardo Collado Torres (15:56:43): > Good luck with the Bio”Pack”athon tomorrow@Kozo Nishida:smiley:

2020-08-14

Laurent Gatto (10:44:24): > I am summarising here some thoughts based from my notes of the recent TAB and CAB discussions at the Bioc2020 conference and some older TAB meetings. > > I think it would be useful to have some mentoring activities as part of the Bioconductor project. I believe there is limited funding available for small projects. In parallel, there are regularly job ads that are posted on the Bioc slack and the support site. Mentoring would be a great way to help people transitioning from small Bioc projects to Bioc-related jobs and create links between newer and more senior members of the community. > > I remember that several years ago, there was a short livedBioconductor mentored projects. With the advent of the CAB, I think it might make sense to consider something like that again.

2020-08-18

Leonardo Collado Torres (16:22:55): > Virtual event funding opportunity. Deadline Aug 25 > > Code for Science and Society is enthusiastic to announce its first call for applications for virtual events centered around improving or connecting research-driven data science tools, practices, and the communities themselves. Proposals must demonstrate the educational and scientific purposes of the event and specifically how it advances Code for Science and Society’s goal to create inclusive knowledge-sharing spaces and support the development of diverse leaders. We aim to invest in both emerging or established events that demonstrate a commitment to making science inclusive and accessible. International applicants are welcome! > > > Awards will range from $5,000-$20,000 and the submission deadline is August 25th. Please contactconference.fund@codeforsociety.orgwith any questions. > https://eventfund.codeforscience.org - Attachment (eventfund.codeforscience.org): CS&S Event Fund > We support events that promote inclusion and broaden participation in research-driven open data science.

Leonardo Collado Torres (16:23:09): > might be of interest to several here, I’m thinking of sending an application for CDSB2021

Leonardo Collado Torres (16:23:32): > I made a template of the info you need to fill out athttps://docs.google.com/document/d/1QY0MKKCC1uzU4-HQpTSAt_1RsyOYctvZcdkpe13I1Kg/edit?usp=sharing

Leonardo Collado Torres (16:23:44): > in case it helps others

2020-08-19

Levi Waldron (05:39:59): > @Levi Waldron has joined the channel

Simone Bell (05:40:05): > @Simone Bell has joined the channel

2020-08-24

Leonardo Collado Torres (08:55:47): > Just a reminder that this application is due tomorrow. I’ll write the one for CDSB later today. Note that you can apply for a single event or a series of events

Leonardo Collado Torres (08:56:05): > I’m not sure if you/we want to apply also for BioC events/confs

Leonardo Collado Torres (08:56:21): > they have to be virtual though

2020-09-23

Kevin Rue-Albrecht (07:43:57): > That’s be a fun opening on the CAB…:smile:https://twitter.com/beau_elliot/status/1306749903561842688?s=21 - Attachment (twitter): Attachment > Over the past 4 weeks, I’ve made at least 1 meme/gif a day for @budlight trying to become their new #ChiefMemeOfficer. This is my last post; highlights of all the posts I made. Good luck to everyone who applied! :)

2020-10-08

Laurent Gatto (04:57:54): > Hello - the EuroBioc 2020 conference will be run using thehttps://hopin.to/platform. Hopin organiser accounts can be paid for monthly or yearly. Our first impressions were very positive and if the conference works out well, hopin could be used more regularly for conferences and workshops. This could be offered as a platform for members of the community to organise their workshop and promote their packages. Feel free to get in touch with me or@Davide Rissoif this is something the CAB is interested in. - Attachment (hopin.to): Hopin: Online venue for virtual events > Hopin is an online events platform where you can create engaging virtual events that connect people around the globe.

2020-10-10

Matt Ritchie (06:39:57): > Thanks@Laurent Gatto- sounds like a great platform that I hope performs well for your meeting. Do you have a sense for how much this might cost for a year (I couldn’t find such info on their website, but maybe I wasn’t looking hard enough)? We are drafting a budget for CAB activities for 2021 at the moment, and it would be good to have a ballpark figure of how much we would need to allocate in the budget for something like this. Cheers!

Davide Risso (06:42:28): > Hey@Matt Ritchiethe platform is $99/month/organizer. Each organizer comes with 100 attendees

Davide Risso (06:43:47): > Our plan is to start the account on Nov 1st when registration to EuroBioc opens

Matt Ritchie (06:44:56): > Bargain! Can you increase the number if more people register for a particular event, or do you need to scale up the number or organisers?

Davide Risso (06:45:23): > You can, it’s 50 cents per additional attendee

Davide Risso (06:45:53): > So $100 buys you either 1 organizer + 100 attendees or 200 attendees

Matt Ritchie (06:46:21): > How many organisers would you suggest, or can you set the organiser up from a generic email account?

Davide Risso (06:47:04): > Our plan was to start with 1-2 organizers in November and add up to 10 for December when the actual event takes place

Davide Risso (06:47:52): > I can see a $99/month account to keep throughout the year with additional co-organizers added and removed when needed

Davide Risso (06:48:29): > Perhaps using specific conference budgets to pay for the extra organizers

Matt Ritchie (06:49:05): > Cool - so you can you scale up / down the number of organisers per month? Also the number of attendees (does the 50c per attendee cover for up to a whole month or just a day)

Davide Risso (06:50:33): > That’s a good question.. I would assume for a month? But I can ask them

Davide Risso (06:50:46): > I mean the one for the attendee

Davide Risso (06:51:47): > The organizers can indeed be scaled up/down on a monthly basis

Matt Ritchie (06:53:04): > Too easy - when you sign up in November we can cover the base account for 1 organiser for the $99 / month recurring and get you to add more to it as you need for your event if that helps

Davide Risso (06:55:36): > That would be great! In that case it would make sense to create the account as Bioconductor and share the login credentials with future event organizers when needed

Davide Risso (06:56:58): > If the account is recurring it can be used also for smaller workshops and events throughout the year

2020-10-13

Laurent Gatto (08:07:46): > Hello - I believe several members of the CAB are interested in the current efforts in developing a Bioconductor curriculum. We have agoogle docwhere we keep notes (also clipped to this channel) and meet monthly (2nd Monday). Meeting reminders and general info is posted on thebioc-teaching google group. - File (Google Docs): bioc-teaching

Laurent Gatto (08:13:53): > As with additional instructor trainings, there is currently a long waiting list due to the covid backlog.Carpentries member organisationscan organise courses with privileged access for their members. Is this something the CAB would be interested in? If relevant, I could also bring it up with the TAB. I would also be happy to liaise with the Carpentries if this is something to be pursued. - Attachment (The Carpentries): Our Current Member Organisations > The Carpentries is a fiscally sponsored project of Community Initiatives, a registered 501(c)3 non-profit organisation based in California, USA. We are a global community teaching foundational computational and data science skills to researchers in academia, industry and government.

Laurent Gatto (08:15:30): > Details about becoming a member organisation -https://carpentries.org/membership/ - Attachment (The Carpentries): Become a Member Organisation > A Member Organisation is an organisation which has made a commitment to the growth and spread of The Carpentries

2020-10-28

Lluís Revilla (11:42:39): > Was there a meeting on September?

Lori Shepherd (11:45:29): > For the CAB. Yes. I’ll get the minutes up in the next few days

Lluís Revilla (11:49:06): > Great. Thanks!

2020-10-29

Sean Davis (16:39:42): > I think this is a valuable experience to share, even if it is only one side of the story:https://www.fast.ai/2020/10/28/code-of-conduct/ - Attachment (fast.ai): I violated a code of conduct > Making neural nets uncool again

Federico Marini (16:53:44) (in thread): > Came across this piece this morning as well, and I also meant to post it in our slack!

2020-10-30

Nitesh Turaga (15:44:49) (in thread): > https://numfocus.org/blog/jeremy-howard-apology - Attachment (NumFOCUS): Public Apology to Jeremy Howard - NumFOCUS > NumFOCUS’s Code of Conduct Committee’s apology to Jeremy Howard

2020-10-31

Federico Marini (17:25:03) (in thread): > Jeremy also updated his post, at the same address linked above

2020-11-27

Sean Davis (13:05:04): > How does one propose an agenda item for the next CAB meeting?

Lori Shepherd (13:27:46): > Emailcab@bioconductor.org

2020-12-02

Konstantinos Geles (Constantinos Yeles) (05:42:44): > @Konstantinos Geles (Constantinos Yeles) has joined the channel

Konstantinos Geles (Constantinos Yeles) (05:46:23): > @Konstantinos Geles (Constantinos Yeles) has left the channel

2020-12-12

Huipeng Li (00:40:38): > @Huipeng Li has joined the channel

2020-12-17

Kelly Street (11:06:26): > @Kelly Street has joined the channel

2020-12-19

Sean Davis (20:18:47): - Attachment: Attachment > Anybody knows if it’s possible to publish workshop material on F1000Research?

2020-12-20

Laurent Gatto (04:33:26): > Hello - what is the best way for people to get in involved with conference organisation (referring specifically to EuroBioc here, but of general interest). Is there a web page with current members of the various organising committees and instructions on how to participate/contribute? (ping@Leo Lahti)

Leo Lahti (04:33:54): > @Leo Lahti has joined the channel

Leo Lahti (04:34:32) (in thread): > Thanks!

2020-12-21

Lluís Revilla (10:52:06): > I’ve read on the last report of the CAB: “One informal incident addressed”. What is an “informal incident”? I checked the code of conduct and couldn’t find anything regarding classifying incidents in informal and formal incidents, or what were the “Code of Conduct Procedures” changed

Lluís Revilla (10:52:08): > (Not sure if this is the right place to ask on in the general channel or the mailing list as this might affect us all)

saskia (20:04:55) (in thread): > We have used informal incidents to denote complaints that we received before the CoC was officially announced. I hope this clarifies it. We will clarify this in the future.

2020-12-22

Lluís Revilla (03:11:07) (in thread): > And what were the procedures changed? I think that if all the community should follow the CoC we should be notified of changes related to it.

saskia (18:41:34) (in thread): > The procedures weren’t changed. These complaints were received before the CoC was officially announced on the 10th of October. The community will be informed of all changes to the CoC.

2021-01-14

Lori Shepherd (16:26:25): > For anyone that is interested we do post the minutes from each months meeting on theCAB Bioconductor WebpageThe December minutes are now posted.

2021-01-22

Kozo Nishida (04:11:47): - Attachment: Attachment > I would like to update https://github.com/Bioconductor/bioconductor.org/blob/master/content/about/community-advisory-board.md to look like https://ropensci.org/about/ (tiled pictures of people). > But I don’t know the syntax (or some config file?) to do that for https://github.com/Bioconductor/bioconductor.org . > Please let me know if there is a suitable channel for this discussion (about requesting the website update).

2021-01-26

Matt Ritchie (23:15:41): > That would be great@Kozo Nishida(although I’m not sure how to do this…)

2021-01-27

Matt Ritchie (06:10:06): > Bioconductor’s Community Advisory Board are seeking new members - details on how to nominate have been posted on the support site athttps://support.bioconductor.org/p/p134374/. Nominations close 26th Feb 2021. Please help spread the word - thank you!

Sean Davis (07:29:18) (in thread): > Just edit the file and make a pull request. The file is markdown which is not great for html formatting. In short, you may want to consider a simple list rather than trying to make a more complex tabular-like design. > > For the images themselves, one convenient method is to upload the pictures to img.ur or some service like that and link to them from the markdown. The alternative is to commit them to git directly in animagesfolder.

Sean Davis (07:30:23) (in thread): > Perhaps@Lori Shepherdhas some thoughts from the core team perspective.

Lori Shepherd (07:34:09) (in thread): > I believe martin pointed@Kozo Nishidato the core team page for ideas – we arent web designers so we went with simple html table format on that page (you can mix some html syntax in markdown) - hardest part I found is trying to standardize image sizes and still make them look good) using table format

Aedin Culhane (21:48:48) (in thread): > Hi Lori, imageMagick is good for editing image sizes.https://imagemagick.org/script/identify.php - Attachment (ImageMagick): ImageMagick > Create, Edit, Compose, or Convert Bitmap Images

Aedin Culhane (21:51:22) (in thread): > > mogrify -path output/ -resize 300 *.jpg > > will convert all i*.jpg mages in path to 300 pixels wide

Aedin Culhane (22:02:31) (in thread): > https://imagemagick.org/script/command-line-processing.php

Aedin Culhane (22:05:44): > Hi for the webpage, and for the joint CAB/TAB meeting we want a short 2-3 line Bio for everyone. Also twitter or any other social media handle you want to provide (linkedin/ github/orc etc). Do you want to post here, or will I make up a google form/template? Whats easiest?

Aedin Culhane (23:39:42) (in thread): > I’ll try and put them up, this seems to resize them but I need to check they all look ok

Aedin Culhane (23:39:56) (in thread): > > mogrify -format png *.jpg > mogrify -resize 300x300^ *.png > magick identify *.png >

2021-01-28

Aedin Culhane (02:32:14) (in thread): > I made an attempt at this… have a look and give me commentshttps://github.com/aedin/bioconductor.org/blob/master/content/about/community-advisory-board.md

Aedin Culhane (02:32:24) (in thread): > I made an attempt at this… have a look and give me commentshttps://github.com/aedin/bioconductor.org/blob/master/content/about/community-advisory-board.md

Aedin Culhane (02:33:20) (in thread): > You can make tables in markdown… but I haven’t worked it out yet. a mouse over info would be good too, but I don’t know how to do that in git markdowm

Aedin Culhane (02:36:29) (in thread): > mmh,, should the photos be smaller?

Kozo Nishida (14:38:09) (in thread): > I sent a pull requesthttps://github.com/aedin/bioconductor.org/pull/1We can’t see the images on Github, but (I think) they can be seen once deployed onbioconductor.org

2021-01-29

Johannes Rainer (02:24:46) (in thread): > To me a google form/template sounds like a good idea - in order to have astandardizedresponse from everyone.

Aedin Culhane (16:14:57): > merged. I can see the photos… I wonder if its a permission issue?

2021-01-30

Kozo Nishida (00:16:53) (in thread): > Thanks you. > By the way, I couldn’t build the website (using Docker).https://github.com/Bioconductor/bioconductor.org/issues/81(So I couldn’t check if its a permission issue.) > > I can see the photos… > How did you build aedin/bioconductor.org ?

Lori Shepherd (11:42:01): > There is instructions locally building the website in the README

Kozo Nishida (20:03:20) (in thread): > (I think) what I did in this issuehttps://github.com/Bioconductor/bioconductor.org/issues/81 > > cd ~ > git clone[https://github.com/Bioconductor/bioconductor.org](https://github.com/Bioconductor/bioconductor.org)docker run -v /home/kozo2/bioconductor.org:/bioconductor.org/ -p 3000:3000 bioconductor/website:latest > > is the same as the README instructions. > (And it failed as I wrote in the issue81.) > > Is theinstructions locally building the website in the READMEsomething different from this docker command?

Kozo Nishida (20:18:17) (in thread): > I clonedBioconductor/bioconductor.orgto create an issue forBioconductor/bioconductor.org, but of course I checked the same thing foraedin/bioconductor.org. (Both failed in the same way.)

2021-01-31

Lori Shepherd (07:51:22) (in thread): > There are also institutions for building the website not using docker. What I don’t remember is if those commands are specific to Linux…

Kozo Nishida (20:40:55) (in thread): > Sorry, I did not tried the other instructions other than the firstdocker runinstruction. > (Now) It seems that I can buildbioconductor.orgusingDeveloper Setup. (still in the middle of building…, it seems that the first build takes time…)

Kozo Nishida (21:43:20) (in thread): > I don’t know why, but the build seems to stop here. > > create [6.99s] output/help/events/BrazilFeb2014/index.html > create [6.20s] output/help/events/BiocAsia2017/index.html > create [5.62s] output/help/events/SeattleMay12/index.html > create [5.60s] output/help/events/Brixen2013/index.html > create [5.50s] output/help/events/index.html >

Nitesh Turaga (23:06:17): > Hi kozo, I’m able to help with the website docker image. Do you see an error??

2021-02-01

Kozo Nishida (07:11:40): > @Lori Shepherd@Nitesh TuragaSorry, I found that the cause of the problem was that I was running the Docker command from “Ubuntu on WSL2”. When I run the Docker command from a non-WSL2-Ubuntu, I can see the website without any problems. And it can be built without waiting.

Kozo Nishida (07:31:16) (in thread): > @Aedin CulhaneIt’s not a permission issue. > It’s image path issue. > See the line 111 ofhttps://github.com/Bioconductor/bioconductor.org/edit/master/content/developers/how-to/git/faq.mdThe image path does not haveassetsin the file path. > If you want to render the image (in the md) on GitHub, you need to addassetsto the file path, but if you do it for the built website (==bioconductor.org), you need to removeassets(from the image file path).

Kozo Nishida (07:48:00) (in thread): > @Aedin CulhaneI sent another pull request.https://github.com/aedin/bioconductor.org/pull/2This should fix the following problem (that the CAB sticker is not displayed). - File (PNG): image.png

2021-02-05

Aedin Culhane (02:29:09) (in thread): > Thanks

2021-02-08

Lori Shepherd (08:43:02): > <!channel>The January 14th minutes have been posted to the website:Jan 14, 2021

Lluís Revilla (09:40:17): > Nide idea@Aedin Culhaneabout the Buddy program for new developers! There was any decision to make a pilot test or something?

Kevin Rue-Albrecht (10:32:12): > Indeed. I just submitted my application to the Software Sustainability Institute Fellowship programme 2021, with one of my 3 focus areas being to consolidate BiocChallenges and in particular the networking aspect. I’d be keen to hear about future developments in this kind of community initiatives!

Aedin Culhane (17:48:45) (in thread): > Thanks. I’d love input. We haven’t discussed it yet in the meeting. Our last CAB meeting was a joint TAB/CAB meeting to approve the new project wide Code of Conduct.

Aedin Culhane (17:50:16) (in thread): > Great. Can we help? Do you want to present this at an upcoming CAB meeting ??

2021-02-09

Kevin Rue-Albrecht (04:06:03) (in thread): > That would be great indeed! I could describe the status of the BiocChallenges, and get some feedback/advice on ways to consolidate them into a sustainable way forward. The more the merrier, when it comes to brainstorming:slightly_smiling_face:

Lluís Revilla (05:54:03) (in thread): > Well, i think that one way to improve package reviews and facilitate new packages submission is to suggest or contact with maintainers of existing package of similar BiocViews. Yhey have domain knowledge and they have at least experienced the process once (although a bit different probably with all the changes from svn to github then togit.bioconductor.org).

Lluís Revilla (05:58:17) (in thread): > However, not sure that that providing many different material would help, perhaps after some cycles or number of buddies-mentors some common and individual experiences could be written together.

Lluís Revilla (06:02:36) (in thread): > Also, not sure about the motivation for senior developers. In the descriptions, it seems that senior developers == Principal investigator. Which I don’t think PI will be doing much of this mentorship. But definitely the motivation for the mentors is something to think about, otherwise it won’t succeed. If this has to be a community effort it cannot be from a vertical/hierarchical structure, imho.

2021-02-12

Janani Ravi (15:52:19): > @Janani Ravi has joined the channel

2021-02-19

Leo Lahti (04:39:45): > Bioconductor’s Community Advisory Board are seeking new members and the nominations close on Feb 26. Considering to volunteer but it is good to make well informed decisions regarding potential commitments. I would be curious to know what the expected work load is. Any comments from the current CAB members would be welcome.

Lori Shepherd (08:03:30): > Monthly meeting attendance. The group identified projects and areas concerning the community and started forming smaller working groups to tackle items. Members help on working groups they find most appealing. Those working groups may have additional meetings and longevity determined mostly by the nature and goals.

2021-02-22

Aedin Culhane (15:02:54): > I spoke to Curtis Kephart at RStudio about their community outreach/meeting organization. He will be presenting a talk about this tomorrow Tuesday, February 23, 2021 6:30 PM to 7:30 PM PST . He will speak about organization of RStudio:conf (they have 17,000 people register for it) , what steps they took to ensure high quality recorded talks, engaging with participants etc .https://www.meetup.com/Santa-Barbara-R-Users-Group/events/276258798 - Attachment (Meetup): Community engagement at rstudio::global > Tue, Feb 23, 2021, 6:30 PM: TALKLet’s talk about growing and sustaining communities that support open science and open source software. These projects are fueled by people dedicating their time to cre

2021-03-15

Lluís Revilla (05:32:34): > Is there any update on the meetings from the CAB and TAB? The last listed minutes are from 2021-01

Charlotte Soneson (05:52:55): > Huh, strange - I uploaded the February minutes last week (and I can see them in the GitHub repo). Perhaps@Lori Shepherdor someone else with better insights than me into the website has an idea of why they are not visible.

Lluís Revilla (06:26:28): > Found it thanks!

Lori Shepherd (07:17:41): > i’ll investigate why not appearing

Lori Shepherd (07:19:13): > I forgot to push to the building location. It should propagate shortly and be visible on the website within the next hour or so

2021-03-31

Lisa Cao (12:50:24): > @Lisa Cao has joined the channel

2021-04-02

Lluís Revilla (14:28:59): > Congratulations to the new CAB members!

2021-04-05

Aedin Culhane (14:37:39): > The CAB will welcome 5 new members at our monthly meeting this Thursday. The CAB now has 15 members. They new members are > * Daniela Cassol, University of California, Riverside, USA > * Katerina Kechris, University of Colorado, Denver, USA. > * Estefania Mancini, Centre for Genomic Regulation, Spain. > * Kevin Rue-Albrecht, University of Oxford, UK. > * Mike Smith, EMBL, Germany. - File (PNG): image.png

Aedin Culhane (14:42:03): > Each year, 5 new members will be elected to the CAB. Members serve a 3 year term

2021-04-12

Lori Shepherd (08:01:59): > The CAB march minutes have been posted on the websiteMarch Minutes

2021-04-14

Aedin Culhane (11:10:43): > Community Award Nominations are open. Information about the awards and a link to the nomination form is athttps://bioconductor.org/about/awards/

2021-04-19

Aedin Culhane (08:57:16) (in thread): > Re-reading this thread. I don’t think senior package developers are PIs. I think people who have developed 2 packages are senior developers. Most are likely students or postdocs

Lluís Revilla (09:41:09) (in thread): > Great! I think many reviewers on rOpenSci (which would be a similar figure perhaps to the buddies here) are not PI nor motivated by a potential new recruit. I was just saying that because I’d expect few developers interested in recruiting students/post-docs which is mentioned as a possible motivation to do so on the minutes.

Aedin Culhane (12:23:31): > Please tweet, email and tell all your colleagues on zoom about the Bioconductor community awardshttps://bioconductor.org/about/awards/

Heather Turner (16:40:23): > @Heather Turner has joined the channel

2021-04-30

Sean Davis (10:39:54): > I’m asking my university communications folks to work on some publicity around the the recent 2-day workshop delivered to African participants. To include the key involvement of the CAB in making that happen. Others on CAB might want to think about doing something similar at their own institutions.

2021-05-01

Arjun Krishnan (21:41:03): > @Arjun Krishnan has joined the channel

2021-05-03

Heather Turner (05:37:38): > The African workshop sounds great, well done to all involved:slightly_smiling_face:

Heather Turner (05:38:11): > Is there an easy way to keep track of such outreach events? I think Forwards and AfricaR both missed this and so missed the chance to raise awareness among their followers/community at the point when registration was open.

Lluís Revilla (05:41:56) (in thread): > There’s a Bioconductor calendar with all the official events:https://bioconductor.org/help/events/and some CAB members tweet about these activities too

Heather Turner (06:22:00) (in thread): > Yes, but this workshop doesn’t seem to be on the calendar. I do follow H3ABionet and@Sean Davisbut I don’t think they tweeted about it in advance. I just realised I’m not following Bioconductor on Twitter - will do that now! - but it seems they didn’t tweet/re-tweet about it either. Probably I could have found it by following the CAB minutes, but it would be great if CAB/workshop organizers can advertise a bit more in future.

Lluís Revilla (06:48:55) (in thread): > Agreed, with all the things around Bioconductor it would be nice if the official account promoted them more.

Matt Ritchie (21:37:00) (in thread): > Thanks for the feedback. The calendar is a good way to keep track of events. In this case, the hands-on training workshops were run as a pilot and were only open to H3Africa fellows (held in the training week following their annual meeting, alongside many other events). Our colleagues at H3Africa handled the advertising and polled the attendees to ask what courses they were most interested in from the list of workshops presented at BioC2020. > > Our longer term goal is to offer training that is open to all and would definitely be promoted more widely in the usual manner (Bioconductor support site, event website, twitter, FaceBook + add event to the calendar). If there are other ways we can promote such events, it would be great to make use of these as well.

2021-05-04

Heather Turner (05:09:40) (in thread): > Thanks for the explanation, that makes sense! I think it would get picked up if it was advertised more widely as you describe.

2021-05-12

Aedin Culhane (23:59:16): > Nominations for joining theBioconductor Technical Advisory Boardare now open. Nominate yourself or someone else (please first confirm that they are interested), by completing thisshort form. Nominations close on May 31, at midnight in a time zone of your choice. > If you have questions, feel free to ask them in the#tech-advisory-boardchannel. Please help spread the word! - Attachment (Google Docs): Nomination Form: Bioconductor Technical Advisory Board (TAB) > Complete this form to nominate a candidate for a three-year appointment to the Bioconductor Technical Advisory Board (TAB). Self-nomination and nomination of others are acceptable; if nominating someone else please check with them first that they intend to accept the nomination. The composition of the TAB is determined through a nomination and selection process defined in the Bioconductor TAB Governance Document (https://bioconductor.org/about/technical-advisory-board/TAB-Governance.pdf). The TAB should: - constitute a broad representation of the Bioconductor scientific community - include emerging and established researchers in biological, statistical, and computational domains - represent diversity of gender, race/ethnicity, geography, and other aspects of the Bioconductor community Participation in the TAB obligates the member to regular participation in a monthly TAB teleconference and to follow the Bioconductor TAB Governance Document. Nominees are encouraged to be specific about any committees they would like to participate in or initiatives they would like to lead. Some existing and planned committees within the Bioconductor project are: Code of Conduct, Education and Outreach, Infrastructure, Governance, various conference organizing committees. The TAB helps determine the overall direction of the project, providing guidance to developers and investigators on new concepts in computational biology and genome research, and acts as an incubation group for the collaborative pursuit of funding for the project.

2021-05-13

Aedin Culhane (00:01:36) (in thread): > I agree with you. What do you think are the most effective communication channels? Should we have blogs/mailing list etc, or do you think we just need to use twitter more frequently/effectively?

Aedin Culhane (00:02:27) (in thread): > and populate and promote the calendar better? There is an option for users/developers to add events to the calendar if they wish to promote something.

Aedin Culhane (00:04:36) (in thread): > I think H3ABionet and@Sean Davistweeted after the workshop. We relived on H3ABionet to promote the workshop in advance and to register users for the workshop. I think they registered over 150 people, so I think we assumed they were doing an effective job of promoting the workshops.

Lluís Revilla (06:59:53): > Not sure this month CAB meeting has already taken place, but I don’t find last March minutes on the website.

Lori Shepherd (07:08:53) (in thread): > March minutes were postedhttp://bioconductor.org/about/community-advisory-board/2021-03-11-minutes.pdfif you are talking about April we will vote on acceptance at today’s monthly meeting and it will be posted by later this morning (the meeting is the second thur of the month)

Lluís Revilla (07:40:19) (in thread): > Oh, yes I was talking about April, sorry. Great! Looking forward to it

Aedin Culhane (12:12:59) (in thread): > Thanks for following what we are doing. Please let us know your suggestions for what we should be doing

Lluís Revilla (13:05:42) (in thread): > @Aedin CulhaneHaving delayed notes is already much better than the available information about CRAN or R core meetings, but sometimes it is a bit hard to know what the CAB is doing and how outsiders can help when one read reports of actions done 3 months ago (the April notes will be released now with the information on what the CAB was doing on March). Faster minutes release will make it easier to know what’s up and maybe participate. > I have provided some links to what I though it was relevant content to events@bioconductor, I didn’t receive a reply and three months later I see it was brought up on the CAB (but it was not mentioned on any channel from Bioconductor I was aware). A simple acknowledgment would have gone miles to encourage further participation. Last, I think the CAB could make more frequent use of Bioconductor’s Twitter account, as the official channel of communication to broaden the reach of any message or new packages accepted.

Aedin Culhane (16:56:18) (in thread): > Thanks, I was trying to think of ways to broaden the reach of new package contributors. Using the @Bioconductor Twitter is good, I wonder how this could be streamlined so its not a ton of work on the Bioc Core Team who manage the account. The CAB are all volunteers and we are only in existence for a year… so I am grateful for your patience as we work out communication paths.

Aedin Culhane (16:57:26) (in thread): > @Lori Shepherdand@Kozo Nishidamanage the event calendar, I will let them know that notice of receipt of event submission would be appreciated. I think we were trying to work out what should and shouldn’t be on the Bioc event calenadar.

Aedin Culhane (16:59:18) (in thread): > We recently started a CAB/TAB boards github so working groups can share docs.. Thttps://github.com/BioconductorBoards

Aedin Culhane (17:00:30) (in thread): > @Kozo Nishidaand@Lori Shepherdare working the events, what is a Bioc event, what should be added, what are the requirements for adding an events etchttps://github.com/BioconductorBoards/CABWorkingGroups/

Aedin Culhane (17:01:57) (in thread): > If you know of calendars that are widely used to publish conference/R/Bioinformatics events, please share, maybe we can ask them to include the Bioc calendar to better communicate our events.

Aedin Culhane (17:03:07) (in thread): > CAB/TAB Minutes are released a month later, because we approve the minutes at the subsequent meeting

Aedin Culhane (17:06:43) (in thread): > Regarding new packages… perhaps new package contributors could be encouraged to upvote and build threads on posts about their package in the slack channel#package_submissionsand#new_packages. Currently these have an automated feed about packages that are submitted and accepted

2021-05-14

Lluís Revilla (05:31:31) (in thread): > The bioc-bot could automatically post on twitter upon acceptance of a package. This is some upfront cost that would remove the burden on any person.

Lluís Revilla (05:31:54) (in thread): > I am aware that CAB is on volunters good will. On other similar organizations, minutes are posted the day after the meeting without further approval. What would happen if the minutes are not approved on the next meeting? I haven’t found anything on the governance document (also it doesn’t mention anything about approval of minutes).

Lluís Revilla (05:34:27) (in thread): > #package_submissionsis too crowded with many notifications, and it is the same feed if someone followed the github repository. (It has no description and no topic)#new_packagesdescription is what#package_submissionsdoes#package-submissionis almost the same as new_packages but with a description that match its content

Lluís Revilla (05:36:00) (in thread): > Anyway if the goal of package contributors is to increase awareness it is better in a more public venue, as many potential users will not be on the slack channel.

Lluís Revilla (05:37:38) (in thread): > Hope this helps, and looking forward to the progress of the project.

Lori Shepherd (09:10:26): > TheApril minutesare now available on theCAB website

Aedin Culhane (13:58:36): > How many languages can the CAB members speak??

Aedin Culhane (14:03:08): > English (all of us), French (@Yagoub Ali Ibrahim Adam,@Kevin Rue-Albrecht,@Susan Holmes,@Leonardo Collado Torres) , Spanish (@Leonardo Collado Torres@Estefania Mancini,@Benilton S Carvalho), Portuguese (@Yagoub Ali Ibrahim Adam,@Benilton S Carvalho,@Daniela Cassol,@Estefania Mancini), German (@saskia), Japanese (@Kozo Nishida), Italian (@Johannes Rainer) How are my guesses????? What have I missed??? Arabic (@Yagoub Ali Ibrahim Adam) I can speak Irish and little French !! What about@Matt Ritchie,@Lori Shepherd,@Katerina Kechris?

Benilton S Carvalho (14:08:58): > I’m able to not starve in Spanish, if needed.

Aedin Culhane (14:23:33): > I can order beer in Spanish and maybe a meal but thats the extent of my Spanish

Estefania Mancini (14:24:02): > @Estefania Mancini has joined the channel

Yagoub Ali Ibrahim Adam (14:25:13) (in thread): > Arabic

Lori Shepherd (14:43:33): > :disappointed:not well enough in anything – long time ago learned spanish and I’m doing duolingo right now for german – but like@Aedin Culhanejust said – mostly can order a beer:slightly_smiling_face:

Aedin Culhane (15:08:01) (in thread): > :fast_parrot:

Aedin Culhane (15:14:46) (in thread): > We’re got 9 languages…

Mike Smith (15:21:44): > Unfortunately, it would be vastly overselling my German to say I speak it.

Aedin Culhane (16:30:38): > Thanks Mike, I’ll drop you from the German list.

Leonardo Collado Torres (18:07:55): > I can speak French too, but I haven’t written French in a long time (and I barely practice nowadays)

2021-05-15

Susan Holmes (09:16:34) (in thread): > Wish I could speak:flag-pt:, it would make my life so much easier right now, but google translate is problematiuc in not separating Brazilian and European Portuguese.

2021-05-16

Estefania Mancini (12:19:07): > Hello everyone! I can understand some Portuguese as well

2021-05-24

Kozo Nishida (17:22:41): > Now conference is virtual, it might be better to set up a community room in one conference like this Dockercon instead of dividing it into regional conferences. (just for reference purposes)https://docker.events.cube365.net/dockercon-live/2021/community - Attachment (docker.events.cube365.net): DockerCon 2021 > Attend DockerCon 2021 to see how Docker helps make it easy for you to focus more of your time on coding the next great application: from code to cloud. Submit your registration now to attend DockerCon 2021– designed for developers by developers.

Kozo Nishida (17:25:25): - File (PNG): image.png

2021-05-27

Aedin Culhane (13:11:45): > @Martin Morganmentioned in the developer forum today, that he would like if core Bioc packages supported different languages. If you run BiocManager in different language, are the error messages in that language or they in English? Do you need better support for multiple languages from core Bioconductor packages such as BiocManager?

Martin Morgan (13:11:48): > @Martin Morgan has joined the channel

Andres Wokaty (13:15:56): > @Andres Wokaty has joined the channel

Henrik Bengtsson (14:42:25): > @Henrik Bengtsson has joined the channel

Robert Castelo (16:04:03): > @Robert Castelo has joined the channel

Robert Castelo (16:57:42) (in thread): > From a Windows with localeSpanish_Spain.1252(Spanish -International) I get an error in English when doing the following: > > > BiocManager::valid(checkBuilt="hola") > Error in valid(checkBuilt = "hola") : is.logical(checkBuilt) is not TRUE > > while R catches correctly the locale and gives translated errors: > > > hola > Error: objeto 'hola' no encontrado > > I don’t recall any of my students having difficulties with understanding English messages in R/Bioc because of the language, but I guess students at a university are a biased subset of the user base of R/Bioc. If the CAB needs support for European Spanish (es_ES), I’ll be happy to help. I’d be also happy to give support to translating messages intoCatalan, but I guess I’d have first to translate R messages since I’m afraid R has no support for that language.

Lluís Revilla (18:33:14) (in thread): > FYI There’s a package (potools:https://github.com/MichaelChirico/potools) to help set up translation of error messages. On the coming useR!2021 conference there is a tutorial/workshop: Translating R to your Language:https://www.conftool.org/user2021/index.php?page=browseSessions&presentations=show&form_tracks=10.

Kevin Blighe (22:01:49): > @Kevin Blighe has joined the channel

2021-05-28

Lluís Revilla (03:19:06) (in thread): > I could also help with both Spanish and Catalan

Heather Turner (10:35:16) (in thread): > @Aedin Culhanepicking up on this old thread. For me Twitter is great, but it probably misses a lot of people. A blog post or a submitted news item to R Weekly might be a good idea (https://github.com/rweekly/rweekly.org#how-to-have-my-content-shared-by-r-weekly), for one-off events especially. There’shttps://jumpingrivers.github.io/meetingsR/events.htmlfor bigger events - I see some of the Bioc events added there already. Those might catch people who don’t think to look directly at the Bioc website and/or subscribe to the calendar. - Attachment (jumpingrivers.github.io): Events | A list of R conferences and meetings > Events | A list of R conferences and meetings.

2021-05-29

Martin Morgan (13:58:43) (in thread): > Great to see this enthusiasm! I tried to feel my way through what needs to happen in the ‘po-translations’ branch of BiocManagerhttps://github.com/Bioconductor/BiocManager/tree/po-translations. There’s a README-Translations.mdhttps://github.com/Bioconductor/BiocManager/blob/po-translations/README-Translation.mdthat can serve as a starting point. This is still highly experimental but if any of you would like to try a translation it would be great to learn of your experience. Including the ‘meta’ experience — it feels like establishing the infrastructure for translation opens the door to some better practices when it comes to tests and so on.

2021-06-03

Kozo Nishida (01:05:12) (in thread): > This useR! 2021 tutorial seems to be related to that topic.https://www.conftool.org/user2021/index.php?page=browseSessions&search=Translating+R

Kozo Nishida (01:06:32): - File (PNG): image.png

2021-06-07

Sean Davis (09:45:15): > We got a recent inquiry fromhttps://www.outreachy.org/about working with Bioconductor. > Outreachy provides internships to work onopen source to underrepresented groups.Internships are::dollar:Paid- $6,000 USD total internship stipend:earth_africa:Remote- both interns and mentors work remotely:mantelpiece_clock:3 months- internships run May to August, or December to March > They have a pretty strong track record::female_sign:92% women:rainbow-flag:4% transgender, genderqueer, or non-binary people:person_with_headscarf:64% people of color:adult:12% people from a historically disadvantaged caste or tribe - 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!

Sean Davis (09:46:04): > Anyone interested in a chat with them, just drop a reply here and I’ll try to arrange a meeting.

Arjun Krishnan (18:21:02) (in thread): > Hi Sean, I’m not part of any board but I’ll be happy to help out with this effort in any way.

2021-06-09

Janani Ravi (00:57:29) (in thread): > Sean, same here:point_up:. I’m not on the board, but happy to help with this effort too.

2021-06-11

Martin Morgan (06:52:22) (in thread): > There are now Spanish, Chinese, and French versions of error messages in the ‘po-translation’ branch of BiocManager —https://github.com/Bioconductor/BiocManager/tree/po-translations— thanks to Robert, Jiefei, and Marcel! See notes athttps://github.com/Bioconductor/BiocManager/blob/po-translations/README-Translation.md > > $ LANGUAGE="es" R -e "BiocManager::install(repos = 'foo')" > > BiocManager::install(repos = 'foo') > Error: argumento 'repos' no permitido en 'install()' > Ejecución interrumpida >

Martin Morgan (06:55:58) (in thread): > @Robert Castelo@JiefeiWang@Marcel Ramos Pérezthanks for the translations and working through the initial glitches! There are four new error strings at the end of the.potfile; so I guess the next step is figuring out how to update an existing.po.

Robert Castelo (10:00:44) (in thread): > Thanks Martin for making it easy for us to translate the messages. I think the concerns summarized in theREADME-Translation.mdfile and brought up by@Hervé Pagèsin thisPRneed to be addressed to minimize language-related problems at the support site. Maybe one approach would be to ask users to report the errors in English and showing how can they switch language, for instance: > > > BiocManager::install(repos='foo') > Error: argumento 'repos' no permitido en 'install()' > > Sys.setenv(LANGUAGE="en") > > BiocManager::install(repos='foo') > Error: 'repos' argument to 'install()' not allowed >

2021-06-13

JiefeiWang (00:20:16): > @JiefeiWang has joined the channel

2021-06-14

Lori Shepherd (09:22:53): > May minutes have been posted on the websitehttp://bioconductor.org/about/community-advisory-board/2021-05-13-minutes.pdf

2021-06-16

Kevin Rue-Albrecht (10:10:41): > Hi all > As part of the ideas to celebrate the 20 years of Bioconductor, discussed at the BioC2021 organisation meetings, I have started a GitHub repository to host a carousel of slides (using xaringan,https://github.com/yihui/xaringan) where community members are welcome to add slides reminiscing highlights of the project over the years: > * Source:https://github.com/kevinrue/Bioconductor20YearsSlides > * GitHub Pages:https://kevinrue.github.io/Bioconductor20YearsSlides/ > I’m aware that not everyone usesxaringanon a regular basis, if at all, and I am happy to help those who would like to contribute but don’t know how. I’ve added a few bits of FAQ in the contributing section of the repository:https://github.com/kevinrue/Bioconductor20YearsSlides/blob/master/.github/CONTRIBUTING.md

2021-06-25

Heather Turner (04:10:05): > Hi Folks, There are several community-focused incubators at useR!, that I expect would be of high interest to this group: > * “Five principles to grow up your R community” (@Leonardo Collado Torresis co-organizing) > * “Strategies to build a strong AsiaR Community” (@Janani Raviis co-organizing and I posted about here:https://community-bioc.slack.com/archives/C01S6BCPA5N/p1624608174000900) > * “Expanding the R community in the Middle East and North Africa (MENA)” (not sure it involves anyone on this Slack yet?) > See all incubators here:https://www.conftool.org/user2021/index.php?page=browseSessions&presentations=show&form_tracks=9&form_topic=0 - Attachment: Attachment > From @Janani Ravi : > > To anyone interested in attending useR! 2021 + building a strong AsiaR community > > Hello, > Hope you are doing well and are safe. > > Please join our AsiaR incubator discussion at useR! 2021. The goal of this incubator is to discuss strategies for building a diverse and vibrant R community within Asia, connecting various useRs/developeRs, and down the line, hosting an AsiaR conference within the next couple of years. > > Do invite people from your R community to join the incubator discussion and register for useR! Asian R-users can avail themselves of reduced registration fees. Also, if they do not have institutional support, we encourage them to apply for waivers. So, please spread the word, and write to us with questions, if any. > > Here are some topics that we could address during our discussion. > •  Shared struggles of the local communities. > •  Motivation for creating/joining these communities. > •  Long-term goals for the AsiaR global community. > •  Current lack of online social platforms for the R community in Asia. > •  The focus is on Python instead of R, though R is a great language for data analysis. Academia/industries are much more invested in learning Python than R, starting with how students are educated. > •  Need for financial assistance – what are resources we can tap into? >   > Few invited participants from across Asia > •  Binod Jung Bogati from Nepal > •  Noman Khalid from Pakistan > •  Meenakshi Kushwaha from Taiwan > •  Joel Nitta from Japan > •  Young Suk-Lee, Woo June Jung, & Eun-Kyung Lee from South Korea > •  Aarthi Ravikrishnan from Singapore > •  Emi Tanaka | originally from Japan but now in Australia > •  Matthias Bannert | will help us connect with the R community in China, but based in Switzerland >   > Moderators > • @Adithi R. Upadhya from Bangalore, India > • @Janani Ravi | originally from India but now in the US > > SESSION DETAILS > Topic: Strategies to build a strong AsiaR community > Time: 08 July 2021 3:40—4:40am UTC > > useR! 2021 conference schedule: https://user2021.r-project.org/program/schedule/ > > Code of Conduct: https://user2021.r-project.org/participation/coc/ > > Conference details > useR! 2021: July 05–09, 2021 > Website: https://user2021.r-project.org/ (incl. registration) > FAQ: https://user2021.r-project.org/participation/faq/ > > Looking forward to building a wonderful AsiaR community with you all!

Heather Turner (04:10:12): > Note that registration to useR! is required to attend and registration closes today

Heather Turner (04:11:26): > However, the idea of the incubators is to produces some sort of output and/or kick-start longer-term initiatives, so hopefully, there will be blog posts and more to share after the event (incubators will not be recorded).

Lluís Revilla (11:18:38): > I’ve seen some activity around the idea of a having reviewers from the community (mainly on github Bioconductor package development book:https://github.com/Bioconductor/pkgrevdocs/pulls).

Lluís Revilla (11:19:02): > Is there any information about how it will be done? I don’t know if this was discussed on the latest meeting. (Were the minutes approved 2 hours later or do we need to wait 1 month more?)

Lori Shepherd (11:39:35): > We expect to be announcing more details in the next week or two once we finalize documentation and requirements

Lori Shepherd (11:40:13): > As previously stated, minutes from the last meeting are announced after they are approved at the following meeting

2021-07-07

Aedin Culhane (01:47:44) (in thread): > Thanks.@Hedia Tnaniis involved with R Ladies MENA and Bioconductor. We have been talking with her to understand how the CAB can support Bioconductor in the MENA region

Hedia Tnani (01:47:49): > @Hedia Tnani has joined the channel

2021-07-09

Kozo Nishida (09:02:56): > https://twitter.com/tatsuya_amano/status/1413369391194902528 - Attachment (twitter): Attachment > #languagebarriers have multiple major consequences for scientists, the advance of science, and its impact on societies. We need a concerted effort from all – both non-native & native speakers. Here we’ve listed ten things you can start doing today. > https://rdcu.be/cnZQf https://pbs.twimg.com/media/E51LyBrVcAsHpUu.jpg

Lori Shepherd (15:26:34): > June minutes have been posted on the websitehttp://bioconductor.org/about/community-advisory-board/2021-06-10-minutes.pdf

2021-07-12

Lori Shepherd (12:02:14): > Bioconductor is pleased to announce a call for community volunteers to > assist with Bioconductor Package Reviews. This is an excellent way to get > involved with and give back to the Bioconductor Community. The minimum > requirement to volunteer is to be actively maintaining an existing Bioconductor > package. Please readReviewer Expectationsfor full details and information.

2021-07-16

Kozo Nishida (02:43:21): > I’m from the CAB Event Calendar Working Group. > I would like to usethis GitHub issue formto manage theBioconductor event calendar. Currently, we are accepting the event addition by email toevents at bioconductor.org. > I would like to replace that email with the GitHub issue form. > Is there anyone who would like to suggest anything? > If there is no problem about the replacement, I would like to ask you to create a new repository (for the GitHub issue from) underhttps://github.com/bioconductor/

2021-07-30

Tom Sinden (04:19:02): > @Tom Sinden has joined the channel

2021-08-06

Aedin Culhane (11:28:19): > We will be doing a meet the CAB session to discuss what we have been doing this past year today. Join us at#bioc2021at 2pm PST/5pm EST/ 10pm GMT.

Marcel Ramos Pérez (17:38:37): > @Marcel Ramos Pérez has joined the channel

2021-08-11

Sean Davis (14:39:07): > F1000Research pointed out a blog post on the Bioconductor Gateway. Tweet about it is here:https://twitter.com/seandavis12/status/1425449147369361408 - Attachment (twitter): Attachment > Five years on: Best of The Bioconductor Gateway: Top 5 Most Impactful Articles blog.f1000.com/2021/08/04/bes… > #Bioinformatics @F1000Research

2021-08-16

Yagoub Ali Ibrahim Adam (08:56:08): > Dear all > Last Friday, I had a meeting with the H3Africa group about continuing to offer Bioconductor courses. The group agreed that it would be great to have a follow-up Bioconductor workshops. They proposed to have a Bioincoductor workshop in the first week of November 2021. I will try to set a second meeting for more discussions and it will be good if more CAB members can attend.

Sean Davis (09:28:32) (in thread): > Hi,@Yagoub Ali Ibrahim Adam. We can very easily recycle some of the workshops from this year and previous ones, reducing work on everyones’ parts. We have about 50 such workshops ready on Orchestra and can prepare others that are perhaps more basic if desired.

Nitesh Turaga (10:21:35): > Would a generic talk/workshop about “Bioconductor using containers” be of interest? If so, i’m happy to give one.

Lou Woodley (12:03:00): > @Lou Woodley has joined the channel

2021-09-06

Eddie (08:22:25): > @Eddie has joined the channel

2021-09-30

Sean Davis (08:42:55): > Demographics from usage stats might be really useful. - Attachment: Attachment > Is it possible to get statistics on which country the package is downloaded from? > I’d like to show that the number of Japanese Bioconductor users is not small (although there are few Bioconductor developers in Japan). > If it can be shown, it can be said that the barrier in Japan is that the information for developers is not available (or accessible==language barrier?).

Mike Smith (09:20:43) (in thread): > I’m no expert, but I think there’s some real GDPR issues that would need to be thought through before processing or sharing any information like that. I’m fairly sure the Bioconductor website isn’t currently GDPR compliant since there’s Google Analytics tracking cookies but no consent form. I suspect you could claim geolocation analysis is a legitimate interest for the project, but it would probably need to be accompanied by declarations on the IP logging policy, anonymization, retention times, etc. > > I also have no idea how something like tracking consent is managed for server requests that don’t involve a browser e.g. runninginstall.packages(). It’s clear that IP address have to be retained for some period of time for a download to work, and Bioconductor must store them for >1 month to generate the existing download stats, but the rest is opaque to me.

Martin Morgan (10:17:28) (in thread): > I agree with Mike, nonetheless in pre-GDPR there are for instance web site visitor stats in Annual reports, e.g., p.5 ofhttp://bioconductor.org/about/annual-reports/AnnRep2019.pdfsays “The web site served 2.378M sessions (777,981 unique visitors) in the trailing 12 months (statistics from Google analytics). Visitors come from the United States (31%), China (12%), the United Kingdom (6%), Germany (5.1%), Japan, India, Canada, France, Spain, Italy, and 213 other countries.” so we could speculate that Japan accounted for about 5% of 777981 web site visitors. There are likely to be similar statements in earlier reports; I think I remember that the ranks were relatively similar across years.

Martin Morgan (10:18:27) (in thread): > Hmm, but Japan isn’t covered by GDPR, so is it legitimate to expose that information? Or are there Japanese regulations that govern this, too? Nightmare!

Mike Smith (10:25:32) (in thread): > Japan has the APPI, but I don’t know the details. Nonetheless, GDPR applies to any website that has EU visitors, and IMO publishing details (even if only for non-EU visitors) might highlight how there is no current GDPR provision and some processing must be happening even if it’s only to eliminate EU traffic from an analysis. I agree it’s a complex problem!

Kozo Nishida (21:48:46): > This “key moment” information seems to be automatically annotated by Google (or YouTube?). > I have only seen one, but the detection accuracy seems to not bad. > It may be useful to add this information as chapters in the video. > (The YouTube video itself doesn’t have the key moments info as the chapters.) - File (PNG): image.png

2021-10-04

Kevin Rue-Albrecht (13:07:53): > Somewhat puzzled why the CAB meeting agendas are more popular/prominent than the About page of the Bioc website. Always a bit of a pain when I want to share the link to the page (shame on me, I haven’t bookmarked it yet ^^ ) - File (PNG): image.png

2021-10-05

Martin Morgan (15:33:46): > Are a few stickers (e.g., CAB / TAB; BiocAsia 2020/2021) missing from the README ofhttps://github.com/Bioconductor/BiocStickers?@Johannes RainerI thought also there were one or more additional ‘diversity affirming’ stickers?

2021-10-06

Johannes Rainer (02:09:23) (in thread): > I didn’t add some of the stickers to the readme (like for the boards or the awards) but I can add them, no problem (they for sure are in the repo, just not linked in the readme). I remember there were some additional diversity affirming stickers, but I can’t recall who wanted to design them (or actually designed them)

Johannes Rainer (02:26:55) (in thread): > I’ve just added some missing stickers to the README. The BiocAsia stickers are still missing - as well as the diversity affirming ones

Aedin Culhane (15:21:38) (in thread): > The diversity ones are therehttps://github.com/Bioconductor/BiocStickers/blob/master/Bioconductor/README.md

2021-10-15

Wes W (11:01:53): > @Wes W has joined the channel

Wes W (11:06:43): > Hey everyone, I am not sure if you are taking on any more volunteers or members , but I am keen to get involved. Not sure if I have to wait till next year to get involved if there are specific in take periods , but finally have more time to take on more community volunteer work. Let me know what and how I can help out. Thanks!

Lluís Revilla (11:19:27): > Hi Wes! Welcome! I’m not a CAB member, but you don’t need to be member of the CAB to volunteer your time. There are many tasks you can do for the community: > * Bioconductor is always accepting new reviewers:http://contributions.bioconductor.org/review-volunteer-chapter.html > * Answering questions onsupport.bioconductor.org > * Answering questions on the bioc-devel mailing list - Attachment (contributions.bioconductor.org): Chapter 19 Volunteer to Review | Bioconductor Package Guidelines for Developers and Reviewers > Anyone from the Bioconductor community can volunteer to become a Bioconductor community reviewer to review incoming packages submitted through the New Submission Tracker. Please review the…

Lori Shepherd (11:20:44): > We also are generating a list of working groups and suggested working groups that we hope to advertise shortly to the community for volunteers

Sean Davis (13:37:47): > And conference planning has already started for Bioc2022.

2021-10-16

Wes W (09:06:53) (in thread): > sounds fund

2021-10-17

saskia (23:03:47) (in thread): > Hi Wes, also would love to have you as a member of the code of conduct commitee! To apply fill outthis form. - Attachment (Google Docs): Bioconductor Code of Conduct Committee Elections 2021 > The Bioconductor Code of Conduct Committee updates, disseminates, upholds and enforces the Code of Conduct (http://bioconductor.org/about/code-of-conduct/) across all platforms of the Bioconductor project. Each year the Code of Conduct Committee invites applications to become a new member of the committee. If you are interested in becoming a member of the committee, please fill out the following short application. The applications are then voted on by the current committee. The Bioconductor Code of Conduct Committee strives for a diverse and inclusive committee and thus encourages applications from members of underrepresented groups. Find out more about the Code of Conduct Committee and its work! (https://docs.google.com/presentation/d/11c1_LjiZbEJ-4S5jgcJnEzdcVo5yhxHICKdI4e95oVM/edit?usp=sharing) Applications close 21st of October. If you have any questions regarding serving on the Bioconductor Code of Conduct Committee or the application process, please contact Saskia Freytag (mailto:sas.freytag@gmail.com|sas.freytag@gmail.com).

2021-11-08

Kevin Blighe (12:16:29): > Forgive me if channel is incorrect. Does Bioconductor have any arrangement with ‘La Piana Consulting’ for conducting independent interviews with developers (like me)?

Vince Carey (12:58:15): > @Vince Carey has joined the channel

Vince Carey (12:59:44): > @Kevin Bligheyes. I am sorry if you were not notified of this previously. We tried to allow opt-out. Contact me directly with any issues.

2021-11-09

Aedin Culhane (02:29:59) (in thread): > Hi Wes. There is a call in spring each year for new members but we have multiple working groups and anyone can join those. We are trying to set a space on GitHub where everything is more visible and it’s easier for people to contribute

Aedin Culhane (02:32:12) (in thread): > You can also start your own group if there is something you’d like to work on. You can announce & create channel in slack. Cab can give advice, advertise through cab etc

2021-11-11

Shilpa Garg (09:28:12): > @Shilpa Garg has joined the channel

2022-01-24

Lori Shepherd (08:00:10): > The community advisory board is seeking nominations for new members. Please seehttps://support.bioconductor.org/p/9141753/for more information and a link to the nomination form. The deadline for submission is February 25 2022. New members will be elected from the list of submitted nominees by the current community board members.

2022-01-30

Aedin Culhane (17:14:39): > Let’s try to spread this msg far and wide. Can we post in #general and tweet

Lori Shepherd (18:28:32): > I thought I tweeted already…. So please share and re tweet…

2022-01-31

Lori Shepherd (07:58:34): > it was tweeted and on the mailing list and support site as well too – I keep bumping the post on the support site to stay visible

2022-02-25

Joshua Sodicoff (16:20:11): > @Joshua Sodicoff has joined the channel

2022-03-15

Lori Shepherd (10:37:34): > BiocAwards 2022 nomination is now open. Please seehttp://bioconductor.org/about/awards/

2022-03-31

Nicole Ortogero (22:26:48): > @Nicole Ortogero has joined the channel

2022-05-09

Xueyi Dong (00:14:55): > @Xueyi Dong has joined the channel

2022-05-18

Lluís Revilla (16:03:27): > Was there a meeting of the community advisory board last month? I cannot find the minutes for April

Lori Shepherd (22:33:46): > Yes. Sorry they were approved last week and I forgot to post before I went on vacation this week. They will be posted next Monday.

2022-05-19

Lluís Revilla (03:20:15): > Thanks. Enjoy the vacation!:sunglasses:

2022-05-24

Sean Davis (15:05:23): > FYI:https://www.cscce.org/resources/cpm/ - Attachment (CSCCE): CSCCE Community Participation Model - CSCCE > Members of a community participate in different ways. Our Community Participation Model helps you design programming to engage every member.

Lou Woodley (15:10:58) (in thread): > Not sure what the context is for this, but if anyone has questions, feel free to add them here:slightly_smiling_face:

Sean Davis (15:14:24) (in thread): > Really just informational. I’ve seen these ideas in multiple forms before and have always thought of them as sort of the social network version of Bloom’s Taxonomy. This is perhaps the most succinct and informative figure for thinking about community engagement.

Sean Davis (15:15:01) (in thread): > @Lou WoodleyI guess you know a bit about it.:wink:

Lou Woodley (15:57:28) (in thread): > I like the description “social network version of Bloom’s taxonomy”!

2022-06-09

Kozo Nishida (11:41:15): > Hi all, > I’m Kozo, a member of CAB. > I would like to share information about > * https://bioconductor.github.io/biocblog/ > * https://github.com/bioconductor/biocblog > . > This is for sharing some little news with the community. > I will mainly use this to tell the community what the CAB working group is doing now. > However, people other than CAB are also welcome to use it (to share information with the community). > All you have to do is adding a post (==an Rmd) with the R commands below > > library(distill) > create_post("Your post title") > > and send it as a PR. > Let me know if you have any opinions/questions/ideas.

2022-06-10

Nicole Ortogero (16:12:42) (in thread): > @Kozo Nishida. My only suggestion is if we could add a mission statement or intro to the blog under the title, “Bioconductor community blog”. This will help users understand what type of articles will be found in this blog. Same with the contributing page, can we add a small blurb of what types of articles we are hoping to post here. I can help with wording if you provide the details.

2022-06-29

Kozo Nishida (12:53:19): > Hi all, > I was interviewed byCSCCEand talked about the Bioconductor community.https://twitter.com/TheCSCCE/status/1541802988720750596Please have a look if you’d like. - Attachment (twitter): Attachment > This week in our case study series, we’re highlighting > @kozo2, a volunteer community manager for several communities including @Bioconductor, @carpentries, and @PyData. https://doi.org/10.5281/zenodo.6578362

2022-07-01

Aedin Culhane (14:52:27): > @Kozo Nishidadid you post your event to the chat ? Kozo is organizing a really exciting event on July 9th, a translate-a-thon… so we can make Bioconductor more friendly for those for whom English is not their first language. If you want to make Bioconductor more multi-lingual and inclusive… Kozo has the info

Kozo Nishida (18:25:32) (in thread): > I haven’t posted the event to the chat yet.https://www.meetup.com/boston-r-bioconductor-for-genomics/events/286908674/is the event page! > If there’s anything you are unclear on, please let me know!

2022-07-09

Kozo Nishida (07:28:35): - Attachment: Attachment > I will be holding this document translation event two and a half hours from now. > If you like, please feel free to join us. > The introduction slide is https://docs.google.com/presentation/d/1yvC6ylG2eK6qnwv9MRPrRUJ0pfYc-7H4zbkhSWnlEos/edit?usp=sharing.

2022-07-15

Ashley Robbins (15:21:24): > @Ashley Robbins has joined the channel

2022-07-27

Andres Wokaty (18:14:50): > Is there a website for working groups?

Aedin Culhane (18:50:48): > http://workinggroups.bioconductor.org/currently-active-working-groups-committees.html - Attachment (workinggroups.bioconductor.org): Chapter 2 Currently Active Working Groups / Committees | Bioconductor Working Groups: Guidelines and activities > The following describe currently active working groups listed in alphabetical order. If you are interested in becoming involved with one of these groups please contact the group leader(s). 2.1…

2022-07-28

Alex Mahmoud (13:29:59): > @Alex Mahmoud has joined the channel

Lambda Moses (13:48:20): > @Lambda Moses has joined the channel

Krithika Bhuvanesh (13:52:08): > @Krithika Bhuvanesh has joined the channel

2022-07-29

Margaret Turner (20:16:39): > @Margaret Turner has joined the channel

2022-08-05

Andres Wokaty (16:09:05): > This monthoutreachy, which provides open science/source internships for those underrepresented in technology, will open applications for communities (which have mentors + projects for which potential internship applicants can apply). We previously applied with R but were not successful. Outreachy suggested that we apply as an individual Bioconductor community, which I plan to do. I wanted to see if anyone might be interested in working on this with me. I would even appreciate if anyone would look at our application, so that I’m making us look good, but I would really like help find funding for the intern. Feel free to reach to help or if you have questions. Thanks :)

2022-08-06

Aedin Culhane (19:35:20) (in thread): > What’s the timeframe for the application? Do you want to present the idea to the CAB at our monthly meeting?

2022-08-07

Sean Davis (11:16:22) (in thread): > I’m happy to take a look,@Andres Wokaty.

2022-08-08

Andres Wokaty (15:30:17) (in thread): > Thanks,@Sean Davis! The application will open this month (still waiting on exact date).@Aedin CulhaneIt’d be great to present it at the next CAB meeting–when is it?

Andres Wokaty (15:38:22) (in thread): > I believe the application will close in September, which is when potential Outreachy internships can also start submitting contributions to be considered for projects. I believe the application isn’t too long. Bioconductor will also need to submit potential projects with 2 mentors each. I’ve had experience with these two areas, but there’s also the funding issue which I haven’t participated in previously.

2022-08-11

Susan Holmes (03:49:08) (in thread): > @Andres WokatySorry for the late reply but the CAB meeting for this month is today at 6am Pacific time, please feel free to email me atsph@stanford.eduif you want to join briefly to talk about this at this month’s CAB, but I understand if it’s too short notice and we could still set up a meeting to have a quick discussion.

Andres Wokaty (10:35:36) (in thread): > Thank you for messaging. I’m sorry I missed the meeting this morning. I’ll send an email so that maybe we can set up a meeting for a quick discussion.

Susan Holmes (12:07:24) (in thread): > It’s my fault, I had missed your message until last night. Feel free to ping me by email and we can talk about the application and the many possible types of internship that the BioC CAB has thought of.

Aedin Culhane (12:22:18) (in thread): > We discussed outreachy ar the cab meeting. There were several ideas for projects. Should the 2 mentors be at different institutes ? What level of R coding experience will interns have. Should we have a range of projects which range from. Technical or no coding experience How many projects should we have ? It would be great to chat to get a better idea of projects

Aedin Culhane (12:29:05) (in thread): > Potential ideas from me 1) supporting CURE project (creating Bioconductor oncology research project material for under represented minorities high and undergraduate students) 2) working with@Sean Davisto expand orchestra 3) working with new community manager to do user survey and outreach 4) do assessment of graphics in Bioconductor for colorblind palettes usage with@Dan Bunisand other mentors in accessiblevis channel 4) working with multi lingual and teaching committees to organize translation or translate carpentries courses into other languages 5) Python and R. Reticulate/basilisk 6) creating a bioc style for Quattro and developing Quattro materials for Bioconductor users. Others might have better ideas

Andres Wokaty (13:39:15) (in thread): > Thanks again for discussing Outreachy! > > In regards to projects, we should select projects that we’d have a mentor. My plan is to act as the community contact for Outreachy and as a mentor so we at least one more member for a project. The time commitment for mentors is a bit high, about 5 hours a week. The project should also be one where we can teach skills. > > In the last application cycle, where I was also applying for Google Summer of Code, we came up with the following project ideas (so they could do double duty):https://docs.google.com/document/d/19nWvgnxW3S0MKafj6-Mr0WF-Fx8ttwMs11t1GHNuVrk/edit#heading=h.b0xosrr9chen

Andres Wokaty (13:41:43) (in thread): > I also made a brief presentation about the differences between the two projects, which is a little outdated:https://docs.google.com/presentation/d/1_MvtPptdwGRXzn57NN61MubrGRGGc6w75-izXEAOb8M/edit#slide=id.g110fd4dffbf_0_26The Community application for Outreachy just opened. I am going make a document of the bioconductor application so that I can share and get your input so we can have a successful application. I really appreciate your interest and enthusiasm. I’d be really happy if we could get one Outreachy intern:slightly_smiling_face:

2022-08-13

Heather Turner (12:02:19) (in thread): > @Andres WokatyGreat to see that you are going to put in an application for Bioconductor. A couple of things: > * Good news: Bioconductor will be eligible to apply directly to Outreachy as a open science community (https://www.outreachy.org/docs/community/#funding-requirements,https://www.outreachy.org/docs/community/#community-types-open-science-projects). You can do this when you submit your application as a community, so you don’t need to secure funding in advance. You can see how I did this when the R project applied:https://developer.r-project.org/etherpad/p/PHHJ_0WSFUOTPebl63dW- that shows what I entered into the web forms. > * The deadline for interns to apply isAugust 29, 2022, i.e. one week before the community application deadline. So if you want to attract people from within the R/Bioconductor communities, you should be encouraging people to put their applications in now. I’m happy to retweet things from the Forwards and R Contributors Twitter accounts, please ping me if you’d like this as I’m just starting 2 weeks vacation, so may not be reading Slack so much.

2022-08-15

Andres Wokaty (09:13:13) (in thread): > @Heather TurnerThank you for all the great information!!

2022-08-20

Kozo Nishida (18:12:54): > Does anyone know of any local Bioconductor groups other than those listed below? > * https://www.meetup.com/boston-r-bioconductor-for-genomics/ > * https://www.meetup.com/biocnyc/events/287804371/ > I would like to invite Bioconductor groups around the world to this Translation-a-thon.https://www.meetup.com/boston-r-bioconductor-for-genomics/events/287802282/ - Attachment (Meetup): Boston R/Bioconductor for Genomics (Boston, MA) > This group will meet regularly to discuss topics related to the application and development of R and Bioconductor workflows and packages for data analysis and visualization of genomics data. - Attachment (Meetup): Bioconductor community Translation-a-thon, Sat, Aug 27, 2022, 10:00 AM | Meetup > Hello! Hola! Bonjour! 你好! こんにちは! We want to open up Bioconductor to the whole world and we’d love your help to achieve [our goal](https://chanzuckerberg.com/eoss/proposals - Attachment (Meetup): Bioconductor community virtual Translation-a-thon, Sat, Aug 27, 2022, 10:00 AM | Meetup > Hello! Hola! Bonjour! 你好! こんにちは! We want to open up Bioconductor to the whole world and we’d love your help to achieve [our goal](https://chanzuckerberg.com/eoss/proposals

2022-08-21

Xueyi Dong (22:51:47) (in thread): > I know a few groups of people doing bioinformatics analysis a lot in China and I believe most of them are Bioconductor users, but most of them aren’t using Meetup. I will send them the link to the Boston group for now, but I’m still considering is there a better way to promote for them.

2022-08-22

Andres Wokaty (11:04:40) (in thread): > This is the initial Outreachy Community application:https://docs.google.com/document/d/1AmslXgbAUneypp2Az_hCNermI9MTx5VCDy93uTae7_o/edit#.@Sean DavisCould I ask you to take a look? Anyone comment or edit to improve it. Thank you.

2022-08-27

Kozo Nishida (09:53:18): > The Bioconductor Translation-a-thon will start in about 8 minutes.https://www.meetup.com/boston-r-bioconductor-for-genomics/events/287802282/Sorry, I forgot to advertise it on this channel and add it to Bioconductor’s calendar…. - Attachment (Meetup): Bioconductor community virtual Translation-a-thon, Sat, Aug 27, 2022, 10:00 AM | Meetup > Hello! Hola! Bonjour! 你好! こんにちは! We want to open up Bioconductor to the whole world and we’d love your help to achieve [our goal](https://chanzuckerberg.com/eoss/proposals

Kozo Nishida (09:55:32): > The translation can be started by accessinghttps://bioconductor.crowdin.com/without participating in the Translation-a-thon. > But I think it would be better if we do the translation together!

2022-09-01

Kozo Nishida (00:00:39): > Discord Watch Together feature may be of interest to the community.https://support.discord.com/hc/en-us/articles/4409342945687-Watch-Together-FAQI don’t mean moving from Slack to Discord, but I’m interested in features that help watch parties. - File (PNG): image.png

2022-09-08

Maria Doyle (04:25:29): > @Maria Doyle has joined the channel

Andres Wokaty (09:42:45): > Seeking Outreachy internship project proposalsBioconductor is planning to participate in the Outreachy internship program. Outreachy’s goal is to support people from groups underrepresented in the technology industry. Interns will work remotely with mentors from our community. > > We are seeking mentors to propose projects that Outreachy interns can work on during their internship. > Sept. 23, 2022 at 4 pm UTC is the deadline to submit projects:https://www.outreachy.org/communities/cfp/bioconductor/If you want help crafting your project proposal, please contact the Bioconductor coordinator: “Wokaty” <jennifer.wokaty@sph.cuny.edu>. > > Mentors should read the mentor FAQ:https://www.outreachy.org/mentor/mentor-faqFull details about the Outreachy program and the internship timeline can be found on the Call for Participation page on the Outreachy website:https://www.outreachy.org/communities/cfp/

2022-09-16

Zuguang Gu (06:14:38): > @Zuguang Gu has joined the channel

2022-09-28

saskia (19:31:21): > The Code of Conduct Committee is seeking feedback regarding our member election process. In particular, we would like to know whether the community thinks the form for new member applications is appropriate. We would be grateful for any comments by the 7th of October.https://docs.google.com/forms/d/e/1FAIpQLSeTRs3m3-XNM7iGs0kyHfoaXNiwRVsgebmce10t0ieKfamaPg/viewform?usp=sf_link

2022-10-03

Aedin Culhane (15:28:28) (in thread): > Can you turn off “required” answers so we can see page 2. Otherwise I need to fill in fake answers to get to page 2.

Aedin Culhane (15:29:38) (in thread): > I’d be tempted to have a question at the start “I have the Bioconductor code of conduct” yes/no

saskia (16:53:42) (in thread): > Will do thanks for letting me know

saskia (16:55:58) (in thread): > https://docs.google.com/forms/d/e/1FAIpQLSeTRs3m3-XNM7iGs0kyHfoaXNiwRVsgebmce10t0ieKfamaPg/viewform?usp=sf_linkfixed now

2022-10-04

Susan Holmes (07:09:55) (in thread): > I have read the form and think it is good, one little change to the last question might make it slightly easier for candidates and the committee, maybe replace Briefly describe how you would approach a report on an alleged Code of Conduct violation?

Susan Holmes (07:10:58) (in thread): > With : What are two important things to ensure a thoughtful response to a Code of Conduct violation…I think “briefly” is doing too much work there.

saskia (18:20:13) (in thread): > Thanks Susan will do!

2022-10-06

saskia (21:13:18): > Could someone from the CAB please post on the Bioconductor twitter about the opportunity to become a new CoC member:https://community-bioc.slack.com/archives/C35G93GJH/p1665104555965749 - Attachment: Attachment > The Code of Conduct committee is seeking new members. If you are interested in serving on the committee with other dedicated and friendly faces, please apply. We particularly encourage applications from candidates identifying as belonging to minority groups. https://docs.google.com/forms/d/e/1FAIpQLSeTRs3m3-XNM7iGs0kyHfoaXNiwRVsgebmce10t0ieKfamaPg/viewform?usp=sf_link

2022-10-07

Kozo Nishida (00:06:44) (in thread): > @saskiahttps://twitter.com/Bioconductor/status/1578235084481921024Let me know if there is any problem in the tweet. > (BTW, I replaced theCode of ConductwithCoCdue to the tweet character limit.) - Attachment (twitter): Attachment > The CoC committee is seeking new members. If you are interested in serving on the committee with other dedicated and friendly faces, please apply. We particularly encourage applications from candidates identifying as belonging to minority groups. https://bit.ly/3CEUht7

saskia (00:12:42) (in thread): > Thank you!!!

2022-10-10

Maria Doyle (18:24:24): > I was thinking to send a tweet from Bioconductor about Hacktoberfest as we decided at today’s teaching meeting that we’d add the other Bioc Carpentries repos into it. I made a draft tweet herehttps://docs.google.com/document/d/1j-n8ZtGYyXI2yHqp0NIr0JMYsK2gKvuCeMaYCHufwC4/editWhat do you think@Kozo Nishida@Kevin Rue-Albrecht@Laurent Gatto@Charlotte Soneson?@Andres Wokatywould you want to add in any outreachy repos? Or anyone else?

Lluís Revilla (18:32:20) (in thread): > Great message, the first one, I’m not sure if is a bit too long, each link is 23 characters length. And it would be nice to have the #rstats tag and ping @R_Contributors and/or the R_Foundation too for amplifying the message

Lluís Revilla (18:33:10) (in thread): > The second one seems too long at the moment

Maria Doyle (18:52:43) (in thread): > Thanks for those tips! They fit now. I had to sacrifice a little grammar:sweat_smile:If anyone wants to suggest more edits (or edit) they can

2022-10-11

Kevin Rue-Albrecht (04:24:28) (in thread): > Both look great to me! I’m trying to decide a day, time, and video call platform for a meetup on bioc-project, after which I’ll update the linked Google Doc with the details

2022-10-12

Maria Doyle (05:06:52) (in thread): > Ok, tweeted:simple_smile:

2022-10-14

Maria Doyle (08:51:15): > CoC committee and CAB, I was thinking of adding the text below into theworking groups guidelines pageas it was in CAB minutes but not on that page. I’ve made aPR herebut let me know if I shouldn’t, or if I should make any changes. > > Adding new membersNew members to Working Groups, who are not already members of > > CAB/TAB/Committees/Working Groups, should be passed through the Code of Conduct > > committee (code-of-conduct@bioconductor.org) to make sure there are no issues > > against them as a final approval.

Lori Shepherd (10:03:48): > being upfront is always a good idea:slightly_smiling_face:

saskia (19:53:46) (in thread): > @Kozo Nishidawould you mind sending another tweet and reminding people that the deadline is the 31st of Ocotober

2022-10-15

Kozo Nishida (04:38:15) (in thread): > OK, I will do it.

Kozo Nishida (05:00:16) (in thread): > I sent it likehttps://twitter.com/Bioconductor/status/1581208207984238593. - Attachment (twitter): Attachment > The deadline of Code of Conduct Committee application is the 31st of Ocotober. > Your early application will be greatly appreciated. https://twitter.com/Bioconductor/status/1578235084481921024 - Attachment (twitter): Attachment > The CoC committee is seeking new members. If you are interested in serving on the committee with other dedicated and friendly faces, please apply. We particularly encourage applications from candidates identifying as belonging to minority groups. https://bit.ly/3CEUht7

Vince Carey (06:43:15): > I have now been informed by NumFocus that we must guarantee that all packages and processes in Bioconductor are governed by Code of Conduct. Does anyone have suggestions on how this is established?

Vince Carey (06:44:10): > A periodic, open review of compliance? Perhaps every third CAB call?

Lori Shepherd (07:46:46): > We have a code of conduct committee; shouldn’t this fall under them? > Or the package triage/clinic group? > > Do we need a reconfirmation for all existing packages? It would be interesting and perhaps a massive clean out/deprecation from unresponsive maintainers if we set up something that existing packages have to do to reconfirm coc and open source/licensing

Lluís Revilla (10:53:54): > I also have questions about the meaning of this “guarantee that all packages and processes” . Does it mean that each package should have a CoC in their development site, that there should be a CoC for Bioconductor and/or that the CoC should supervise that all theprocessof the TAB, CAB and Scientific committee follow the existing CoC? There is a CoC meeting in a couple of weeks we can discuss this,

2022-10-16

Vince Carey (20:11:49): > @Lluís Revillaand@Lori Shepherd, thanks for your input. It seems to me that the material athttps://bioconductor.github.io/bioc_coc_multilingual/index.htmlcovers almost everything needed. Any unwelcoming interactions or code components or comments (in code, on fora, or in person) appear to be subject to (optionally anonymous) reporting, evaluation and enforcement by the code of conduct committee. The timeliness of evaluation is covered athttps://bioconductor.github.io/CodeOfConduct/incident_response.html. A very brief executive summary of CoC capabilities and scope would be appropriate at the CoC site and could be conveyed to NumFocus to show our compliance. The exact request from NumFocus was > > The board has approved Bioconductor under two conditions 1) all packages meet the NF licensing criteria - all projects (including sub-projects and packages) are under an OSI-approved license, and 2) all packages are under the Bioconductor Code of Conduct. > > I broadened clause 2 a little bit.

2022-10-20

Lluís Revilla (10:54:41): > TheCAB pageshows the minutes of the meeting of the CAB on 07/2022. Have been any meetings in 08/2022 or 09/2022? (I assume this October there have been a meeting that approved previous minutes). I would like to read the minutes and know about the updates of the board including the new community manager.

Kozo Nishida (11:05:36): > We are inhttps://meet.google.com/zym-zhin-vtq! > Feel free to join us! - Attachment: Attachment > The call has started. One person has joined so far. From what I can see, people need to request to join the call, following the link on the meetup page. Then I can let them in. - Attachment (meet.google.com): Meet > Real-time meetings by Google. Using your browser, share your video, desktop, and presentations with teammates and customers.

Kozo Nishida (12:38:23): - Attachment: Attachment > Discussions from this Hacktoberfest meetup can be continued here. > https://github.com/carpentries-incubator/bioc-project/discussions

Lori Shepherd (14:31:00) (in thread): > I’ll make sure they are posted tomorrow. Sorry for the delay; I think I staged but forgot to push up

Lluís Revilla (16:08:50) (in thread): > Thanks Lori! No problem, I wasn’t sure if this was a summer pause or not.

2022-10-21

Kozo Nishida (18:01:42): > https://twitter.com/Bioconductor/status/1583578580012847104 - Attachment (twitter): Attachment > #hacktoberfest > We reschedule this meetup to next Wednesday in order to gather more attendees! > We would be happy if you could join us on the new date! > The http://Meetup.com URL remains the same. You can also register at > https://www.meetup.com/boston-r-bioconductor-for-genomics/events/289261203/ > as well as the following URL. https://twitter.com/Bioconductor/status/1582117168816132096 - Attachment (twitter): Attachment > Join our meetup to learn how to create a post for Bioconductor community blog! :writing_hand: > You can be rewarded on @hacktoberfest if you make a blog post PR that’s merged :tada: > :spiral_calendar_pad:Saturday 22 October > :clock9: 3pm JST > :world_map: https://www.meetup.com/bioconductor-community-in-asia/events/288949678/ > #hacktoberfest #rstats @R_Contributors @_R_Foundation

2022-10-24

Lori Shepherd (11:23:25) (in thread): > They should appear within the next hour on the website – again I apologize for the delay

2022-10-25

Lluís Revilla (03:57:53) (in thread): > Cool, you even included this month meeting! Many thanks!!

2022-10-31

Heather Turner (13:19:05): > FYI:https://community-bioc.slack.com/archives/C9EJJD6KT/p1667236692219259. There is a corresponding iCal link if you want to import the events into the Bioconductor calendar. - Attachment: Attachment > Starting this week :sparkles: R Contributor Office Hours:sparkles:! > > On the first Thursday of the month, join an Office Hour to > - discuss how to get started contributing to R > - get help/feedback on contributions you are working on > - look at open bugs/work on translations together > > Details: https://contributor.r-project.org/events. > > Note this is for contributor to the core R project vs Bioconductor, but hopefully of interest to some folk here!

2022-11-07

Kozo Nishida (05:23:55): > https://mobile.twitter.com/Bioconductor/status/1589560084899954689 - Attachment (twitter): Attachment > A contribution post by @JauntyJJS has been added to the Bioconductor community blog. > https://bioconductor.github.io/biocblog/posts/2022-10-22-awesome-lists/ > This blog post is made possible from an online Biocondutor meetup for @hacktoberfest . > Thank you, @JauntyJJS ! https://twitter.com/Bioconductor/status/1584640429307592704 - Attachment (twitter): Attachment > Feel free to join our Hacktoberfest event! > > You don’t need to have articles ready for the blog! > We are thinking a big barrier might be finding time for solo blog writing. > We could try help you co-write, proof-read etc. > You can come with just ideas and get help! https://twitter.com/Bioconductor/status/1583578580012847104

Susan Holmes (06:14:27) (in thread): > Thanks, great blog entry, I “tooted” it onfosstodon.orgas a “trial” to gather interest in #Bioconductor on Masstodon…we’ll see.

2022-11-14

Laurent Gatto (09:47:21): > Should we have a Bioconductor presence on Mastodon?fosstodon.orgwould be a good instance to create an account. Happy to help/discuss.

Johannes Rainer (09:50:17) (in thread): > I think it’s a good idea. I would even suggest that we form a “social media working group” that has access to all official Bioconductor channels.

Laurent Gatto (09:51:04) (in thread): > Or… a Bioconductor instance !

Lluís Revilla (09:51:14) (in thread): > That instance only allows English, as language…

Johannes Rainer (09:52:34) (in thread): > we had a short discussion on a Bioconductor instance (mastodon server). Generally I love the idea, the question is who will run and admin that? needs computational resources and manpower and BioC core doesn’t have the time

Laurent Gatto (09:52:36) (in thread): > The language thing is for moderation purposes.

Laurent Gatto (09:56:47) (in thread): > @Johannes Rainer- and moderation!

Johannes Rainer (09:58:16) (in thread): > Having abioconductor.orgserver would be awesome - and we could avoid the language restriction. but then access needs to be manually accepted (only package maintainers?). And yes, moderation - I guess that goes the same way like all other channelsviaCoC

Laurent Gatto (10:12:27) (in thread): > No, it’s more involved, it’s a day to day moderation, banning other instances, checking on mutes/bans of accounts on our instance, …

Johannes Rainer (10:22:25) (in thread): > So, we would need some volunteers to act as admins then… I really like the idea of having our own instance - but am afraid it will be too much work (at least I will not be able/willing to be admin:wink:)

Laurent Gatto (10:23:18) (in thread): > I would volunteer:slightly_smiling_face:with some help from others

Laurent Gatto (10:52:17): > In the meantime,@Maria Doyle(I think you are managing the Bioc twitter account), are you OK with me re-posting Bioc tweets? Or are you on Mastodon yet? Or anyone with an access to Bioc twitter account?

Maria Doyle (12:50:59): > Fine by me to re-post! I’m not on Mastodon yet. I have Tweetdeck team member access to Bioconductor Twitter, along with Kozo and I think a few others but I don’t know who. Probably good to have a doc with info/guidelines somewhere e.g like herehttps://osf.io/tzmhp/wiki/Public%20Communications/. At last week’s CAB meeting we said we’d set up a social media working group that could discuss these things. Will I make a Slack channel #social-media for it?

Laurent Gatto (15:23:00) (in thread): > OK, I’ll post on Mastodon. Feel free to ping me if there’s something important that I should miss.

Martin Morgan (21:12:25) (in thread): > Maybe team up with another communitylike rOpenSci?

2022-11-16

Laurent Gatto (04:26:58) (in thread): > FYI - pricing of running our own instancehttps://masto.host/pricing/ - Attachment (Masto.host | Fully Managed Mastodon Hosting): Pricing | Masto.host > Pricing for Masto.host fully manages Mastodon hosting plans. Starting at $6/month.

Laurent Gatto (04:27:25) (in thread): > (all temporarily unavailable)

Maria Doyle (11:04:46): > #social-mediachannel now created, feel free to join

2022-11-17

saskia (22:43:22) (in thread): > @Vince Carey,@Lori Shepherdand@Lluís Revilla: We had a chat during the CoC meeting about this. We came to the conclusion that it may be helpful if the CoC explicitly stated that packages are covered and will implement this change in the coming weeks. We have also discussed whether it would be possible to link the CoC on the landing pages (e.g.https://bioconductor.org/packages/release/bioc/html/RUVSeq.html) for each package. We could then ask if any developers are against this and would like to opt out, in which case their package may be subject to removal. We also discussed whether for new packages, a new field could be introduced in the Description file that would be called Code of Conduct and list the link to the Bioconductor Code of Conduct. Let me know what you think.

2022-11-18

Vince Carey (08:57:33) (in thread): > It sounds good to me.

2022-11-20

saskia (16:14:21) (in thread): > @Aedin Culhanesee the conversation above. Does this work?

2022-11-21

Aedin Culhane (08:38:18) (in thread): > I think new packages that are submitted have to tick a box to say that will comply with the CoC. Lori and I discussed emailed bioc-devel and updating developers about the change. It might be helpful if the CoC wrote a short paragraph about the CoC committee (number of members, how people are elected, a bit about generating the CoC, the book you read, that we are adhering to international best practice). I also think this is a publication (at ISMB).. how Bioconductor adopted a CoC across the entire project, where issues have arisen (github issues) etc. Adding a field in the DESCRIPTION file and including that as a check in biocCheck could be done but would require additional work by@Lori Shepherdwhich might be a lot. However including the Bioconductor CoC in the footer of every page on the website, might be an easier fix.

Aedin Culhane (08:39:23) (in thread): > @saskiathe CoC blog could be similar tohttps://bioconductor.github.io/biocblog/posts/2022-01-31-join-the-bioconductor-community-advisory-board/ - Attachment (bioconductor.github.io): Bioconductor community blog - Join the Bioconductor Community Advisory Board > Each year the Bioconductor Community Advisory Board (CAB) puts out a public call for new board members. This post tells you more about what the CAB does and how you can apply to become a member.

saskia (16:07:16) (in thread): > I will write something this weekend

2022-11-27

saskia (16:47:14) (in thread): > https://docs.google.com/document/d/17z-UGgnAzGT3YnFdXHsyBx2s5BNTm171o6W37kQCC7M/edit?usp=sharing

saskia (16:47:20) (in thread): > Let me know if this works

Vince Carey (16:49:02) (in thread): > That looks good to me.@Maria Doylethis should be of use in dialogue with NumFocus. Thanks all.

2022-11-28

Maria Doyle (14:51:36) (in thread): > I’ve added some info on that into the email drafted to NumFocus.

2022-11-30

Shixiang Wang (23:12:47): > @Shixiang Wang has joined the channel

Kozo Nishida (23:21:42): > https://docs.google.com/presentation/d/1Wgs6y2ZMmbYGFk3WhEQ7Vc3NbvQxXjRFuyimidM1JxA/edit?usp=sharingis the link to my BioCAsia2022 short talk slides. > If you are interested in the community working groups, please click the links in the slides. - File (Google Slides): BioCAsia2022 - 5mins

2022-12-09

Kozo Nishida (06:45:55): > ChatGPT may be useful for the Bioconductor community. - File (WebM): Screenshare - 2022-12-09 8:45:27 PM.webm

Martin Morgan (11:37:26) (in thread): > StackOverflow isn’t in favor of this…https://stackoverflow.com/help/gpt-policy - Attachment (Stack Overflow): Why posting GPT and ChatGPT generated answers is not currently acceptable - Help Center > Stack Overflow | The World’s Largest Online Community for Developers

Susan Holmes (12:58:56): > But it does write great first drafts, which nearly always contain some mistakes, but getting a first function and the right libraries and an idea of a worflow is nice.

Maria Doyle (16:21:42): > I agree, personally I think we can’t ignore or dismiss it as it’s a current a hot topic, it’s fascinating and I wonder could we harness it. > Related to what Susan said, could we use it in teaching to demo an initial (draft)workflow, but then question it - is it right, are there errors, how would we verify it, are there other/better alternatives…

Kevin Rue-Albrecht (17:28:04): > Well, like illustrated herehttps://community-bioc.slack.com/archives/CMVC2F78U/p1670336970488259?thread_ts=1670336849.404969&cid=CMVC2F78UIt’s pretty fun to generate content with, but it takes an “expert” reviewer to pick up some details… on his second reading ^^ - Attachment: Attachment > (small mistake by the AI though: it’s installing version 3.16 or BiocVersion not BiocManager, but that’s pretty tricky for the AI to figure out without going into a pretty deep thorough analysis of the code in BiocManager::install)

Kozo Nishida (22:39:55): > Rather than relying entirely on or banning ChatGPT, I’m wondering that usingsupport.bioconductor.orgwith ChatGPT will make the Bioconductor community more active.:slightly_smiling_face:

Kozo Nishida (22:50:14): > We need good questions to get good answers from ChatGPT. > And the good questions are insupport.bioconductor.org. > I think thatsupport.bioconductor.organd ChatGPT can have a good relationship.

2022-12-10

Kevin Rue-Albrecht (11:53:48): > Honestly, I would be very careful about the use of any fully automated system that may be seen as giving “advice” or anything that looks like instructions to potentially naive new users. I agree that the impressive and frankly jaw-dropping contents may stimulate engagement from the community (e.g., to stimulate conversation), but if anything, I would strongly recommend highlighting any content generated by ChatGPT with a clear warning that it was automatically generated, that it wasn’t reviewed by a human, and that it may contain wrong or misleading statements, and maybe even that it is not endorsed by Bioconductor.

Lambda Moses (14:35:38) (in thread): > I agree. Yesterday I tried it. It gave wrong answers when it comes toaes_string()being deprecated. I suppose the deprecation happened too soon for ChatGPT to learn. I as a human already know what to do with the deprecation.

Vince Carey (16:00:17) (in thread): > Not “currently” acceptable? Anyway, the advice is wrong … forgot BiocManager! Is there a way to “tweak” the system when inaccuracies are found?

2022-12-12

Susan Holmes (15:03:25) (in thread): > With the examples I tried it gives a first draft with some errors, but quite useful to experts, I think that for beginners it can be unsettling because they won’t know what parts are right. You can give feedback with the thumbs up/ thumbs down icon and they are appreciative of extensive feedback, I received nice feedback on my feedback and of course it’s a chat so you can tell it: Your answer should be improved by remembering that…etc.

2022-12-14

Lori Shepherd (11:54:52): > CAB is seeking nominations for new members. If interested please fill out the following form by January 31:https://forms.gle/2nb2fJE4jgca3nqi7 - Attachment (Google Docs): Community Advisory Board Nomination Form > Information about the Community Advisory Board can be found at https://bioconductor.org/about/community-advisory-board/ . Yearly there are elections for new members to the board. Currently the board consists of 8-20 members. Members are elected to 3 year terms but may step down early at any time. Anyone from the community is welcome to run. We aim to have a diverse board from varying geographical and professional level stages in order to help Bioconductor be more inclusive to every background. The current advisory board will consider all nominees and vote to fill the limited number of vacant board positions. If interested please fill out the following form: asterisk questions are required, non asterisk are optional.

Leo Lahti (12:33:11) (in thread): > I assume that this can be freely circulated?

Lori Shepherd (12:33:47) (in thread): > yes

2022-12-15

Matt Ritchie (23:36:14) (in thread): > There’s also this resourcehttps://twitter.com/Physacourses/status/1602730176688832513 - Attachment (twitter): Attachment > This is just amazing! > Have a look at RTutor (http://RTutor.ai). It can generate & test R code just by “chatting” with it. > RTutor will then generate functional code to answer your question, making it easy for those without R experience > #RStats #MachineLearning #DataScience

2022-12-16

Kozo Nishida (16:23:30): > Bioconductor and Galaxy are added to NumFOCUS sponsored projects - Attachment (NumFOCUS): Sponsored Projects | pandas, NumPy, Matplotlib, Jupyter, + more - NumFOCUS > Explore NumFOCUS Sponsored Projects, including: pandas, NumPy, Matplotlib, Jupyter, rOpenSci, Julia, Bokeh, PyMC, Stan, nteract, SymPy, FEniCS, PyTables…

Kozo Nishida (16:26:00): > Now it’s clear where to donate - Attachment (NumFOCUS): Donate for Bioconductor > Donate to help support Bioconductor! Bioconductor is an open source, open development ecosystem of R-based software for bioinformatics.

2022-12-17

Laurent Gatto (11:45:01): > Thanks! A couple of quesitons: > * Is there a link to the donate page onbioconductor.org, and is there a strategy to advertise/promote donations? > * Is there some expectation to get some dedicated funding through donations?

Lori Shepherd (12:10:03): > I think this is a new development so not onBioconductor.orgyet but I can get it on tht home page this week

2022-12-26

Aedin Culhane (08:23:10) (in thread): > Wedon’thave a strategy or plan re donations.But maybe we should discuss this with numfocus if/when they become the fiscal sponsor.

2023-01-10

Robert Shear (14:09:22): > @Robert Shear has joined the channel

2023-01-12

Kozo Nishida (13:59:26): - Attachment: Attachment > I am interested in the workflow described in https://ropensci.org/blog/2023/01/12/multilingual-publishing-en/. > I will share it with the Bioconductor community.

Lori Shepherd (14:49:03): > CAB is seeking nominations for new members. If interested please fill out the following form by January 31:https://forms.gle/2nb2fJE4jgca3nqi7. If you are unable to use google forms please see thispdf of quesetionsand email nomination toshepherd.bioc@gmail.com

2023-03-15

Jiefei Wang (11:17:05): > @Jiefei Wang has joined the channel

2023-04-11

Lluís Revilla (11:22:35): > Inhttps://bioconductor.org/about/community-advisory-board/there is no minutes for the March meeting. Did you held the meeting or is the April’s one is happening later than usual?

Lori Shepherd (11:24:35): > The meeting is the second thur of each month (so this thur) after the minutes are approved then they will be posted

Lluís Revilla (11:46:49): > Thanks! Looking forward to read the minutes

2023-04-17

Lori Shepherd (07:46:58) (in thread): > We should for sure but I’m not sure this is clearly set up yet – I think we still needed to officially sign and were working out details still

Umar Ahmad (13:45:54): > @Umar Ahmad has joined the channel

2023-05-10

Robert Castelo (05:02:41): > Hi, I’m subscribed to every post at the Bioc support site and in the last two days I’m getting massive amounts of SPAM at a scale that I’d say they must be produced by some sort of robot. Is there anything we can do to avoid or minimize this problem?

Maria Doyle (06:22:28) (in thread): > That’s not good, can you ask this in#support-sitechannel?

Lori Shepherd (06:42:46) (in thread): > We are aware. We will be pushing changes later today that will hopefully help/fix the issue

Robert Castelo (08:04:11) (in thread): > Ok, thanks Maria & Lori, if in a couple of days this is still happening, I’ll post at the#support-sitechannel.

Janani Ravi (15:33:02) (in thread): > Has anyone else received 10 junk cab emails in the past hour?

Lori Shepherd (15:46:07): > We are trying to get it under control.

2023-05-11

Stevie Pederson (16:13:00): > @Stevie Pederson has joined the channel

Enis Afgan (16:13:07): > @Enis Afgan has joined the channel

2023-06-02

Simone Bell (08:23:19): > @Simone Bell has left the channel

2023-06-19

Kozo Nishida (22:11:34): > Is there a GitHub template repository for Bioconductor package? > (If not, I would like to create it.) - File (PNG): image.png

2023-06-20

Kozo Nishida (22:37:37) (in thread): > I wasn’t sure if this channel was appropriate for that message(, but I sent it here somehow). > Let me know if there is another channel I should forward this message to. > + > I’m going to create that template project under my account to try it out (since someone sent:+1:emoji).

Shixiang Wang (22:43:01) (in thread): > Great idea.

2023-06-21

Kevin Rue-Albrecht (05:04:26) (in thread): > I’ve been using that, but I haven’t updated it in a while so it might be a bit out of date by now:https://github.com/kevinrue/MyBioconductorPackage

Kevin Rue-Albrecht (05:05:27) (in thread): > e.g. - File (PNG): image.png

2023-06-22

Leonardo Collado Torres (14:50:07): > Isn’t that a lot of work@Kozo Nishida?

Leonardo Collado Torres (14:50:51): > I typically make my new R/Bioconductor packages with: > > usethis::create_package("~/some_name") > biocthis::use_bioc_pkg_templates() >

Leonardo Collado Torres (14:51:27): > and those 4 scripts that it creates underdev/is how you can populate all files needed for a package

Janani Ravi (14:55:35) (in thread): > I have a couple generated like these too.@Kozo Nishida— happy to share them, if you’d like. > * new_project (using workflowr + minor modifications) > * new_package (using Leo’s way) > * new_paper (to share alongside manuscripts) - File (PNG): image.png - File (PNG): image.png

Kozo Nishida (22:23:57): > Thanks@Kevin Rue-Albrecht@Leonardo Collado TorresYou two do a great job. > But I thought that yourhttps://github.com/kevinrue/MyBioconductorPackageandhttps://bioconductor.org/packages/release/bioc/html/biocthis.html, are so perfect that people who want to casually start building package repositories might be put off it. > Therefore, I would like to create a more lightweight template for beginners. - Attachment (Bioconductor): biocthis > This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly.

Kozo Nishida (22:30:36): > Like@Janani Ravi, I’m also thinking of having a template for each type of the repo. > Unlike@Janani Ravi, I have no plans to create workflow[r] or paper templates, > but I think it would be better to have a shared template repository for AnnotationHub package (as well as Software).

Janani Ravi (22:35:50) (in thread): > I like the lightweight idea.I can share my version and you can see ifit’shelpful.If not, happy to help in anyway.

2023-06-23

Alex Mahmoud (13:11:38): > Love that this conversation is happening, and agree that while a lot of technical work already exists, it might be inaccessible/intimidating for some to get started. We’ve been talking among some core team members about the idea of a package/GHA template, especially in the context of more easily providing a standardized set of github workflows à la biocthis in order to surface errors across different platforms before submitting the package to Bioconductor. I personally think it’d be great to take whatever existing work is out there, and consolidate it into a set of templates that stay maintained by a combination of the core and the community going forward. The idea of variations for different types of packages sounds great too. I think this would be a great topic for a working group and happy to help organize conversations and help move it forward however needed. cc@Vince Carey

Laurent Gatto (16:31:14) (in thread): > Yes, thank you@Alex Mahmoudand@Kozo Nishidafor this.I completely agree. I would be happy to help/contribute, in some capacity. I realise that there’s so much implicit knowledge/expertise behind what is done/expected, and I’m not able to make it explicit.

Vince Carey (16:41:55) (in thread): > Thanks for adding me to this thread. What can we do to help understand the acceptability of different possible approaches? Do we need a focus group? Personas reflecting variation among community contributors? Incentives for participation in evaluation processes?

2023-06-24

Shixiang Wang (00:17:23) (in thread): > Feature like convert a existing package to a well-formatted bioc package template is suggested.

2023-07-05

Kevin Rue-Albrecht (15:45:58) (in thread): > @Kozo Nishidanote that the commit history ofhttps://github.com/kevinrue/MyBioconductorPackage/commits/mainis lean and represents the step by step process that I followed from setting up the biocthis template to progressively working my way though the various bits that needed replacing. > I was inspired by a MeteorJS tutorial that took such a commit by commit approach to describe the writing of a small website. I just never completed the job by writing an accompanying tutorial pointing at each commit like they did

Kevin Rue-Albrecht (15:48:12) (in thread): > See bottom of pagehttps://react-tutorial.meteor.com/simple-todos/01-creating-app.html > > Review: you can check how your code should be at the end of this step here

2023-07-28

Konstantinos Daniilidis (13:47:27): > @Konstantinos Daniilidis has joined the channel

2023-08-03

Ritika Giri (15:57:12): > @Ritika Giri has joined the channel

Ellis Patrick (20:12:55): > @Ellis Patrick has joined the channel

Ellis Patrick (20:36:49): > Hi, I don’t know if this is the appropriate channel to voice this but…. In a conversation today about the pros and cons of a hybrid conference, the importance of presenting at conferences was highlighted as being important for both visibility of someone’s research but also for demonstrating research impact on a CV. As an Australian living forever away from anywhere, and a parent of young children, this resonated with me a little. There was a suggestion made that perhaps Bioconductor could be innovative in ways to provide virtual attendees opportunities to achieve both of these goals without necessarily presenting via video stream, which isn’t always a great experience on both sides of the stream and can create logistical challenges. My suggestion was to seek short “invited” perspectives on topical themes to be included in the conference program. I’m too egotistical to remember the other suggestions but I just wanted to flag this conversation, whose themes seemed to sit at the intersection of equity, accessibility and career development, as I’m sure that it is one that has happened before and should keep happening.

Ellis Patrick (20:38:07): > Again, sorry if this isn’t the place to say this or if it comes across as self-interested/insensitive/naive.

Ellis Patrick (22:44:29) (in thread): > Oh, one of the suggestions was for an asynchronous track to emulate the “speaker spotlight” Twitter posts with daily posts of 5 minute videos leading up to the conference.

Kevin Rue-Albrecht (23:07:43): > Sounds great and yeah, having a newborn myself helps me appreciate this fully firsthand myself this time. The YouTube channel in particular seems like an obvious place ready to go. Nothing prevents from uploading invited short videos any time of the year. The rest is about giving those videos a visibility comparable to live talks at the events. Social media posts like “spotlights” sounds again like a great idea!

2023-08-04

Leo Lahti (05:02:14): > Sounds good and well justified

Maria Doyle (08:23:26): > Yes, good suggestions Ellis!

2023-08-08

Kozo Nishida (04:43:15): - Attachment: Attachment > I found out it was already August… > We need to plan for Hacktoberfest (in October). > If anyone has any ideas for actions for Hacktoberfest, please let us know. > > https://community-bioc.slack.com/archives/CEQD45CHK/p1691420966046599

Aedin Culhane (09:19:33) (in thread): > The speaker spotlight was done by@Anna Powellwho is a undergraduate intern in our lab. She is a journalism and social media student and is working with us to see how we can better communicate the work in Bioconductor.@Anna Powellplease connect with@Ellis Patrickto learn how this would work. Maybe we can try this out for the EuroBioc2023 meeting

Anna Powell (09:19:37): > @Anna Powell has joined the channel

Aedin Culhane (09:22:12) (in thread): > I appreciate that the live stream of the meeting is important especially when traveling to a meeting is difficult due to children/elder care responsibilities or budget challenges.

Aedin Culhane (09:26:09) (in thread): > @Ellis Patrickare you involved in the conference committee? Bioc2024 has an open call for people to help on the conference committee (@Erica Feickwill know when this will be). There is also a#biocasiagroup which organize the asia meeting

Erica Feick (09:26:18): > @Erica Feick has joined the channel

2023-08-25

Aedin Culhane (12:41:44): > Announced on the czi slack. I wonder if this might be a mechanism to use the new functionality in R described by JJ at bioc2023 and create a open publication framework for dynamic books, workflows and vignettes. > > ICYMI the Astera Institute recently launched a new program funding a cohort of entrepreneurs-in-residence aiming to build innovative tools for scientific publication/dissemination. Initial awards up to $500K with a possibility of extended funding up to $2M. They also have an open RFI in parallel to the EiR program asking participants to “describe clear technological bottlenecks limiting innovation in life sciences publishing. What is blocking the ability to build advanced tools for open sharing and discussion of scientific information?” More details at:https://astera.org/science-opportunities/@Susan Holmes@Aaron Lun@Vince Carey@Maria Doyle@Anam Akhtar@Stephanie Hicks

2023-09-04

Kevin Rue-Albrecht (05:34:58): - Attachment: Attachment > On my way to work, anyone wants to help me read instructions at https://hacktoberfest.com to figure out what to do to for Bioconductor to participate this year? I’ll have a closer read myself asap

2023-09-13

Aedin Culhane (07:31:04): > @Anam Akhtarhas worked with@Maria Doyleto created a neo4j graph using 1) package download info 2) pkgtools dependencies 3) libraries that are loaded in the same vignettes 4) scrape of website (or GitHub/workflows etc) to identify learning paths and groups of packages that are part of the same workflows. The idea is to learn the learning paths which could re-learned regularly / “updated” as new methods arise.

Aedin Culhane (07:31:14): > https://github.com/js2264/BiocBookBiocBook

Levi Waldron (08:47:27): > I presented two lightning talks at the NumFOCUS summit this week. My overall impression is that it will be a great organization to be a part of, because 1) they’re open-source enthusiasts and good people who have a lot to offer to help Bioconductor grow and do more things, and 2) it brings together an extremely impressive group of software projects with expertise that we will benefit from and developers who are enthusiastic about sharing and collaboration. These were my talks: > * Growth and Governance of Bioconductor > * Bioconductor Developer Experience > By the way - hearing about activities of all these other projects and talking about what our CAB does gave me even greater appreciation for the significance and innovativeness of what the CAB does. You’re amazing, seriously!

2023-09-14

Aedin Culhane (22:30:04) (in thread): > Levi.I think we need to publish some of this more widely so non R folks know differences R/Bioconductor.We probably need a Bioconductor ecosystem paper that people can cite when they use bioc

2023-09-15

Levi Waldron (03:57:13) (in thread): > Should I record a talk from these slides for YouTube?

Leo Lahti (04:54:07): > @Leo Lahti has joined the channel

Aedin Culhane (10:31:19) (in thread): > I think a publication and youtube would be good. Publication of the CAB work and acknowledge of the CZI funds@Maria Doylewould be good.

Aedin Culhane (10:32:44) (in thread): > For the development pipeline, difference between R and BIoconductor. This could be why submit to Bioconductor. and about our standards. The industry group had some great insight into why Bioconductor has the respect in the pharma field and why they allow packages in Bioconductor, but not necessarily other R repos or github

2023-09-18

Michael Love (08:42:41): > @Michael Love has joined the channel

Michael Love (08:43:53): > Dear CAB, I met@TrusharShah at CSAMA this summer, he instructs in Kenya (research in plant genomics) and was interested in setting up a Bioconductor workshop in Kenya or the region (Tanzania, Ethiopia and Uganda). Where would CAB members propose that he start to figure out scope / logistics?

Trushar (08:43:57): > @Trushar has joined the channel

Trushar (12:59:43): > THanks@Michael Lovefor the introduction to the CAB. Would love to have inputs from the CAB about possibilities of setting up workshops in this region.

Michael Love (13:20:21): > @Trushardo you have any links to the local institute / ongoing projects there? Also, are you interested in having Bioc folks provide in person talks, zoom talks, or what other ways can people contribute?

Maria Doyle (16:16:40): > @Trusharwould it help to have Bioconductor experts on topics go to Africa to teach in-person? > As wondering if we could include some funds for that in upcoming EOSS grant application

2023-09-19

Trushar (15:39:38) (in thread): > Yes we have links to local institutes and universities in all the countries mentioned above. Here is an example of one of our projects and the courses we have held.https://journal.embnet.org/index.php/embnetjournal/article/view/1045 - Attachment (journal.embnet.org): EpiCass and CassavaNet4Dev Advanced Bioinformatics Workshop | Gisel | EMBnet.journal > EpiCass and CassavaNet4Dev Advanced Bioinformatics Workshop

Trushar (15:41:10) (in thread): > @Maria Doylethat would be great. I think it would be really good to have an in person course followed later by virtual events and specialised trainings. Would be happy to help with any information for the mentioned grant

2023-09-20

Maria Doyle (04:26:33) (in thread): > Great! Will be in touch

2023-09-22

Aakanksha Singh (05:16:27): > @Aakanksha Singh has joined the channel

2023-09-25

Aedin Culhane (11:43:20): > https://labs.heygen.com/video-translate - Attachment (labs.heygen.com): Video Translate by HeyGen Labs > One-click to translate your spokesperson video with natural voice clone, lip-sync and talking style, powered by HeyGen Labs generative AI.

2023-09-27

Umar Ahmad (18:34:50) (in thread): > Happy to also be involved in this, as we were recently discussing with Africa CDC, to see how we can strengthen our genomics training at NPHIs and National Sequencing Labs across the continent.I coordinate genomics sequencing and bioinformatics across Western Region in Africa.

Umar Ahmad (18:35:56) (in thread): > Although our focus is more into pathogen genomics activities but I initiated a talk to see how we can expand the training capacity to go beyond just pathogen.

2023-09-28

Maria Doyle (05:39:20) (in thread): > Great! Umar, yours and Trushar’s expertise and insights will be key. Let’s align soon to discuss strategy and the EOSS grant. Excited for what’s ahead!

2023-10-08

USLACKBOT (00:00:00): > Some older messages are unavailable. Due to the retention policies of an organization in this channel, all their messages and files from before this date have been deleted.

2023-10-11

Aedin Culhane (14:21:13): > https://www.cell.com/cell-genomics/fulltext/S2666-979X(23)00183-0?dgcid=raven_jbs_etoc_email

2023-10-12

Leo Lahti (07:44:04): > that would be a good inspiration thinking about the CAB paper

2023-10-17

Anna Quaglieri (she/her) (01:56:28): > @Anna Quaglieri (she/her) has joined the channel

Gerry Tonkin-Hill (01:56:37): > @Gerry Tonkin-Hill has joined the channel

Sean Davis (03:06:39): > Just FYI, there is now a Bioconductor Community in Zenodo:https://zenodo.org/communities/bioconductorAnd to submit to the community:https://help.zenodo.org/docs/share/submit-to-community/If anyone would like to join me as a “curator,” (which only entails clicking a button to accept requests) just DM me. - Attachment (help.zenodo.org): Zenodo - Research. Shared. > Zenodo is a free and open digital archive built by CERN and OpenAIRE, enabling researchers to share and preserve research output in any size, format and from all fields of research.

2023-10-20

Aedin Culhane (08:30:32): > Brilliant idea Sean love this

Sean Davis (08:37:50) (in thread): > We’ve already got 7 resources listed! Keep them coming (4 of them from@Johannes Rainer)!

Sean Davis (09:16:40) (in thread): > Spread the word.https://twitter.com/seandavis12/status/1715351568860524819 - Attachment (X (formerly Twitter)): Sean Davis on X > There is a new #Bioconductor community on the open digital repository @ZENODO_ORG. > > https://t.co/MXkZHauMpS > > Zenodo empowers sharing research output of arbitrary size and format and receives @NIH and @NIHDataScience support for data sharing as a Generalist Repository.

Sean Davis (09:41:43) (in thread): > And big thanks to@Wes Wand@Shixiang Wangfor joining the “curation” team.

2023-10-23

Sean Davis (16:37:38): > Bioconductor has a long (and successful) history of requiring a single maintainer for each package. However, I wonder if we can and should consider other models. Github and other social coding platforms encourage a much broader definition of software development, including shared responsibility. PR reviews, discussions, issues, projects, blame, and even automated CI/CD enable and encourage the concept of a team of developers that can be structured according to project needs and (local) community governance and engagement. > > I’m curious to hear what others feel about this. Cross-posting to TAB as well.

Lori Shepherd (16:54:33): > Herve and I comment on the TAB channel posting of this; I recommend posting additional comments there so we only have additional discussion on one thread…

Peter Hickey (17:25:05): > @Peter Hickey has joined the channel

2023-10-26

Daniel Niiaziiev (15:51:09): > @Daniel Niiaziiev has joined the channel

2023-12-01

Sean Davis (11:33:21): - Attachment (datascience.cancer.gov): Sharing Cancer Research Software? NIH Wants to Hear from You! | CBIIT > Are you working with source codes, algorithms, workflows, and other software in your cancer research? NIH wants to hear from you! Respond today to help NIH develop new best-practice guidelines.

2023-12-30

Aedin Culhane (09:37:36): > https://cziscience.medium.com/mapping-the-impact-of-software-in-science-92c1b5126a34 - Attachment (Medium): Mapping the Impact of Software in Science > Notes from the 2023 hackathon hosted by the Chan Zuckerberg Initiative

2024-01-12

Kevin Rue-Albrecht (05:31:18): > Hi all > > After the confusing (let’s say it, failed) attempt to coordinate Bioconductor events duringHacktoberfestlast year, I’m about to kickstart a quarto website onmy ownGitHubaccount, with the goal to transfer ownership to theBioconductorGitHub account once it takes shape and becomes endorsed by the boards and more generally the community. > > In short, I’m looking for volunteers interested in tinkering with the website with me. > > I don’t have a clear view of what the website should look like, what it should or should not contain, etc, so any help and opinion is welcome! > > I’ll message again when I’ve set up the GitHub repository and the GitHub Action automatically deploying the static website, but in the meantime, please contact me here or by DM, so that I can invite you to work directly on the repository without the need to fork. - Attachment (hacktoberfest.com): Hacktoberfest 2023 > Hacktoberfest: a month-long celebration of open-source projects, their maintainers, and the entire community of contributors.

Kevin Rue-Albrecht (06:05:43) (in thread): > Alright, so: > * GitHub repo:https://github.com/kevinrue/hacktoberfest2024 > * GitHub Pages:https://kevinrue.github.io/hacktoberfest2024/

2024-04-02

Leonardo Collado Torres (21:07:45): > FYIhttps://x.com/thelucygarner/status/1775102700784370162?s=46&t=fPqNoppoJ109s623S-JHFw - Attachment (X (formerly Twitter)): Dr Lucy Garner (@TheLucyGarner) on X > Some people on the @Bioconductor forum are really rude when answering questions. If you don’t want to help, maybe just don’t respond, rather than treating people like they are idiots! #Bioinformatics #academia

Gerry Tonkin-Hill (21:11:50) (in thread): > Hi Leonardo, thanks for linking this. The CoC committee is aware and is looking into it.

2024-05-10

Maria Doyle (08:01:55): > :trophy:Last Chance to Nominate for the Bioconductor Awards 2024!:trophy:Time is running out to recognise individuals who have made impactful contributions to our community. Don’t miss this opportunity to honour their hard work and achievements!:star2:Criteria: Significant contributions in one or more ways to the project:busts_in_silhouette:Selection: 4 awardees based on impact:alarm_clock:Deadline: 15th May 2024 > > Nominate Now:Nomination FormLearn More:Bioconductor Awards

2024-06-03

Sean Davis (08:52:28): > Sean Davis[8:50 AM] > Just a reminder that conference presenters (or anyone at anytime) are welcome to submit posters, software, slides, data resources, etc. to the Zenodo Bioconductor community:https://zenodo.org/communities/bioconductor.

Aedin Culhane (09:41:18): > Are we recommending zenedo rather than f1000 for meetings?

Michael Love (10:26:41): > from BioC, I was a point person with F1000R for 2021 and maybe another year… F1000R is not really responsive to our needs these days, basically you can keep using it “as is” for posters and workflows, but they won’t fix any of the known issues, and you have to use workarounds that are sometimes quite clumsy

Michael Love (10:33:48) (in thread): > on the poster side, I was trying in 2021 to clean up this interface

Michael Love (10:33:56) (in thread): - File (PNG): Screenshot 2024-06-03 at 10.33.19 AM.png

Michael Love (10:34:11) (in thread): > we have conference / gateway / year

Johannes Rainer (11:21:23): > I was just used to upload talks and posters to zenodo - for conferences other than Bioc-related. To have a central place where interested people can download/check them

Stevie Pederson (11:34:00) (in thread): > Just a brief comment on F1000R workflows, as someone currently going through the submission process, their new approach requires submissions in MS Word and their formatting tool removes all line breaks from code chunks. Simple things like > > library(pkg1) > library(pkg2) > > become > > library(pkg1) library(pkg2) > > which isn’t really satisfactory, and obviously breaks all submitted code. We’re getting there, but it has been a frustrating experience. Unfortunately, I wouldn’t really recommend F1000R for workflows any more either.

2024-06-04

Johannes Rainer (01:38:21) (in thread): > but is there any alternative for workflows?

Stevie Pederson (02:25:09) (in thread): > I haven’t found anything yet but I should probably look harder. I was wondering aboutworkflowhub.eu, but they’re currently more for automated nextflow/snakemake etc workflows, rather than “Here’s how you go through the steps to analyse your data”

Stevie Pederson (02:28:21) (in thread): > Is this something for CAB to ponder, or is it outside our remit…?

Michael Love (06:39:54) (in thread): > and i also had an email chain about F1000R and workflows and they have no plans to fix the experience for Bioconductor. it’s outside of their plans to allow us to submit from Rmd, they expect a Word doc now

Stevie Pederson (07:23:01) (in thread): > I guess we’re just not a big enough market really. I’ll see if there’s interest in the CAB channel as the gateway seemed to me like it was a really positive thing for our community.

2024-06-12

Lachlan Baer (22:27:08): > @Lachlan Baer has joined the channel

2024-07-10

Enis Afgan (16:00:34) (in thread): > Late to the discussion, but as an alternative toworkflowhub.eu, there is adockstore.org.

2024-08-19

Rema Gesaka (09:38:47): > @Rema Gesaka has joined the channel

2024-09-16

Jasmine Daly (07:11:12): > @Jasmine Daly has joined the channel

2024-10-10

Guangchuang Yu (22:43:23): > @Guangchuang Yu has joined the channel

2024-10-21

Zahraa W Alsafwani (19:04:01): > @Zahraa W Alsafwani has joined the channel

2024-11-01

Sean Davis (13:12:03): > TOTALLY off-topic, but this group is particularly connected with respect to community engagement. I’m being asked to collect “ideas” electronically with additional capabilities including commenting on the ideas and “upvoting.” I can probably do this with something like discourse or another such platform, but are there other engagement approaches that are more akin to something like Ideascale that are free and easy-to-use (or set up if open source)?

2024-11-02

Vince Carey (09:01:24): > ?slido

Maria Doyle (11:44:08): > Interesting question! Slido is great for live interactions, but it doesn’t support commenting on ideas. I haven’t seen anything specifically geared toward that functionality, and a quick look in the CSCCE Slack didn’t reveal anything either. I can ask there if you’d like, though. Otherwise, Discourse might be the best option. A couple of others I’ve come across are Fider and Canny, though I don’t have direct experience with them.

2024-11-05

Laurent Gatto (01:43:12): > What abouthttps://www.wooclap.com/? Its main use case is education, but it might be more widely applicable. - Attachment (Wooclap): Create Interactive Presentations with Wooclap and engage Your Audience > Engage your audience with Wooclap’s free interactive presentation tool. Create dynamic and engaging presentations that keep your audience hooked.

Stevie Pederson (07:30:39): > Just trying to find the list of current working groups on the Bioconductor website & can’t spot it linked anywhere. Have we removed links to that section? I can still seehttps://workinggroups.bioconductor.orgthough, so the page appears to still be there - Attachment (workinggroups.bioconductor.org): Welcome | Bioconductor Working Groups: Guidelines and activities > This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook.

Vince Carey (09:09:06): > Is this linkhttps://workinggroups.bioconductor.org/currently-active-working-groups-committees.htmlnot working for you? - Attachment (workinggroups.bioconductor.org): Chapter 2 Currently Active Working Groups / Committees | Bioconductor Working Groups: Guidelines and activities > The following describe currently active working groups listed in alphabetical order. If you are interested in becoming involved with one of these groups please contact the group leader(s). 2.1…

Vince Carey (09:11:04): > I guess you are right that there is no direct use of that link onbioconductor.org

Stevie Pederson (17:27:18): > Thanks Vince. Yes the site is there for me, but I couldn’t find any links to it from the main page.

Vince Carey (18:03:13): > OK, our webmaster comes back from vaca this week, will make a note.

2024-11-07

Lori Shepherd (07:28:25): > good point. I will get it on the main page under linking with community

2024-12-13

Sean Davis (15:44:46): > Does anyone have any recent experience with a platform that allows folks to drop by poster sessions? Or just a list of zoom rooms? Or other approaches for online poster sessions?

2024-12-27

Zahraa W Alsafwani (17:24:40) (in thread): > Hi Sean, I had two sessions usinghttps://www.gather.town/and it was great interactive platform for poster sessions. - Attachment (gather.town): Gather | Virtual HQ for Remote Teams > Work remotely side-by-side in digital Spaces that make virtual interactions more human.

2024-12-29

Yahya Jahun (04:01:48): > @Yahya Jahun has joined the channel

2025-03-05

Claire Rioualen (10:53:32): > @Claire Rioualen has joined the channel

2025-04-24

Alex Mahmoud (12:14:18): > If you have any ideas for the collaboration fest / hackathon post-conference (GBCC25 joint Galaxy-Bioconductor conference in the US), please submit any and all ideas tohttps://forms.gle/RzrT75DpRh9Vb8Z16 - Attachment (Google Docs): GBCC Cofest Ideas Submission > Submit any and all ideas you want to lead and/or in which you’d like to participate.

Maria Doyle (12:26:10) (in thread): > @Alex Mahmoudyou could post in#bioc-conference-everyoneaswell