#bioc2020

2019-07-08

Stephanie Hicks (22:36:56): > @Stephanie Hicks has joined the channel

Stephanie Hicks (22:36:56): > set the channel description: Discussions for the Bioconductor 2020 conference

Simina Boca (22:41:59): > @Simina Boca has joined the channel

Charlotte Soneson (23:45:05): > @Charlotte Soneson has joined the channel

2019-07-09

Martin Morgan (00:13:46): > @Martin Morgan has joined the channel

Vince Carey (06:42:41): > @Vince Carey has joined the channel

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2019-07-10

James Taylor (14:53:55): > @James Taylor has joined the channel

2019-07-12

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Stephanie Hicks (19:35:43): > ok so following up on@Vince Carey’s comment in#diversebioc(https://community-bioc.slack.com/archives/CL21357E2/p1562242899129600), how do people feel about “Developer Day”? how about adding an additional “Collaboration Day”? or a redesign to the conference structure / schedule? - Attachment: Attachment > Since there are concepts of conference redesign/renaming on this > channel I will raise these points here, but maybe we should have a > bioc2020 channel to get going on planning next conference. > > 1) I think the 3-day format with one optional day has worked well and > may continue to work well for at least the next few years > > 2) I am all in favor of “Collaboration day” as one of the days > > 3) I am not in favor of dropping “Developer day” and I propose some repositioning below. > > 4) Proposal for redesign of conference schedule. > > Day 1: Conference day. Keynotes on cutting edge comp bio and genomics, followed by elementary and intermediate workshops that are few in number, large in class size, and emphasize teamwork. We might think about “flipped classroom” approach to our core workshops, where there is a well-produced video that people watch together, interrupt with questions, and > then tackle problems in small groups. [Does flipped classroom still get used? It > got a fair amount of press a few years ago. The wikipedia entry seems useful. Would > it be helpful in such short term encounters?] > > Day 2: Collaboration day. Early meeting giving overview of objectives of day 2. > Various workshops and meetings throughout the day. Schedule “reporting back” > from groups formed in workshops – one objective of each workshop is preparing > a report for delivery to the whole conference. [This reporting concept is speculative.] > > Day 3: Developer day. Optional. Focus on decisionmaking in software/data structure > design, new assay types and associated problems of ingestion, QC, summarization, > new concepts in R and computational services relevant to state-of-the-art comp bio.

Vince Carey (23:18:29): > I think there is a pretty broad consensus that “Developer day” is unappealing to many people we would want to engage, so I withdraw my objection to dropping/renaming.

Martin Morgan (23:33:06): > I’m also in favor of a name change / refocus for that first day of the conference, or for re-imagining the conference more broadly. I personally like the spirit of the title ‘where software and biology connect’ and have enjoyed the implementation of that through the morning talks / afternoon workshops format of the main conference. > > Maybe a good place to start is to think about what we want from the conference, perhaps particularly the day formerly known as developer day. Originally I think it was meant as something like ‘skills development’ for those actively engaged in writing packages; there was not much of that at the last conference, and the needs of the community have probably changed quite a bit, especially with an expanded breadth of experience (novice to very experienced) and indeed size of the event.

2019-07-13

Domenick Braccia (09:55:40): > @Domenick Braccia has joined the channel

Nitesh Turaga (12:36:45): > I’m also in favor of name change, mostly because there is some amount of the “imposter syndrome” feeling when I think “hackathon” or “developer day”. > > The expanded breadth of the experience at the conference “developer day” is worth focussing on probably. It might be good to have a few workshops taught for people who want intro courses in, parallel tracks are fine, (1.Intro to package development, 2. Intro to package maintenance 3. <Other Bioc 101 courses>, 4….), along with some advanced courses to make people feel more comfortable across their experience levels. Maybe we also need to be more creative about how these courses or workshops are delivered.

2019-07-15

TomCarroll (17:46:52): > @TomCarroll has joined the channel

Stephanie Hicks (20:28:36): > I like the idea of a “Training Day”. This name at least suggests that there could be training for both new users and developers wanting to get more experience in niche or new areas. This year for me, that was learning more aboutDelayedArrayfrom@Peter Hickey@Hervé Pagès. Also, I like@Nitesh Turaga’s idea of being explicit in describing the workshops e.g. “Introductory”-type workshops vs “Intermediate/Advanced” workshops.

Stephanie Hicks (20:34:01): > also as it stands, it’s not super clear to me what the difference is between the workshops on what’s been known as “Developer Day” vs workshops in the afternoon of the Bioc conference? Are they meant to be different?

Stephanie Hicks (20:43:52): > going back to@Martin Morgan’s comment: I like the idea of a “Training Day” with something like > - Welcome session > - Short, thought-provoking presentations (5-15 mins, contributed or invited) from either new users or long-time contributors to bring to the community’s attention either new scientific problems that the bioc community could address, or technical problems that have arisen in the last year (e.g. need for better documentation, data infrastructure is not sufficient for a new type of data, etc). > - Open discussion between a set of panelists and the audience to talk through the thought-provoking session > - lunch > - Afternoon training 1hr workshops that are labeled (e.g. Introductory Workshops 1-4, Intermediate Workshops: 5-8, Advanced Workshops: 9-12) that run concurrently. So if I’m a new user, I can attend 4 1hr workshops and get exposed to a lot of what I need to know as a new user, etc. > - Closing discussion between a different set of panelists and the audience to talk through any other issues that have arisen during the day.

Stephanie Hicks (20:50:31): > Then for the 2-day Bioc conference, I felt like this year the community has expanded so much that I would have greatly preferred to see more contributed talks from individuals and a reduced set of workshops in the afternoon. I do like the afternoon workshops, but I would rather see the training day expanded to two days to able to include all the great workshops and then have more contributed talks at the Bioc conference in the afternoon.

Peter Hickey (21:07:27): > @Peter Hickey has joined the channel

Peter Hickey (21:18:56): > fwiw RStudio pitch their conference as a 2 day conference preceded by 2 Training Days, where training days include what I’d call “developer day” activities

2019-07-16

Martin Morgan (06:24:38) (in thread): > I think of the main conference workshops as targeting the user trying to get through an analysis, DESeq2 being an archetype. ‘Back in the day’ these were smaller and longer, and the idea was to actuallydothe analysis in the workshop; this year with shorter workshops (and more choice, I guess) these become more like presentations / live coding sessions that show the participants what to do, but they never actually struggle with doing it. I know lots of AMIs were spun up, but I wonder how often they were actually used? > > Maybe an archetype for training day would be ‘how to build a package’ or ‘how to debug C code’ or ‘how to write an S4 class’; things that would definitely not be useful for getting an analysis out the door.

Martin Morgan (06:39:11): > Just having a little reservation about ‘training’ day, because it doesn’t really differentiate between training for users of the software and training for developers of the software. Maybe that distinction is mostly lost anyway, and the way to differentiate is in distinct tracks within workshops. > > Also for me I can’t really track a large number of talks, I’m overwhelmed. So I appreciate that the main conference gives us a finite amount of time in this passive learning mode. Also, in terms of learning, I would rather be exposed to a few longer talks that I can reflect on than many short talks – this means of course that I only hear main-stream, curated messages, and that people who would like to convey their message to the community don’t get a chance to do so – we’ve never done poster sessions well, and maybe there are creative ways of doing these (useR preceded the poster session with a ‘lightning poster talk’ session where all poster presenters had 1 minute or less and 1 slide to advertise their poster) talks, e.g., a ‘speakers corner’ at times in the poster session where people stand up and deliver their 5-minute spiel. > > I’m not sure how important it is, but I do think that distinct days helps people justify coming – I have two days worth of commitment to this project, but not three. Developer Day has always been free from a monetary perspective, I’m not sure whether a financial cost would change participation?

Robert Castelo (13:38:00): > @Robert Castelo has joined the channel

Robert Castelo (13:50:00) (in thread): > I think that live coding sessions that show participants what to do, but they don’t struggle with doing it decreases the learning experience, especially in beginners. Keeping attention to live coding is more difficult than to slides.

2019-07-19

Aedin Culhane (16:52:31): > @Aedin Culhane has joined the channel

Aedin Culhane (16:54:35) (in thread): > I think Vince’s idea of doing the main conference (beginner/intermediate) days first and follow with collaboration/developer day. People may stay on or feel more confidence in participation if they attend the two prior days

Aedin Culhane (16:59:42): > I like the mix of talks and training sessions during meeting. I am not sure I could do a full 2 days of training/workshops only. I would like a section where new Bioc developers are recognized. They are given a lightning talk to present new packages or there is a full session on “new in bioc”

Aedin Culhane (17:01:26): > A review of new packages or major package releases would be nice.

Aedin Culhane (17:02:25): > Could we create an award to recognize new developers and established contributors. Awards by nomination /vote

2019-07-23

Lori Shepherd (11:28:34): > @Lori Shepherd has joined the channel

2019-07-25

Levi Waldron (12:58:23): > @Levi Waldron has joined the channel

2019-07-31

Joselyn Chávez (19:27:09): > @Joselyn Chávez has joined the channel

2019-08-02

Leo Lahti (14:32:03): > @Leo Lahti has joined the channel

2019-08-04

Lambda Moses (20:54:06): > @Lambda Moses has joined the channel

2019-08-23

Boris Hejblum (06:11:42): > @Boris Hejblum has joined the channel

2019-09-18

Aedin Culhane (14:05:19): > <!channel>Dear Bioconductor Community, > > The organizing committee for BioC2020, to be held in Boston on July 29-31, needs organizers to help in planning the event. > > Participation involves attending approximately monthly remote meetings plus taking on responsibilities in one or more of the areas of: > > * Outreach (developing materials, promotion) > * Website > * Workshop technical organization > * Program development > * Sponsorship and funding > * Code of Conduct training and enforcement > * Local organization in Boston > > Please register your interest to participate on the Bioc2020 organizing committee athttps://forms.gle/Zs1gn2T9RtQ7Xysv5Thanks > Aedin Culhane, Levi Waldron - Attachment (Google Docs): Bio2020 Committee Application > The organizing committee for BioC2020, to be held in Boston on July 29-31, needs organizers to help in planning the event. Participation involves attending approximately monthly remote meetings plus taking on responsibilities in one or more of the areas listed below.

Qian Liu (16:28:01): > @Qian Liu has joined the channel

2019-09-19

Deepak Tanwar (02:29:28): > @Deepak Tanwar has joined the channel

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Krithika Venkataraman (13:57:45): > @Krithika Venkataraman has joined the channel

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2019-09-20

Aedin Culhane (14:37:57): > Should we incorporate these suggestions into bioc2020.https://www.nature.com/articles/d41586-019-02759-2?utm_source=twitter&utm_medium=social&utm_campaign=crs-&utm_content=200919v2 - Attachment (nature.com): Put participants first in conference design > By using more sophisticated methods of thinking about conferences, organizers can help to ensure that time spent at a meeting is spent well, say Hannah Turbeville and Ruth Gotian.

2019-09-23

Keegan Korthauer (11:59:36): > @Keegan Korthauer has joined the channel

2019-10-04

Lauren Hsu (09:11:30): > @Lauren Hsu has joined the channel

Aedin Culhane (15:15:37): > We have sent out a doodle poll about monthly calls times for the Bioc2020 committee. If you want to me on the committee sign up athttps://forms.gle/woP5jKdKpmboRGKo7 - Attachment (Google Docs): Bioc2020 Committee Application > The organizing committee for Bioc2020, to be held in Boston on July 29-31, needs organizers to help in planning the event. Participation involves attending approximately monthly remote meetings plus taking on responsibilities in one or more of the areas listed below.

Keith Connolly (16:08:02): > @Keith Connolly has joined the channel

2019-10-05

Helena L. Crowell (05:50:21): > @Helena L. Crowell has joined the channel

2019-10-15

Ming Tang (10:04:48): > @Ming Tang has joined the channel

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2019-10-16

Sean Davis (12:19:02): > Bioc Workshop Book notes from today’s call:https://docs.google.com/document/d/1EKerVh-eWviBrWtr3SEH9LwlYOqZ4rHqbgRWGTjJ2Ik/edit?usp=sharing - File (Google Docs): Bioc Workshop Committee working document

2019-10-18

Pratima Chennuri (11:34:50): > @Pratima Chennuri has joined the channel

2019-10-21

Aedin Culhane (13:50:35): > Hi, Can we make a google calendar associated with the google group and ask all of the sub-committees to add calls as “event”s on that calendar. That way we can subscribe to the calendar and easily keep track of meetings for the sub-committees etc@Martin Morgan@Levi Waldron

Aedin Culhane (13:54:08): > https://groups.google.com/forum/#!forum/biocconference

Aedin Culhane (13:54:41): > according to help docs, only owners of group can create group calendar

Aedin Culhane (13:54:45): > https://support.google.com/a/answer/1626902?hl=en - Attachment (support.google.com): Create and share a group calendar - G Suite Admin Help > As a G Suite administrator at work or school, you can create calendars to share with people in your organization. For example, you might want a shared group calendar for company holidays and anot

2019-10-22

Ameya Kulkarni (17:08:47): > @Ameya Kulkarni has joined the channel

2019-10-28

Aedin Culhane (16:10:42): > Hi<!channel>Would you like to work on the Bioc2020 sponsorship committee? The sponsorship committee is vital to the meeting success. It brings in funds that support student and postdoc travel fellowships. From previous years, we have a list of organizations /companies that have funded us. The committee will meet, gather a list of possible companies that may sponsor Bioc2020. We send them a email (using a template that we have from previous years). We may need to send a reminder. We will have our first meeting in November.

Qian Liu (16:23:19): > Hi@Aedin Culhane, I’m interested in helping with sponsorship. Please add me if possible. Thanks!

2019-10-31

Lauren Fitch (15:34:28): > @Lauren Fitch has joined the channel

2019-11-01

Aedin Culhane (18:03:48): > <!channel>Reminder BioC2020 planning meeting on Tuesday, November 5⋅9:30 – 10:30am (EST). Please can all committees prepare update (and post here) and Let us know if you need to add items to the agenda

2019-11-05

Lori Shepherd (09:30:56): > @Aedin Culhaneand@Levi WaldronWere we using the blackboard link again that is in the calendar reminder/invite or the zoom link that is in the original agenda? - just making sure we get everyone

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2019-11-20

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2019-11-29

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2019-12-02

Levi Waldron (04:34:52): > <!channel>we are meeting tomorrow at 9am EST / 3pm CET athttps://bluejeans.com/260305868?src=calendarLink. Calendar invitation has been sent sent to biocconference Google Group, announcement and agenda will be sent there, let me know if you on the organizing committee but not in the Google Group.

2019-12-03

Simina Boca (08:58:25): > Will be a bit late but am on my way

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2019-12-04

Jonathan Carroll (17:38:10): > @Jonathan Carroll has joined the channel

2019-12-11

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Aedin Culhane (14:07:30): > Hi  > > The sponsorship committee and everyone interested in helping, please join a short conference call tomorrow Dec 12th, 2pm EST > > Join Zoom meetinghttps://harvard.zoom.us/j/6176322468Join by telephone+1 929 436 2866US (New York) > Meeting ID:617 632 2468One tap mobile+19294362866,,6176322468#US (New York) >   International numbers available:https://harvard.zoom.us/u/acXhSi1TFgJoin by SIP conference room system > Meeting ID:617 632 24686176322468@zoomcrc.comA tentative agenda for the meeting is athttps://docs.google.com/document/d/1Ce_6lCh14YSDuvo1mSpffYDLRWVjcPpQxfZ5Yc0a0QU/edit#If you can’t join the call, please add your suggestion/edits/comments to the sponsorship letter and put your name next to a company if you will send a letter > >   - The sponsorship letterhttps://docs.google.com/document/d/1yAjRJmFJ22F8CB3DYhj7WwywHh0ZovA1ZEDok-0AJ6A/- the list of companieshttps://docs.google.com/spreadsheets/d/1oxOnUBOB6G7gpSsiiRBuhFwBor0XsytaE6eZzAUDBaE/In the meeting, we hope to finalize the letter and develop a plan for sending out letters.  > > best > Aedin<!channel>

Simina Boca (14:41:14): > 2 pm Eastern?

Aedin Culhane (16:35:42): > Yes

Aedin Culhane (16:36:05): > Thinking of the schedule; Is 3 keynote speakers together a lot together…

Aedin Culhane (16:36:31): > Currently its 8:30 - 9:00 – Speaker 1 – TBA > 9:00 - 9:30 – Speaker 2 – TBA > 9:30 - 10:00 – Speaker 3 – TBA > 10:00 - 10:30 – Break – TBA > 10:30 - 12:00 – Contributed talks Session 4a – Theme 1 – TBA > * Speaker 1 > * Speaker 2 > * Speaker 3 > 10:30 - 12:00 – Contributed talks Session 4b – Theme 2 – TBA > * Speaker 1 > * Speaker 2 > * Speaker 3 > 12:00 - 1:00 – Lunch / Birds-of-a-feather – TBA > 1:00 - 1:50 – [Workshop Session] 5a > * Workshop 1 > * Workshop 2 > * Workshop 3 > 2:00 - 2:50 – [Workshop Session] 5b > * Workshop 1 > * Workshop 2 > * Workshop 3

Aedin Culhane (16:36:55): > On day 1, there will be intro by Martin, CoC etc…so Speakers will start later (possibly 8:45 or 9am)

Aedin Culhane (16:37:43): > Suggest alternative schedule - File (Plain Text): Untitled

Aedin Culhane (16:37:47): > Can we make themes and then ask contributed speakers to tag their abstract talks with a theme. Here are the invited speaker topics..

Aedin Culhane (16:38:46): - File (Plain Text): Untitled

Aedin Culhane (16:42:22): > Ok Apologies every.. The formatting is horrible… I also emailed on biocconference

2019-12-12

Aedin Culhane (15:07:26): > <!channel>I have created a slack channel for the Bioconductor Conference Sponsorship Committee#bioc-conference-sponsorship

2019-12-17

Jean Yang (02:39:22): > @Jean Yang has joined the channel

2019-12-18

Shubham Gupta (11:23:06): > @Shubham Gupta has joined the channel

2019-12-23

dylan (10:34:57): > @dylan has joined the channel

2020-01-31

Stephanie Hicks (20:52:10): > Not sure if there’s is still time to discuss, but I really like this idea of dev days where people collectively work on pull requests or accomplish specific tasks for a packagehttps://twitter.com/juliasilge/status/1223374420170788864 - Attachment (twitter): Attachment > At #TidyDevDay folks are typing away, working on issues on tidyverse packages. I helped someone submit their first PR ever! :tada: https://pbs.twimg.com/media/EPpMi4hUcAEteMP.jpg

2020-02-01

Stephanie Hicks (07:06:49): > “I learned a lot, but more that anything I feel like I belonged”https://twitter.com/revdocgabriel/status/1223445860421230592 - Attachment (twitter): Attachment > Finished a pull request for my first #TidyDevDay at #rstudioconf with @Bouzoulay, @lauragabrysiak, @raymondBalise, and many others from @tidyversetweets and @rstudio. I learned a lot, but more than anything I felt like I belonged. No more #impostersyndrome! #rstats #RockstaR

2020-02-02

Charlotte Soneson (09:37:30): > @Stephanie HicksThere will be an opportunity to have this type of activities during Bioc2020. We also tried it on a smaller scale during EuroBioc last year, which was very nice (https://github.com/bioconductor/eurobioc2019/issues)

2020-02-04

Simina Boca (10:52:08): > I started the caregiver award doc herehttps://github.com/SiminaB/BioC2020/blob/master/docs/caregiver-awards.md

Simina Boca (10:52:17): > I actually got approval from NAVBO for using their language

Simina Boca (10:53:32): > Just made a pull request as well

Simina Boca (10:55:42): > We’ll need to create a submission form as well, but I saw there isn’t one for the poster/talk submission form eitherhttps://github.com/Bioconductor/BioC2020/blob/master/docs/TBA.

Aedin Culhane (12:59:43): > Connect with@Matthew McCallI think he did the travel form.

Matthew McCall (15:58:55): > The submission forms are all in the google drive shared folder entitled bioc2020

Simina Boca (18:02:03): > Can we link them from GitHub?

2020-02-05

Matthew McCall (17:20:12): > One of the folks working on the website did it for me.

Martin Morgan (17:30:06): > Poster / talk / workshop forms are linked on the ‘Call for submissions’ pagehttps://bioc2020.bioconductor.org/call-for-abstracts; The link to the form for travel applications might be a bit hidden – at the bottom of the travel & accommodation pagehttps://bioc2020.bioconductor.org/travel-accommodations. Maybe should (also?) be linked in the ‘Call for submissions’ and / or ‘Registration’ page? - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. June 24 - 27, New York City, USA. - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. June 24 - 27, New York City, USA.

Simina Boca (20:09:56): > Sorry, I was referring to the link from the Scholarship pagehttps://github.com/Bioconductor/BioC2020/blob/master/docs/scholarships.md

Simina Boca (20:10:50): > Ie if you click on “Poster / Talk Submission Form” you get an error. I guess the Scholarship page isn’t on the official website yes though?

2020-02-11

Simina Boca (13:02:00): > We should make the Travel Awards form more prominent. Also I don’t think we have a Caregiver Award form yet. Mentioning it since they’re noted in this tweet:https://twitter.com/Bioconductor/status/1227283205188988931 - Attachment (twitter): Attachment > Bioc2020! Registration is open! Now accepting abstracts for workshops/talks/poster deadline March 3. Now accepting applications for travel and caregiver scholarships deadline March 3. More information on the website: https://bioc2020.bioconductor.org/ #bioconductor #rstats #rladies

Simina Boca (13:02:33): > But the Travel Award form is at the very bottom of this pagehttps://bioc2020.bioconductor.org/travel-accommodations, so if you go to the website via the link it’s not easy to find - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. June 24 - 27, New York City, USA.

Lori Shepherd (15:25:11): > sorry about the care giver award - I saw the emails for PR and didn’t realized they weren’t merged yet

Simina Boca (15:40:53): > No problem!

Simina Boca (15:41:22): > I also didn’t make a submission form for it yet:disappointed:

2020-02-13

Noor Pratap Singh (00:19:57): > @Noor Pratap Singh has joined the channel

2020-02-14

Andrew Skelton (05:03:54): > @Andrew Skelton has joined the channel

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2020-02-18

Simina Boca (14:03:34): > Oops, I didn’t see Lorena’s and Martin’s comments on Github until now

Simina Boca (20:39:39): > Quick question I got from someone interested in submitting: does the presentation have to center around a new BioC package or can it be a CRAN package?

2020-02-19

Daniel Newhouse (11:26:24): > @Daniel Newhouse has joined the channel

Aedin Culhane (18:52:16): > Hi Simina.@Martin Morganand@Levi Waldroncan clarify. Someone can submit an abstract about a github or R package, and we like it if they plan to submit to Bioc. Most Bioconductor packages start as R packages. The conference hopefully provides support that enables the R-> Bioc package submission step

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2020-02-20

Joan (14:30:26): > @Joan has joined the channel

2020-02-22

Lambda Moses (22:27:07): > Can I submit an abstract for an early stage project that does use R and Bioconductor for data analysis, but isn’t a package yet? I plan to submit the package to Bioconductor eventually, but right now it’s still experimental R code not yet packaged.

2020-02-25

Hena Ramay (12:50:00): > @Hena Ramay has joined the channel

Levi Waldron (14:18:50) (in thread): > Yes, certainly.

2020-02-26

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2020-02-27

Yi Wang (14:05:56): > @Yi Wang has joined the channel

2020-03-01

Simina Boca (10:10:06): > Perhaps a silly question, but is the deadline on March 3rd at 11:59 PM Eastern time?:joy:

Simina Boca (10:10:13): > If not, what is the exact time?

2020-03-02

Peter Hickey (02:43:42): > scholarship info suggests talk/poster presenters, but not workshop presenters, are eligible for travel awards (http://bioc2020.bioconductor.org/scholarships.html). > However, travel award form suggests workshop presenters are eligible (https://docs.google.com/forms/d/e/1FAIpQLSdr__Ox7kWpTV0lwjJ7skD617HcWFQmPrJqyMpVN27darvZQg/viewform). > Could this please be clarified - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 29 - 31, Boston, USA.

2020-03-03

Levi Waldron (11:13:13) (in thread): > Workshop presenters are also eligible for travel awards - sorry for the confusion.

2020-03-04

Aedin Culhane (13:17:56) (in thread): > Erica said 5pm EST in an email. But in practice, its a google form and I don’t think anyone will be checking the time stamp:wink:

2020-03-07

Federico Marini (02:38:23): > @Federico Marini has joined the channel

Federico Marini (02:39:44): > Hi there:wave:I’m writing here as a member of the Orga committee of the eRum2020 conference in Milan (end of May). > Just wondering what the current policy re: Coronavirus is in your case.

Federico Marini (02:40:40): > We have been having constant calls to explore a variety of plans B, and keep on working with the original schedule, in case the emergency state gets lifted

Federico Marini (02:41:35): > I see Bioc this round is one good month later “than usual”, so that makes you a little more on the safe side

Federico Marini (02:42:15): > Any pointers are very appreciated:wink:

Vince Carey (05:19:40): > Hi Federico – the policy just circulated at Harvard Medical School > > indefinitely prohibits employees across the system from attending all conferences, locally, domestically or internationally. In addition, the hosting of conferences that draw individuals from outside our organization is also indefinitely prohibited. > > Apropos Bioc2020 we have had limited discussion regarding options for an electronic conference, should such be necessary.

USLACKBOT (05:22:21): > This message was deleted.

Federico Marini (05:59:26): > being not there in person I cant get a hold of the situation - also the perceived one

Federico Marini (05:59:38): > but yes, looks like it hit harder than what we all hoped

Federico Marini (06:00:37): > similar policies to the one you posted@Vince Careyare being issued around. so far we got a nice feedback from potential attendees. thing is authorities will have the saying in this

2020-03-08

Levi Waldron (03:58:36): > Our discussion in the last meeting concluded with, 1) we will follow the lead of the conference facilities, which are not at the point of cancelling events, 2) clarify our cancellation policy (refunds only if the conference is cancelled, because most of our costs are fixed), and 3) discuss web streaming for participants who can’t attend. We haven’t yet discussed the possibility of an entirely electronic conference.

Federico Marini (04:11:09): > re: point 3, it would be interesting to inspect feasibility aspects

Federico Marini (04:11:55): > not saying that nowadays we would indeed have all tech ingredients to do so, but almost. Then of course depends on the scale of the event.

Federico Marini (04:12:24): > FWIW, the R group in Neuchatel (CH) did meet like that a few days ago (just read indirectly over twitter)

Federico Marini (04:13:20): > I do not have local contacts there, maybe it is worth reaching out with them. > On one side, our devel forum might be interesting as a way to pave the road to such e-meetings

Charlotte Soneson (04:13:41) (in thread): > On Saturday actually:https://neuchatel2020.satrdays.org/ - Attachment (neuchatel2020.satrdays.org): satRday > R conference in Neuchâtel

Federico Marini (04:14:09) (in thread): > oh

Federico Marini (04:14:35) (in thread): > thanks Charlotte! Got any direct connections over there?

Charlotte Soneson (04:16:14) (in thread): > Not really, I have met one of the organizers a couple of times.

Stephanie Hicks (22:04:01) (in thread): > fwiw — in the US, Delta Airlines and American Airlines have also canceled flights to milan through beginning of April

Stephanie Hicks (22:05:32) (in thread): > maybe@Davide Rissocould provide some insights here? I’ve been communicating with him weekly and it seems things are still incredibly… fluid.

2020-03-09

Davide Risso (04:00:34): > @Davide Risso has joined the channel

Davide Risso (04:14:01): > Re: eRum and the situation in Italy, I think it is pretty bad. RECOMB was supposed to be in Padova in May and they canceled it, I would strongly consider canceling eRum if you ask me…

Davide Risso (04:14:40): > I know it’s a difficult decision to make because of all the time and effort that people put in organizing it:cry:

Davide Risso (04:15:56): > Even if the emergency state is lifted, people might not want to travel to Milan, even if flights are restored

Federico Marini (04:37:15): > We will be having a general call on this regard tomorrow

Federico Marini (04:37:28): > And I can confirm the feelings are not good from my side either

Federico Marini (04:38:25): > Without entering too much in the reasons why I hate the “smart-ass-philosophy” which seems to be among the causes of the underestimation/complete ignoring of the risks

Federico Marini (17:02:59): > FWIW, Italy is in full lockdown now- Well, “zona protetta”, where people should indeed limit at most their movements & co.

2020-03-10

Aedin Culhane (01:15:53): > I have cancelled in-person R/Bioconductor meetups in Boston during March but have not cancelled BIRSBiointegration in June. DFCI, partners and Harvard have prohibited business travel from March 9th until April 15th or April 31st or until future notice respectively. I think anything during March/April and early May is likely to be cancelled.

Aedin Culhane (01:16:20): > DFCI have also prohibits external visitors to buildings with patients

2020-03-13

Hirak (17:27:19): > @Hirak has joined the channel

2020-03-17

Jianhong (20:03:42): > @Jianhong has joined the channel

2020-03-22

Simina Boca (09:58:18): > Still working on reviewing abstracts but will be done soon

Simina Boca (09:58:21): > But I just realized…

Simina Boca (09:58:32): > Even if the in-person conference is not cancelled

Simina Boca (09:58:52): > International folks may not have time to get visas, tickets etc because of what’s going on

Simina Boca (09:59:24): > So we may want to discuss a possible on-line component as well for people who want to listen in and also those international people who abstracts are selected

Sean Davis (14:20:02): > That seems pretty rational,@Simina Boca.

Federico Marini (15:07:25): > We as eRum2020 in Milan opted to reschedule - trying now to find a date in November. Of course, hoping the corona hard phase will be done by then

2020-03-23

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2020-03-24

Lauren Fitch (16:29:56): > are notifications still planned to go out today or are there any covid-related delays anticipated?

Lori Shepherd (16:43:31) (in thread): > I believe it is delayed until later in the week but perhaps someone could verify@Matthew McCall?

Matthew McCall (17:26:04) (in thread): > Aiming to send out notifications by Friday.:crossed_fingers:Apologies for the delay.

2020-03-27

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2020-03-31

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Lori Shepherd (11:48:54): > Bioc2020 is proceeding with planning for the conference to be held July 29-31, with contingency planning for an online-only conference if necessary.https://bioc2020.bioconductor.org/As part of the program we want to encourage community involvement and interactive projects. This may take the form of birds-of-a-feather discussion topics (like an open forum discussion) but could extend to ideas like short hack-a-thon projects (e.g., create a Pull Request for feature x in package y) or the compilation of short FAQ/how-to topics (e.g., how do I liftover hg19 coordinates to hg38 with Bioconductor resources). We encourage submissions from novice R/Bioconductor users and minority groups. > > We want to have some of these sessions planned and will also encourage spontaneous sessions to form on the day of the conference (pending an in-person meeting). In an effort to schedule topics that are of most interest to the Bioconductor community at large, we encourage submission of session ideas on the bioc2020 github as an open issue. (https://github.com/Bioconductor/BioC2020/issues) > > Please include in the issue title if it’s a birds-of-a-feather (BOF), hack-a-thon (HAK), or how-to/FAQ (FAQ), and include a short description of the goals of the session. > > For example: > (BOF) Annotation harmonization > (HAK) Add metadata column to package > (FAQ) How to do a lift over from hg19 to hg38 > > Please announce your session suggestion in this Bioconductor slack channel#bioc2020. This will encourage the Bioconductor community to contribute to the session. > > Thank you > > Lori Shepherd on behalf of the Bioc2020 planning committee - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 29 - 31, Boston, USA.

Koen Van den Berge (11:49:55): > @Koen Van den Berge has joined the channel

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Hena Ramay (19:22:02) (in thread): > Did the notification go out on Friday? I haven’t received any email so just wondering if it was postponed. Thanks!

2020-04-01

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2020-04-02

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2020-04-03

Simina Boca (13:41:27) (in thread): > I got mine on Friday…

2020-04-11

Kylie Bemis (13:48:34): > @Kylie Bemis has joined the channel

2020-04-15

Koen Van den Berge (20:01:47) (in thread): > We haven’t heard back yet from our workshop, just wondering if that’s the case due to delays, or whether we weren’t selected? Thanks.

2020-04-16

Lori Shepherd (10:07:38) (in thread): > There were delays. Notifications should be going out hopefully by next week.

Petr Smirnov (13:51:04): > @Petr Smirnov has joined the channel

2020-04-17

Lori Shepherd (13:44:30): > Bioconductor is excited to announce an opportunity to recognize those making significant outstanding contributions to the Bioconductor community. The Bioconductor project proudly launches the first call for Bioconductor Awards, honoring various forms of contributions to the project. Four awardees will be selected, each having contributed to the project in an outstanding way based on one or more of the criteria foundherePlease fill out the nomination form by June 15 :Nomination Form

2020-04-18

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2020-04-24

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2020-04-29

Federico Marini (17:13:05): > Hi there, given the St. Louis cancellation (probably complete) I wanted to ask & offer something at the same time.

Federico Marini (17:14:33): > If you plan to go remote for Bioc2020, this is what we as eRum2020 (now e-Rum2020) have set. We are exploring platforms to host the event, and among the concurrent solutions, we are thinking of Hopin and Zoom webinar

Federico Marini (17:15:43): > If you have questions about these, we have been in touch with the Hopin representatives (they’re new, but the system looks very promising), and I can either pass some information directly, or “just” do the messenger:wink:

2020-04-30

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2020-05-01

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2020-05-02

Levi Waldron (06:22:28) (in thread): > @Federico MariniI’d love to talk to you about this. We have a BioC2020 meeting on Tuesday, could we talk before then?

Federico Marini (08:29:25) (in thread): > Would tonight at around 21 work for you?

Levi Waldron (08:29:44) (in thread): > Yes it should

2020-05-06

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2020-05-07

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Levi Waldron (17:06:39): > <!channel>it is official that BioC2020 will be an online-only conference, during the same week as planned. We on the BioC2020 committee are actually pretty excited, because we have time to design it well and to develop an innovative, interesting, productive, inclusive, community-building online conference. It is not too late to get involved if you are excited about planning a great online conference. A couple things: > 1. If you’d like to take part in some brainstorming, check outhttps://app.sli.do/event/gvh5mzfq/live/questions(# 52549) to toss out ideas and up/down-vote, read/add to our more detailed brainstorming document athttps://docs.google.com/document/d/12mBgGjQRsmbxj3g8Qi73k1fMAckJHxJbHtdMn7S4Jgc/edit?usp=sharing, or write your thoughts here in this channel. > 2. if you already registered, we’ll be in touch about your refund. The online conference fee is TBD but will be significantly less expensive.

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2020-05-08

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Jenny Drnevich (12:06:50): > Can we be mailed a registration packet with stickers? I just got a new laptop and want to bling it out some. Only partially joking…:grin:

James MacDonald (18:10:14) (in thread): > I’ve seen your laptop. That’s absolutely not a joke.:grin:

Jenny Drnevich (22:59:58) (in thread): > It’s just that I saw the cool BioC2020 Boston sticker onhttps://bioc2020.bioconductor.org/right about the same time my son started to try to peel the stickers off my old laptop I’ve been letting him use for school Zoom and it made me sad…:cry: - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 29 - 31, Boston, USA.

2020-05-09

Levi Waldron (13:27:00) (in thread): > I do kind of like the idea of still getting very special virtual conference stickers out to registrants……

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2020-05-10

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2020-05-11

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2020-05-12

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2020-05-14

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Aedin Culhane (14:20:32): > Hi.. Still thinking about the Bioc2020 stickers. Do we go virtual stickers only.. or we could off stickers sheet as part of registration, or could be a $5 add-on extra at registration. A sticker sheet could include Bioc2020 sticker and some other stickers (maybe new packages or packages that received awards this this). Additional sticker sheets could be offered for sale. A 4” x 6 costs $1-2 and then postage would be anything from around 50 cents to $2 depending on location. If shipped at or soon after registration, then they might arrive on time for the meeting.https://www.stickermule.com/products/sticker-sheets - File (PNG): Screen Shot 2020-05-14 at 2.20.02 PM.png

Federico Marini (17:53:11): > If this can be of any help: we had for eRum a sponsorhip of the in-kind type with stickermule

Federico Marini (17:53:33): > that got transmuted into the virtual event

Federico Marini (17:54:03): > from our side, all they needed was a banner on the website, with the personalized link (to track the visits I guess)

Federico Marini (17:54:19): > what we will get is > * about 1000 stickers, “kiss-cut” type

Federico Marini (17:54:53): > * and a special offer for 10 stickers -> 1 euro, kind of an appetizer

Federico Marini (17:55:33): > Probably an almost crazy thing to do, but I’ll plan to send around the stickers to who would request that:slightly_smiling_face:

Federico Marini (17:56:03): > anyway, relevant for you organizers@Aedin Culhane-> they told me they are open to more of such sponsorships

Federico Marini (17:56:21): > so it might be the matter of putting you all in touch

Aedin Culhane (20:09:20): > Thanks a million. Who was your contact at StickerMule

Aedin Culhane (20:12:08): > Suggestion.. Manubot of meeting report of Bioc2020. ?? Would it might encourage engagement…https://greenelab.github.io/meta-review/Each session chair gets to provide a short report of the session.. So Q&A/panel discussions etc.. are coupled with writing an XX word section report of that part of the meeting - Attachment (greenelab.github.io): Open collaborative writing with Manubot

Peter Hickey (20:35:46) (in thread): > FWIW I basically did this on Google Docs last yearhttps://twitter.com/PeteHaitch/status/1143495621636251648 - Attachment (twitter): Attachment > In case it’s useful, here are my notes from Developer Day at #BioC2019 https://docs.google.com/document/d/1ylziUypDwwuKKC3J5_6KaW-OJVxs_gu1x6LjJOQ6olk/edit?usp=sharing (inspired by @jxtx last year) > I’ll try to continue over the next few days and write something up following the meeting

2020-05-15

Federico Marini (04:42:10) (in thread): > I had a call yesterday with Luca

Federico Marini (04:42:34) (in thread): > their email is generic, but I always got assisted from him

Federico Marini (04:43:09) (in thread): > Happy to follow up on this also in DM if you want:wink:

2020-05-18

B P Kailash (08:43:58): > @B P Kailash has joined the channel

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2020-05-19

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Stephanie Hicks (15:12:34): > not sure if this is helpful, but another conf that went virtual wrote up a post on what worked and what didn’t:https://medium.com/@iclr_conf/gone-virtual-lessons-from-iclr2020-1743ce6164a3 - Attachment (Medium): Gone Virtual: Lessons from ICLR2020 > From today, all content for the ICLR2020 Virtual Conference is available in open-access for anyone across the world to learn from. A…

Shraddha Pai (15:42:45): > @Shraddha Pai has joined the channel

Dan Bunis (15:48:01): > Perhaps this perspective will also be helpful? > > My PI was scientific program chair for the AMIA 2020 INFORMATICS SUMMIT which took place right around the start of when the pandemic was growing large in the US. So it pretty hastily went fully virtual. Even so, it ran super smoothly from her perspective and my own as a post-virtual-swtich-registrant. They even opened registration up, albeit to a limited number of people, for free. > > Unfortunately my PI wasn’t on the technical side of things — those were all handled by AMIA — so I don’t have much access to the logistics other than these: they collected slides ahead of time and had them as backup. Then they did practice runs with presenters before all talks.

Lori Shepherd (15:57:24): > It might be worth talking with some of the carpentries training participants too – some feedback on the current training session that is going on was that they made it very interactive and engaging to keep focus – there might be some pointers to collect for presenters of what they were finding effective

2020-05-20

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2020-05-22

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2020-05-25

Simina Boca (23:17:17): > Do we have a meeting tomorrow?

Simina Boca (23:17:45): > Not sure if I would be able to attend it either way

Simina Boca (23:19:14): > Quick question: How many people registered? Asking because for example my university apparently pay for the “Business” version of zoom which allows only 300 participants, so I wasn’t able to attend one of our online town halls

Simina Boca (23:19:57): > This may have been discussed last meeting (which I also missed), but something to consider

2020-05-26

Levi Waldron (03:00:02) (in thread): > Yes, 9am EDT - here’s a link to add the invitation to your calendar:https://calendar.google.com/event?action=TEMPLATE&tmeid=X2I1c2phY2oxYnRtM2NxOWljdDU1ZXEzOWQxMDVjbTFqODU5azRqYjhmMHE3ZWRiNWExaDBfMjAyMDA1MjZUMTMwMDAwWiBsd2FsZHJvbi5yZXNlYXJjaEBt&tmsrc=lwaldron.research%40gmail.com&scp=ALL - 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.

Levi Waldron (03:02:02) (in thread): > We haven’t yet started registration for the virtual conference, but should be able to do so in the next week or two.

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2020-05-28

Maria Doyle (00:12:01): > @Maria Doyle has joined the channel

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Sean Davis (11:36:16): > <!channel>I dropped some workshop package details in#biocworkshops.

Aedin Culhane (13:14:23) (in thread): > Thanks , sorry for followup delay, my to-do list keeps getting interrupted by kids !

Federico Marini (13:41:56) (in thread): > no problem. I can easily relate to that, I’m the one juggling with the homeschooling of the twins:slightly_smiling_face:

Aedin Culhane (16:45:38) (in thread): > Ouch.. I have 3 elementary kids (Kindergarten- 5th grade) who I am home schooling, its rough

2020-05-29

Federico Marini (14:31:38): > In case you’re still in the choosing phase for the platform, we had today a pre-conference event for eRum, namely CovidR

Federico Marini (14:32:00): > We had a smaller warm-up thing, and used that also to check the tires of the Hopin platform

Federico Marini (14:32:08): > gotta say it worked out pretty smoothly

Federico Marini (14:32:25): > If you need more information, I am happy to pass it over:wink:

2020-05-31

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2020-06-01

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2020-06-02

Lori Shepherd (08:34:17): > Friendly reminder: Please submit your nominations for Bioconductor Awards in by June 15 th. Nominations are open to the public. For more information and links to the nominating form please seehttps://support.bioconductor.org/p/130094/

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Aedin Culhane (16:59:02): > POSTER: In this meeting, they asked poster presented to prepare a 4-slide poster template, that was optimized for display on twitter (and used the conference hashtag)https://www.nature.com/articles/s41578-020-0194-0 - Attachment (Nature Reviews Materials): How to organize an online conference > The first online-only meeting in photonics, held on January 13th 2020, was a resounding success, with 1100 researchers participating remotely to discuss the latest advances in photonics. Here, the organizers share their tips and advice on how to organize an online conference.

Aedin Culhane (17:00:16): - File (PNG): Screen Shot 2020-06-02 at 4.59.58 PM.png

Aedin Culhane (17:00:36): > Examples of twitter poster sessionhttps://twitter.com/hashtag/POM20?src=hashtag_click - Attachment (twitter.com): #POM20 hashtag on Twitter > On Mar 18 @NatRevMater tweeted: “With travel restricted for the foreseeab..” - read what others are saying and join the conversation.

Aedin Culhane (17:04:10): - File (PNG): image.png

Martin Morgan (17:43:40) (in thread): > awesome idea!

Aedin Culhane (18:13:26): > We didn’t take down (or publicize) the caregiver awardshttps://bioc2020.bioconductor.org/caregiver-awards.htmlIf that defunct now with the meeting going online, or use we maintain it so single parents or parents in need of assistance could apply for child care to participant in the meeting or use it to create a child-friendly side event (zoom pre-k crafts, lego competition etc) to entertain kids while parents participate in the meeting - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 29 - 31, Boston, USA.

Aedin Culhane (19:06:46): > Hi I make a quick word cloud of the new packages so we can promote the new Bioc2020 new package awards.. Please share - File (PNG): Bioc2020_newPkgAwards.png

Aedin Culhane (19:08:03): > If anyone wants to do better, please.. I’d appreciate it. The list of new packages ishereand I usedhttps://www.wordclouds.com/to make the basic word cloud@Johannes Rainer

Aedin Culhane (19:12:32): > If anyone wants to make a image for each award category that would be amazing…

Aedin Culhane (19:29:12): - File (JPEG): Slide2.jpeg

2020-06-04

Satoshi Kume (04:32:33): > @Satoshi Kume has joined the channel

Sangram Keshari Sahu (08:57:59): > Hi! May I know if there are any scholarship for bioc2020 registration?

Aedin Culhane (13:13:17): > Yes, Need to check, but i think you can apply for a scholarshiphttp://bioc2020.bioconductor.org/scholarships.html - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 29 - 31, Boston, USA.

Levi Waldron (13:28:23) (in thread): > Yes! The scholarships will be extended and we expect to make more, website will be updated soon.

Aedin Culhane (13:55:08): > Hi levi and@Lorena PantanoI just put in a pull request on the website to make this clearer.

Keegan Korthauer (14:20:47): > The website currently says the conference is July 27 - 31, 2020. But the correct dates are July 29-31, 2020, correct? > > edit: it states both of these dates in different places

Dan Bunis (14:58:22): > I think 27 - 31 are the corrected/new dates for the conference’s now virtual form

Keegan Korthauer (15:00:32): > Got it - thanks!

Stephanie Hicks (15:30:30): > @Keegan KorthauerI believe the idea is to spread out the conference across 5 days and across different time zones to allow a bigger international community

Stephanie Hicks (15:30:48): > (someone correct me if I misunderstood though)

Keegan Korthauer (15:33:41): > That’s a great idea.

Benjamin Reisman (17:21:57): > Is the call for poster submissions for the virtual conference coming up or has it already passed?

2020-06-05

Levi Waldron (02:26:51): > @channela few things we know about the virtual conference: 1) it will be spread across 5 days (July 27 - 31) and has a $50 registration fee to partially cover the cost of the conference platform and technical support (the rest covered by sponsorship, registration already open), 2) the call for poster submissions will be re-opened, 3) we will shortly make “registration scholarships” available, 4) it will include its usual core of keynote talks, contributed talks and posters, and ~20 workshops, and 5) most content will be prepared or recorded in advance with the conference focused on shared study and interactive discussion of that content with the authors and other participants across multiple modes (ie live Q&A and workshop instruction, Slack, Twitter), and in that spirit we will facilitate registrants to add conference event “watch parties” with others in their time zone to the programme.

Aedin Culhane (23:12:06): > zoom meetings and conference are tough when you have young kids at home. I just heard abouthttps://campkinda.org/CampKinda which is a free, virtual summer experience for children in grades K-8. Programming consists of five educational adventures per week, without feeling like homework. Kids will get 3 to 4 hours’ worth of activities each day, all connected to fun weekly themes, such as unlocking the mysteries of history and jumping into the world’s craziest sports. It’s like camp… kinda.

2020-06-06

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2020-06-08

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2020-06-09

Shankar Shakya (10:05:57): > @Shankar Shakya has joined the channel

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Taoyu Mei (17:16:25): > @Taoyu Mei has joined the channel

2020-06-10

MounikaGoruganthu (11:23:59): > @MounikaGoruganthu has joined the channel

Ye Zheng (12:05:03): > @Ye Zheng has joined the channel

Vandhana (16:03:22): > @Vandhana has joined the channel

2020-06-16

Andre Sim (23:57:08): > @Andre Sim has joined the channel

2020-06-17

Andre Sim (00:01:12): > Apologies if this is the wrong place to post such a question but I didn’t find a contact email. I have been trying to register for BioC2020 however Paypal will not work citing having to “comply with international regulations”. For context, I am paying with Singaporean Dollars, and this occurs both when I try using my paypal account or using the Paypal credit option. Has anyone else had similar issues or know a trick to get it to work?

Levi Waldron (14:07:38) (in thread): > @Erica Feickdo you know anything about this?

2020-06-18

Marco Chiapello (10:57:08): > @Marco Chiapello has joined the channel

Levi Waldron (14:15:35) (in thread): > @Andre Simthere is an answer on the way, thanks for your patience.

Erica Feick (14:18:47): > @Erica Feick has joined the channel

Erica Feick (14:19:06) (in thread): > Andre, I just sent you an email to clarify. We will figure it out!

2020-06-19

Mikhael Manurung (14:13:54): > @Mikhael Manurung has joined the channel

Jelmer Poelstra (15:34:21): > @Jelmer Poelstra has joined the channel

Atul Deshpande (19:17:54): > @Atul Deshpande has joined the channel

2020-06-22

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2020-06-23

Kevin Rue-Albrecht (16:39:40): > @Kevin Rue-Albrecht has joined the channel

Lambda Moses (21:16:13): > Just curious, why are talks that are not keynotes in this conference only 10 minutes long while such talks in most other conferences I’ve been to are 20 minutes? Is this to make more time for the workshops or more keynotes?

2020-06-24

Levi Waldron (05:35:14) (in thread): > I guess it is historical, that’s how we’ve done it in the past and the format has been popular, giving a taste of more projects in a short format. Probably the main difference between the BioC conference and many others though is its focus on workshops - I don’t think we could keep that and double the length of contributed talks without reducing the number of contributed talks or having a lot of parallel sessions. We’re open to feedback though, here and through the feedback we’ll seek during and after the conference!

2020-06-25

Robert Castelo (02:40:33): > hi, one question about the Bioconductor registration form. i’d like to register myself along with two other people in my group and when i select “Qty=3” and press “REGISTER NOW” then i get a form with three blocks of information, one per attendee. for attendee 1 i have to fill up “Personal Information” and “Conference Information”, while for attendee 2 and attendee 3 i have to fill up “Personal Information”, “Address Information” and “Conference Information”. If I select “Qty=1” then i also do not get the “Address Information” part either. so, why the “Address Information” is lacking for attendee 1 and how can i put my address information to get a proper bill to get reimbursed at my university? should i register as attendee 2 or 3? why there’s this inconsistency between attendee 1 and the rest?

CristinaChe (15:57:20): > @CristinaChe has joined the channel

2020-06-26

Levi Waldron (09:48:32) (in thread): > @Erica Feickdo you know about this?

Erica Feick (09:48:37): > @Erica Feick has joined the channel

2020-06-28

Jonathan Goeke (01:21:26): > @Jonathan Goeke has joined the channel

2020-06-29

wisam (07:18:18): > @wisam has joined the channel

2020-06-30

Frank Rühle (06:20:15): > @Frank Rühle has joined the channel

Erica Feick (12:26:34) (in thread): > Hi, sorry for the delay. I wasn’t aware for this error and other people registering for multiple people have not mentioned it. I looked into it and you can register without the address and I would be able to provide you with a detailed receipt that shows all 3 of your registrations as well as your registration info. I will ask our platform to look into the address issue, but if you want to register now, you could.

Federico Marini (12:45:10): > Hi everyone! Together with@Charlotte Sonesonand@Davide Risso, I just posted a proposal for a BOF session ->https://github.com/Bioconductor/BioC2020/issues/105We’d like to stimulate an exchange to talk aboutTen simple rules for thriving in bioinformatics research. > If you want to signal some interest in participating, just leave a comment or a reaction to the issue - looking forward to a fruitful discussion all together!

Robert Castelo (13:00:23) (in thread): > Hi, ok, I’ve just done now the three registrations and sent you an email about the invoice. I was afraid I was doing something wrong. Thanks for your help!

2020-07-02

Kevin Rue-Albrecht (18:27:16): > Hi all. Similarly to the above, I just submitted a proposal for BOF ->https://github.com/Bioconductor/BioC2020/issues/106In this one, we’d like to exchange experience, best practices, and advice on the usage ofReproducible environments for integrated computational workflowsAs above, you can show interest in participating by leaving a comment or a:thumbsup:on the issue. I personally look very much forward to it!

2020-07-03

Jonathan Goeke (03:28:00) (in thread): > Hi@Erica Feickis there any solution? I have also tried to register from Singapore and it was never successful. I tried with multiple cards from different banks, but it never seems to work

Atul Deshpande (11:18:05): > Hi everyone! I submitted a proposal for a BOF session here:https://github.com/Bioconductor/BioC2020/issues/107Over the last couple of weeks, there have been discussions about strategies to make the default visualizations in Bioconductor packages accessible to people with color-vision deficiency. With that in mind, I am proposing this BOF sessionOn Standards for Accessible and Interpretable Visualizations. > > I have provided some perspective of the problem and outlined a few thoughts on the topic, addressing them from my personal perspective as someone with red-green color blindness. > I have also outlined the scope of strategies we would like to identify as an output of this session, but it is by no means an exhaustive list. Please feel free to comment on the issue, to either contribute more information, possible outputs for the session, or to signal your interest in the BOFwould love to get more perspective regarding the problems faced due to other vision impairments and successful strategies being used in other fields to make visualizations more accessible in general.

2020-07-04

Umar Ahmad (08:20:12): > @Umar Ahmad has joined the channel

Gian Marco Franceschini (09:57:30): > @Gian Marco Franceschini has joined the channel

Kasia Kedzierska (19:28:33): > @Kasia Kedzierska has joined the channel

2020-07-05

Dan Bunis (13:45:28): > Can I ask when we plan to order the stickers for the conference? Also how many per participant? And which stickers?

2020-07-06

Levi Waldron (03:23:30) (in thread): > There’s an order going in imminently if it hasn’t already (@Aedin Culhaneknows the details) of the virtual conference sticker now shown onhttps://bioc2020.bioconductor.org/. Actually distributing them is a chunk of work that will likely have to wait until after the conference :) - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 27 - 31, Boston, USA.

Levi Waldron (03:24:11) (in thread): > Great session proposal,@Atul Deshpande.

Levi Waldron (03:24:58) (in thread): > Very timely proposal,@Kevin Rue-Albrecht.

Kevin Rue-Albrecht (03:26:36) (in thread): > are you referring to anything specific?

Levi Waldron (03:28:22) (in thread): > The whole thing. There’s so much new work in this area regarding containers, mixing languages, and use of workflow systems.

Kevin Rue-Albrecht (03:34:20) (in thread): > Agreed! I’ve been working on reproducibility a lot in recent weeks, specifically controlling the version of R packages that a pipeline is meant to run with. > With renv in the ecosystem (in addition to conda, containers, etc.), I think it’s a good time to have another discussion about it.

Lidia Lipinska-Zubrycka (08:21:23): > @Lidia Lipinska-Zubrycka has joined the channel

2020-07-07

Pablo Latorre-Doménech (03:16:12): > @Pablo Latorre-Doménech has joined the channel

Jonathan Goeke (04:53:15) (in thread): > Hi@Levi Waldrondo you know if this is solved? I would like to register, but the payment does not work

Levi Waldron (04:56:46) (in thread): > Argh! Would you send an email to@Erica Feick<efeick@ds.dfci.harvard.edu> and cc me <lwaldron.research@gmail.com>?

Mehdi Pirooznia (09:25:31): > @Mehdi Pirooznia has joined the channel

Sean Davis (12:16:40): - Attachment: Attachment > Hi, > does anyone know whether Bioc2020 conference will only be streamed live, or if the talks will remain online for a few hours/days ? > > Thanks, > Simone

Jonathan Goeke (21:39:33) (in thread): > done! Thanks

2020-07-08

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2020-07-09

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2020-07-10

Rajesh Shigdel (03:39:17): > @Rajesh Shigdel has joined the channel

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2020-07-13

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Aedin Culhane (12:40:01): > I am currently watching the textmining stream from ISMB 2020 and whilst the live zoom is fine, playing of the pre-recorded talks are horrible, the videos seems have reduced audio and visual resolutions, so the audio is really bad

Aedin Culhane (12:46:10): > The second thing with the ISMB platform is that I wish to view the talks that I missed this morning, but there is no way to click on a talk and play the recording. I can’t see how to access recordings of earlier talks

Dan Bunis (13:09:17) (in thread): > This is great to know seeing as my plan was to submit a pre-recorded video for my talk. I know other virtual conferences have not had such quality issues for pre-recorded talks, but are we using the same virtual conference platform as ISMB 2020?

Dan Bunis (13:11:10) (in thread): > This is something I’ve been wondering about as well. Will talks be made available after-the-fact in some way? Perhaps directly through the conference platform, or perhaps via something public like youtube? I would personally love for my talk to become accessible to the public in some way.

Aedin Culhane (14:44:56): > Hi@Dan Bunisno we are using a different platform, we are have a few run through’s of the platform this week and next and will test it

Aedin Culhane (14:48:41): > @Dan BunisI will delete my post as I really only meant it for the organizer, as a note that these are things that we need to check on the Bioc2020 platform

Dan Bunis (14:49:28) (in thread): > gotcha, no worries

2020-07-14

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2020-07-15

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Aedin Culhane (14:09:57): > For anyone who saw my earlier comments about ISMB, they quickly fixed the audio issues and there quality of prerecorded talks was excellent today

2020-07-16

wmuehlhaeuser (03:03:14): > @wmuehlhaeuser has joined the channel

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Gabriel J. Odom (09:44:15): > Hi everybody! Looking forward to this conference

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2020-07-17

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2020-07-18

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2020-07-19

Ludwig Geistlinger (11:34:03): > For those of you that also have problems uploading a profile picture on the conference community website (https://bioc2020.pathable.co), I am just reporting that several attempts uploading a profile picture using mozilla firefox failed, using google chrome instead resolved the problem. - Attachment (bioc2020.pathable.co): BioC 2020 > BioC 2020

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Hyun-Hwan Jeong (22:38:54): > @Hyun-Hwan Jeong has joined the channel

Hyun-Hwan Jeong (22:48:47): > Hi, I want to register the conference but can’t. It seems that every option on the page has been expired.https://datasciences.eventsmart.com/events/bioc2020/Is there another way to register the conference? - Attachment (Bioconductor): BioC 2020: Where Software and Biology Connect - Bioconductor > BioC 2020: Where Software and Biology Connect - When: July 27 - 31, 2020 Where: Virtual Conference Slack: Bioconductor Team (#bioc2020 channel) Twitter: #bioc2020 BioC2020 highlights current

2020-07-20

Dr Awala Fortune O. (02:08:11): > @Dr Awala Fortune O. has joined the channel

Dr Awala Fortune O. (02:10:18): > Hello just registered, hope to see you at the conference virtually.

Hyun-Hwan Jeong (02:12:49): > @Dr Awala Fortune O.Hi did you register today? I tried it but it doesn’t work for me.

Bishoy Wadie (04:07:18): > @Bishoy Wadie has joined the channel

Bishoy Wadie (04:09:43): > Hello, I am trying to register but apparently the link expired due to limited seats or something. Does anyone know whether it’ll reopen or not ?

Bishoy Wadie (04:10:25) (in thread): > Same here:disappointed:

Hyun-Hwan Jeong (04:10:42) (in thread): > I have the same problem and reported both registration page and slack but haven’t heard any response yet.

Bishoy Wadie (04:11:01) (in thread): > Yeah,

Bishoy Wadie (04:11:26) (in thread): > I’ve also sent them an email, but I don’t think they’ll respond now as it is still 4 am EST

Bishoy Wadie (04:12:17) (in thread): > I guess we’re gonna have to wait till someone responds. I’ll keep you updated

Hyun-Hwan Jeong (04:12:31) (in thread): > I will do, too. Thanks!

Mariela (05:22:47): > @Mariela has joined the channel

Bishoy Wadie (07:18:29) (in thread): > @Hyun-Hwan JeongThey have reopened registration. You can now register till 5 pm (EST)

Hyun-Hwan Jeong (07:23:03) (in thread): > Thanks for letting me know!

Bishoy Wadie (07:24:50) (in thread): > No problem:slightly_smiling_face:

Vince Carey (08:18:25) (in thread): > although it says “expired” ignore that. just pick the virtual conference rate, select number of tickets, and proceed.

Jennifer Doering (09:59:43): > @Jennifer Doering has joined the channel

Anthony Sonrel (10:13:45): > @Anthony Sonrel has joined the channel

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Shashi Ravishankar (14:45:26): > @Shashi Ravishankar has joined the channel

Gabriel J. Odom (16:56:26): > Can someone point me to a blog post or discussion on how the poster session will happen? Will it be one large Zoom call with breakout rooms?

Spencer Nystrom (17:53:09) (in thread): > “During the poster sessions, presenters should be present in the virtual room for their poster during their entire time slot. Since our videoconferencing platform allows you to be in multiple rooms at once, if you’re not occupied with interested visitors at your poster, you should feel free to visit other posters – just remember to keep your own room open in a separate window and monitor it. When a visitor arrives at your poster, you should politely leave your other conversation to entertain your visitor, much like you would at a real poster session.”

Spencer Nystrom (17:53:25) (in thread): > From the veeeeery bottom of the instructions for presenters page.

Spencer Nystrom (17:55:22): > Is anyone else having issues with their posters showing up in the Bioconductor gateway? Not sure if I uploaded incorrectly, or what. Does it need human approval that hasn’t happened yet?

Brianna Barry (18:28:33): > @Brianna Barry has joined the channel

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Kirill Tsyganov (20:16:42): > @Kirill Tsyganov has joined the channel

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2020-07-21

Manoj Teltumbade (00:14:49): > @Manoj Teltumbade has joined the channel

Helen Horkan (07:27:39): > @Helen Horkan has joined the channel

Matthew McCall (09:03:06): > I think the F1000 Bioc2020 gateway is now working properly. Please let us know if you’re still having issues submitting / viewing the posters.

Will Arnold (09:24:14): > @Will Arnold has joined the channel

Aedin Culhane (12:37:37) (in thread): > The expired options were for the physical conference. Just pick the virtual rate - File (PNG): Screen Shot 2020-07-21 at 12.37.13 PM.png

Aedin Culhane (12:39:48) (in thread): > We are not using zoom for the posters, we are using another platform which allows you to be in >1 room at the same time. You will have a web link to the meeting room for your poster, but will be free to visit other poster rooms during your session

Aedin Culhane (12:40:01) (in thread): > Posters should be uploaded onto F1000 in advance of the meeting

Hyun-Hwan Jeong (12:40:02) (in thread): > I have registered, and at that time when I opened the thread, the virtual conference was also expired. But thanks for letting me know!

Aedin Culhane (12:40:42) (in thread): > seehttps://f1000research.com/gateways/bioconductor?selectedDomain=posters - Attachment (f1000research.com): Posters from gateway Bioconductor - F1000Research > Read the latest peer reviewed Bioconductor articles and more on F1000Research

Aedin Culhane (12:41:39) (in thread): > Hi Spencer I can see your posterhttps://f1000research.com/posters/9-726 - Attachment (f1000research.com): Poster: {memes}: an R interface to the MEME Suite has been published by F1000Research. > Read this work by McKay D, at F1000Research.

Aedin Culhane (12:42:31): > Posters and slides for Bioc2020 -https://f1000research.com/gateways/bioconductor/bioc2020 - Attachment (f1000research.com): Posters from gateway Bioconductor - F1000Research > Read the latest peer reviewed Bioconductor articles and more on F1000Research

Carl McIntosh (12:48:38): > @Carl McIntosh has joined the channel

Philippe Boileau (17:32:14): > @Philippe Boileau has joined the channel

kipper fletez-brant (17:38:59): > sorry to be “that” guy but am I correct that registration is actually closed?

Hyun-Hwan Jeong (17:41:17) (in thread): > I think so, now it says the ticket has been sold out.

kipper fletez-brant (17:43:51) (in thread): > Yes, I see that. I am asking bc this concept is a bit out of place given that this year is purely virtual

Hyun-Hwan Jeong (17:54:50) (in thread): > I am not sure I understand correctly, do you mean you expect you can still register to the conference because it’s virtual?

kipper fletez-brant (17:55:41) (in thread): > It seems weird to me that there is a seat limit in a virtual conference and so I was asking if I was reading it right, or if the website is in error.

Marcel Ramos Pérez (17:56:26) (in thread): > I think the registration cap has been reached.@Erica Feickor@Levi Waldroncan clarify.

kipper fletez-brant (17:57:28) (in thread): > OK, then the website is probably not in error. Thx

Erica Feick (20:58:27) (in thread): > @kipper fletez-brantyes, unfortunately the registration cap has been reached and registration is closed. Due to the large number of workshops we did want to keep the conference to a manageable number.

2020-07-22

Anke Busch (03:54:47): > @Anke Busch has joined the channel

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Dr Isha Goel (09:34:39): > @Dr Isha Goel has joined the channel

Stephanie Hicks (10:36:09): > hi@Erica Feick— is it still possible to test out our slides on the webinar test run today?

Erica Feick (10:36:53): > yes it you want to join now the link I sent should still work.

Stephanie Hicks (10:37:12): > I did click it but it says “Waiting for the host to start this webinar”

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2020-07-23

Mindy (11:29:35): > @Mindy has joined the channel

Spencer Nystrom (16:05:31): > Just an FYI, some of the posters that use a series of slides have been moved to the “slides” section of the gateway, so they don’t appear when using the link in the “Poster Titles” page of the website.

Tania Guerrero (22:27:48): > @Tania Guerrero has joined the channel

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2020-07-24

Johannes Rainer (01:18:19): > @Johannes Rainer has joined the channel

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Robert Castelo (10:48:47): > hi, am i right that in this year’s conference there’s no specific “developers’ day” and that kind of event is just scattered throughout the 5 days of the conference (BoF, etc.)? (just checking, i don’t want to miss anything!!)

Lori Shepherd (10:52:22): > yes.

dnusskern (15:05:49): > @dnusskern has joined the channel

Christopher Eeles (15:09:55): > Does anyone know if poster presenters join the virtual discussion room using the same Jitsi Meet link as the attendees, or is there something I am missing?

Sean Davis (15:19:13) (in thread): > Same link.

Christopher Eeles (15:19:46) (in thread): > Good to know, thanks@Sean Davis

2020-07-25

Levi Waldron (02:12:05) (in thread): > Only difference is, whoever is in the room first assumes “moderator” powers, so it would be a good idea for the poster presenter to enter early.

2020-07-26

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2020-07-27

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Jeroen Gilis (04:45:09): > Hi all, > On July 16th I successfully made the payment for the “Virtual Conference Rate - All Attendees” option. However, I did not receive an email frompathable.comwith my login information to the virtual platform. Does anybody know who I should be in contact with for this? > King regards

Shila Ghazanfar (04:47:11): > @Shila Ghazanfar has joined the channel

Charlotte Soneson (04:49:44) (in thread): > I can see you in the backend among the list of participants. However, your email address looks wrong (I suppose it should be spelled like your name here?), so I think this is why you didn’t receive an email. Could you send your correct email address to me in a private message, then I’ll try to fix that before the start of the conference today.

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Nitesh Turaga (09:14:21): > <!here>People who are wondering where the “chat” is, it is available in the pathable link for this specific talk.

Erica Feick (09:15:40): > If you are on the pathable platform, the chat should be the the right of the video.

Kevin Rue-Albrecht (09:16:14): > Fig. 1 - File (PNG): image.png

Lori Shepherd (09:21:42): > <!here>Don’t be discouraged if you get an error at the start of a meeting saying “Meeting has not started” if you wait a few moments and hit retry it should eventually let you in via pathable rather than having to switch directly to zoom. For those of you that have used zoom before it is similar to a “waiting room” where the meeting hasn’t officially started.

Ameek Bhalla (09:32:53): > @Ameek Bhalla has joined the channel

Kevin Rue-Albrecht (09:47:18): > Small technical point: in the Polls, if I start a question and change my mind, there is no way to “cancel”, only “submit”. Which is turning into a series of empty questions as per Fig 2 - File (PNG): image.png

Kevin Rue-Albrecht (09:47:57) (in thread): > Now I can see this, and my empty question - File (PNG): image.png

Izabela Mamede (09:59:45): > @Izabela Mamede has joined the channel

Levi Waldron (10:40:53) (in thread): > One of the moderators or administrators can delete these, which is I guess all we can do. At least, they should stay at the bottom as long as every other question has one upvote.

Leonardo Collado Torres (10:48:08): > Hi! How do attendees know which poster presenters will be available in each of the sessions?

Nathan Sheffield (11:03:07) (in thread): > The posters are assigned to sessions. All the presenters have been asked to be available for their assigned session.

Leonardo Collado Torres (11:18:35) (in thread): > Hm…. I filled the google form to select one session but I don’t have any emails detailing whether the session I preferred was the one I got assigned to (maybe I missed it, sorry!). Though thanks to your message, I found the info athttps://posters.bioconductor.org/Bt7b1YCXccGupnIjMgF80EXuxo9coP9oXKW98GnH:smiley:

Nathan Sheffield (11:21:50) (in thread): > Glad you got it. Everyone was assigned the poster session they requested.

Nathan Sheffield (11:22:37) (in thread): > I think we probably didn’t make that clear enough, sorry about that!

Hervé Pagès (11:23:09): > @Hervé Pagès has joined the channel

Kevin Rue-Albrecht (11:28:04): > I’ve run into an issue: I accidentally launched the wrong workshop (Bioc2020Anno), instead of the “Public data resources in Bioconductor”. Now when I got back and select the “good” workshop, it still takes me to the cloud instance of the “wrong” one. Any idea how I can “reset” my cloud instance to go to any other workshop than the “active” one?

Mike Smith (11:46:34) (in thread): > I guess this is what Levi was alluding to when he suggested using a private browser window for each workshop.

Kevin Rue-Albrecht (11:47:17) (in thread): > Ahhh I didn’t hear the “private”

Nolan Nichols (11:48:27): > @Nolan Nichols has joined the channel

Mike Smith (11:50:04) (in thread): > I assume it’s some sort of cookie/session info that keeps sending you back to the original session.

Sean Davis (12:04:15) (in thread): > For those who might have had the same problem as Kevin, that was a bug in the workshop platform that should be fixed. Sorry about that.

Kevin Rue-Albrecht (12:04:56) (in thread): > No worries - Finding tiny bugs is a skill on my CV

Sean Davis (12:06:21): - Attachment: Attachment > For those who might have had the same problem as Kevin, that was a bug in the workshop platform that should be fixed. Sorry about that.

Leonardo Collado Torres (12:06:56) (in thread): > ahh no worries, thanks:smiley:

Sean Davis (12:06:56) (in thread): > That one was a little larger than tiny. I introduced that this morning.

Matt Paul (12:12:39): > @Matt Paul has joined the channel

Corina Lesseur (12:50:35): > @Corina Lesseur has joined the channel

Aedin Culhane (12:58:39): > @Atul Deshpandeand@Dan Bunisdiscussion on creating figures that work for color blind individuals.  The google doc is athttps://docs.google.com/document/d/1qCYv4vfBeKMTNMf1m6TgRvo9dyfmbR7qx772dHiuX5M/edit#heading=h.8l5xrpwd5sqd

Ray Su (13:25:39): > @Ray Su has joined the channel

Sridhar N (13:56:39): > @Sridhar N has joined the channel

Ana Beatriz Villaseñor Altamirano (17:24:52): > @Ana Beatriz Villaseñor Altamirano has joined the channel

Martin Morgan (20:59:39): > The end of the annotation workshop saw a question about (what I heard the question as…) ‘how to extract the first, and all but the first, intron from a list of introns by transcript’. For some definition of first, the easy answer (after thinking about it for four hours…) is > > introns <- intronsByTranscript(TxDb.Hsapiens.UCSC.hg38.knownGene) > heads(introns, 1) > tails(introns, -1) > > !@Aaron Lun@James MacDonald(the latter may not be a real slacker)

2020-07-28

Johannes Rainer (02:28:31): > In the annotation workshop there was also a question about getting annotation resources for non-standard species (such as bacteria, plants etc). If your species is available inensemblgenomesit is possible to create aEnsDbannotation database for it (which contains likeTxDbresources the genomic coordinates of genes, transcripts and exons and in addition also mapping to gene names, symbols, gene biotypes, description, protein and protein domain annotations). Send me a message if you need anEnsDbfor one of these non-standard species and I’ll create it. Note: all species that are listed in Ensembl core are available throughAnnotationHub.

Will Arnold (07:28:27) (in thread): > Thanks! That was me. This is very helpful! I had previously struggled with this during my PhD work and was just wondering if there was a way through the demo’d process. I eventually ended up merging the gffs from NCBI with the genome fasta to pull transcripts through the RSEM functionality but always struggled to properly reannotate the transcript IDs with gene IDs in the downstream analysis.

Anabella (08:20:56): > @Anabella has joined the channel

rohitsatyam102 (08:27:51): > @rohitsatyam102 has joined the channel

joost groot (08:59:29): > @joost groot has joined the channel

Regina Umarova (09:02:36): > @Regina Umarova has joined the channel

jackgisby (09:06:35): > @jackgisby has joined the channel

Marcin Kaszkowiak (09:47:59): > @Marcin Kaszkowiak has joined the channel

Mikie Phan (09:48:14): > @Mikie Phan has joined the channel

Zuzanna Nowicka (09:49:13): > @Zuzanna Nowicka has joined the channel

Ameek Bhalla (09:59:17): > When the session hosts delete answered questions they become unavailable for people who playback the videos later. Instead of deleting the answered questions outright from the ‘Polls’ if the session hosts copy them into the ‘Chat’ window then they will remain available for people who playback the videos later.

Marcel Ramos Pérez (10:01:30): > They’re not deleted only hidden. They can be made visible by hosts after the session.

Mirko Signorelli (10:04:42): > @Mirko Signorelli has joined the channel

syliu (10:12:34): > @syliu has joined the channel

Yuri Kotliarov (10:20:29): > @Yuri Kotliarov has joined the channel

Levi Waldron (10:39:01) (in thread): > I think they’re unhidden now.

James MacDonald (10:50:19) (in thread): > Ah,heads, nothead! Nice. I came up with > > unlist(introns)[!duplicated(rep(1:length(introns), lengths(introns)))] > > Which produces the same output as > > unlist(heads(introns,1)) > > With, like, more typing involved…

James MacDonald (10:57:55) (in thread): > @Martin MorganBothheadsandtailsare apparently undocumented functions (andlengthsseems to use the base version? Those are super useful functions, and there might be more lurking about. Is this a documentation oversight, or is there a listing somewhere that people can reference for these ‘add an s to existing functions for extended capabilities’ type things?

Johannes Rainer (11:27:00) (in thread): > In theensembldbvignette there is a short description how to do that (seehere) - but that’s a little tricky because you have to install the Ensembl Perl API, BioPerl and set up a MySQL server. I have however all installed on my computer(s) and have the scripts ready to createEnsDbresources for any species available either in Ensemblgenomes or Ensembl core. So, it is possible (for advanced users) - and all thanks to the excellent work from Ensembl:slightly_smiling_face: - Attachment (jorainer.github.io): Generating an using Ensembl based annotation packages > ensembldb

Alejandro Reyes (12:29:31): > @Alejandro Reyes has joined the channel

Nathan Sheffield (12:56:10): > What ‘python integration’ was@Aaron Lunreferring to?

Marcel Ramos Pérez (12:56:59): > Perhaps thebasiliskpackage?https://bioconductor.org/packages/release/bioc/html/basilisk.html

Nathan Sheffield (12:58:00): > Ah. So is the difference fromreticulatethat it embeds python, rather than using the one on the PATH ?https://rstudio.github.io/reticulate/ - Attachment (rstudio.github.io): Interface to Python > Interface to Python modules, classes, and functions. When calling into Python, R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types. Compatible with all versions of Python >= 2.7.

Henrik Bengtsson (12:58:07): > @Henrik Bengtsson has joined the channel

Dan Bunis (13:00:19): > I’m not sure the specific difference/implementation, but I believe basilisk utilizes reticulate internally and basically sort of helps make the connection more stable.

Dan Bunis (13:00:35) (in thread): > cross-posting from#diversebiocfor visibility for anyone interested in continuing the discussion “On Standards for Accessible and Interpretable Visualizations” with a practical focus on how we might implement some of the concrete ideas from the previous session. > The new session will beThursday at 4pm.https://community-bioc.slack.com/archives/CL21357E2/p1595874742034700 - Attachment: Attachment > Sounds like there’s a lot of interest in some sort of ‘practical’ followup to the discussion from earlier. Atul and I would love to have another session later in the conference where anyone interested could gather to discuss some concrete plans. He and I just discussed a few ideas that we have, and here’s the sort of structure we think might work best for the session. > > Session structure: > 1. A few slides giving overview of a few ideas that might “easily” achievable ideas, > 2. Some joint brainstorming: What of these ideas are most achievable? What can we actually do? > 3. Breakout sessions, perhaps one for each idea, to see if we can create some concrete implementation plans > Potentially achievable goals we’ve come up with so far: > • A check of accessibility compliance in BiocCheck > • Default colors - how to make accessible palettes more commonly the default > • A color version of “ggrepel” where colors that are too similar are made more distant > • automated generation of Alt Text - perhaps a basic text description which might encourage people to fill these in > • new visualization possibilities (augmenting with non-color) — example Atul’s > • A set of resources / guidelines that could be posted somewhere in the Bioconductor website > Totally open to suggestions for both structure and individual ideas! If you’d like to suggest anything, you can do that either here or in the googledoc shared above. I’ve copied these examples in towards the bottom of the doc.

Mikhael Manurung (13:58:43): > Will the videos remain to be available after the seminar ends?

Devika Agarwal (13:59:31): > how do we get some stickers?

Devika Agarwal (14:01:12): > i want a holo iSee sticker:slightly_smiling_face:

Marcel Ramos Pérez (14:01:32) (in thread): > Yes, for up to one year

Federico Marini (14:02:27): > Hi@Devika Agarwal, just DM me an address and I’ll be happy to send it over to you!

Kevin Rue-Albrecht (14:02:45): > @Federico Marinidon’t worry, she’s a colleague

Kevin Rue-Albrecht (14:03:15): > I just haven’t met her in person since I started in the same group in April:laughing:

Federico Marini (14:03:17): > Oh awesome:slightly_smiling_face:

Federico Marini (14:03:24): > oh. Less awesome

Devika Agarwal (14:03:37): > COVID-19 problems sadly

Kevin Rue-Albrecht (14:04:50): - Attachment: Attachment > Oxford people: I got stocks

Kevin Rue-Albrecht (14:05:29): > (Cambridge too, if they dare come to the dark side)

Federico Marini (14:07:02): > You said the C-word

Federico Marini (14:07:09): > :smile:

Aaron Lun (14:42:59): > @Aaron Lun has joined the channel

Lucy (14:50:11): > @Lucy has joined the channel

Lucy (14:51:06) (in thread): > Save one for me Kevin!

Aedin Culhane (15:00:09): > Questions for@Kylie Bemis

Aedin Culhane (15:00:10): > * What’s the spatial resolution of MSI? > * What is your recommended strategy for breaking a file/files up into atoms? > * Can you explain more about the PCA and how it was so fast > * Since it is file-based and it already has a C++ backend, do you plan any kind of interoperability with other programming languages? > * Have you tried it on mzML files with Numpress compression? > * how fast is random access operations ? > * Do it support polygon spatial representation

Kylie Bemis (15:02:27) (in thread): > * Spatial resolution of MSI can be down to 1 micron, but more often 10-100 um or so

Kylie Bemis (15:03:22) (in thread): > * Atoms should match the file structure. For us, in imzML, each atom is an m/z array or intensity array of a mass spectrum.

Kylie Bemis (15:05:47) (in thread): > * The PCA is implementation simple straightforward C++ implementation, and could probably be improved much more. The reason it was faster than bigmemory was that the data files were larger than computer memory, and bigmemory’s reliance on mmap leads to keeping too much data in memory and struggling with I/O, while matter was only reading small portions of data at a time, so could be more efficient

Kylie Bemis (15:07:05) (in thread): > * Unfortunately, it would be difficult to port matter to other languages primarily due to some special handling of R-specific things like NAs and double-based indexing (no 64-bit int). Would be very possible, but that’s probably a project for someone else to take up

Kylie Bemis (15:07:59) (in thread): > * Haven’t tried straight-up mzML files due to different handling of binary data (usually embedded in XML). But generally speaking, matter won’t work on compressed files (unless you uncompress them first).

Kylie Bemis (15:08:45) (in thread): > * Random access is about as fast as it can realistically be, but as always is bound by I/O speeds – good SSD is preferred.

Kylie Bemis (15:09:57) (in thread): > * Polygon spatialrepresentation… inCardinal I’m assuming? Unsure exactly what is meant here, but if I understand correctly, then yes, MS images in Cardinal can be any shape.

Kylie Bemis (15:10:09) (in thread): > Thanks everyone!

Aedin Culhane (15:19:21) (in thread): > Kylie, the last question reply include a link to a wesite (probably a slack thing), might be good to remove as I don’t think its related to your reply

Aedin Culhane (15:20:06) (in thread): > With the resolution question (1 micron, but more often 10-100 um or so).. how many cells is that?

Kylie Bemis (15:38:24) (in thread): > Removed preview, but not sure how to remove link… Slack made it automatically

Kylie Bemis (15:39:47) (in thread): > Depends on the size of the cells, but can be single cell resolution. Most MSI experiments aren’t at this resolution though since it’s very difficult and time-consuming. More often a rougher spatial resolution is done in combination with microscopy for finer details

CristinaChe (16:19:54): > General question: for how long will be the recordings available on the pathable platform after Friday? Thanks a lot!

Marcel Ramos Pérez (16:25:37): > For about a year AFAIK

Aedin Culhane (16:29:11): > (Sorry Marcel, what is AFAIK.. as far as I know? (

Marcel Ramos Pérez (16:29:52): > Yes

CristinaChe (16:31:23): > Thanks!

Rajiv Kumar Tripathi (16:33:32): > @Rajiv Kumar Tripathi has joined the channel

Levi Waldron (16:57:18): > Confirming, about a year.

Spencer Nystrom (18:29:59): > Quick question: when providing the link to slides in the lightning talk form, does that lock those slides in for the presentation? If not, I would apply now and finish some formatting things if accepted.

Mikhail Dozmorov (19:16:22): > @Spencer Nystrom, please, apply. It is perfectly fine to continue improving the slides.

Haibo Liu (22:30:26): > @Haibo Liu has joined the channel

beyondpie (22:58:12): > @beyondpie has joined the channel

2020-07-29

Shian Su (04:23:33) (in thread): > Hey@Kylie Bemis, really great talk, and sorry for the delayed question. When performing simple ops like adding two matrices together, is a new disk file created to represent the results? If so, are these cleaned up as the variables drop out of scope, or according to regular R temp file clean-up rules?

Mirko Signorelli (04:44:57) (in thread): > @Federico MariniiSEE that you are the sticker pusher also here!

Federico Marini (04:51:35) (in thread): > Hell yeah:slightly_smiling_face:

Devika Agarwal (08:28:02) (in thread): > btw can i@Federico MariniDM you my address for the other stickers i want or do we need to write to package developers for specific stickers?

Federico Marini (08:35:48) (in thread): > I just have some for my own (iSEE and GeneTonic, plus a handful for ExploreModelMatrix, with@Charlotte Soneson,@Michael Love,@Michael Stadler). The “generic” ones might need to be retrieved otherwise:wink:

Federico Marini (08:38:10) (in thread): > Stickermule has every now and then some promos, you can grab the pdf/ hi res png from the BiocStickers repo:https://github.com/Bioconductor/BiocStickers

Marc RJ Carlson (08:42:56): > @Marc RJ Carlson has joined the channel

Aedin Culhane (09:14:25): > Unanswered poll questions from the CAB session this morning > * Are there rules for the use of the Bioconductor Logo or name for conferences and other activities? > * How is CAB promoting Bioconductor to biologist who doesn’t have any programming background? > * Are there specific scholarships encouraging people from underrepresented groups to attend BioC events? > * If I was nominated, how we find out who nominated us?

Johannes Rainer (09:21:47): > Regarding the rules for the use of Bioc logo and name: best is to ask for permission (seehere) the name and logo are under copyright. Note that most Bioc Stickers list their license in the README, e.g. for theBioC2020sticker. Most are under CC-BY, but it is always good to contact the designer.

Lucy (09:28:48): > How can we get hold of#bioc2020stickers? I am really excited to decorate my laptop!

Aedin Culhane (09:46:01): > Participants in#bioc2020will be mailed a sticker. You can get the image file for#bioc2020, Bioc diversity stickers and package stickers in the Biosticker repository (https://github.com/Bioconductor/BiocStickers). The Bioc2020 sticker is athttps://github.com/Bioconductor/BiocStickers/tree/master/events/Bioc2020. We normally order stickers from Stickermule, a link to the die cut stickers ishttps://mule.to/pdk - Attachment (Sticker Mule): Die cut stickers | Free shipping > Custom die cut stickers are a fast and easy way to promote your business, brand or event. Thick, durable vinyl protects your stickers from scratches, water & sunlight. Get your die cut stickers fast with free proofs, 4 day turnaround & free worldwide shipping.

Aedin Culhane (10:36:16): > Q&A - How is CAB promoting Bioconductor to biologist who doesn’t have any programming background? This is a good questions, currently there are resources on the website, but we need community input to find out whats needed.@Laurent Gattoand others are now Carpentry trainers and hope to develop beginner bioconductor training materials. Please reach out to#community-advisory-board. We are listening and want to hear what you need

Aedin Culhane (10:37:12): > We had 52 responses in the poll that was undertaken during the CAB session and these are the results - File (PNG): Screen Shot 2020-07-29 at 9.06.54 AM.png

Aedin Culhane (10:40:33): > Q&A- Are there specific scholarships encouraging people from underrepresented groups to attend BioC events? Bioc2020 had provide scholarships and we positively consider caregiver and diversity requests. We try to fund as many scholarships as we can, and conferences break even.

Aedin Culhane (10:42:19): > Q&A If I was nominated, how we find out who nominated us? Anyone could nominate a person for an award. There was a public google form. I could be wrong, but I think nominations could be anonymous.@Simone Belland@Charlotte Sonesonmight be able to tell you more about the process.

Aedin Culhane (10:42:52): > If I haven’t answered questions. please reach out to#community-advisory-boardchannel

Kevin Rue-Albrecht (11:01:37): > Fresh feedback for pathable: it’d be nice if on the page of each talk/session, there were links to the ones immediately after, save participants a trip to the agenda page, which seems to get stressed every hour:laughing:(it takes a while to load, and I assume this comes from all he participants simultaneously loading their agenda at the same time)

Leonardo Collado Torres (11:19:49) (in thread): > I tried to avoid this bottle neck by pre-loading the next session like 20 mins before. By that I mean opening the pathable link for the next session on a new tab

Aedin Culhane (11:28:34): > The form for submitting a lightning talk is open… Submit a lightning talk athttps://forms.gle/n2xsTYER4mWLugNh9(you just need a link gdrive/dropbox/web to slides and a title). 4 min talk..

Ayush Aggarwal (11:48:39): > @Ayush Aggarwal has joined the channel

Ayush Aggarwal (11:51:48) (in thread): > Yes, and it’s the same for the workshops also so I load them before the next workshop and it works great:smiley:.

Levi Waldron (12:07:03): > Trying to make an easier way to schedule R/Bioconductor helpdesk and any spontaneous meetings:https://bit.ly/letstalkbioc2020. Also there’s a poster session now athttps://posters.bioconductor.org/Bt7b1YCXccGupnIjMgF80EXuxo9coP9oXKW98GnH, with links to meet each poster presenter. - Attachment (Google Docs): Let’s talk! BioC2020 > Sheet1 Poster area link,What’s the topic?,This page:,https://bit.ly/letstalkbioc2020,Notes:,For more rooms, just invent any URL starting with https://meet.biocondu…

Levi Waldron (12:08:43) (in thread): > (this post will self-destruct in ~10 minutes!)

Jeroen Gilis (12:09:59): > At the moment, the “join live discussion” button at the poster session is not functioning; will they open later or is there a problem from my side?

Federico Marini (12:10:17): > I’m also not able to hear/see anything

Federico Marini (12:11:19): > I’m for example also in Sonali’s room where you’re in Levi, but can’t do anything

Federico Marini (12:12:05): > Could be because of ports being blocked by my university medical center?

Levi Waldron (12:13:54): > Oh dear, I don’t know @Nathan Sheffield? It is working for me which makes me think firewall.

Nathan Sheffield (12:14:21): > It’s working for us in Tania’s poster room

Jeroen Gilis (12:14:28): > Based on what I see on my part, I also think firewall related issues. Will try to find a fix

Federico Marini (12:14:29): > Could well be the firewall

Federico Marini (12:14:33): > ¯*(ツ)*/¯

Federico Marini (12:14:59): > Silver lining: hi there@Jeroen Gilis:smile:

Nathan Sheffield (12:16:37): > try using chrome ?

Jeroen Gilis (12:17:34) (in thread): > Hmm yes I’m already on chrome I’m afraid. Tried safari now (against common sense); didnt solve it

Levi Waldron (12:17:43) (in thread): > Did you try making a cart, that gives you direct links to the rooms for all posters you select?

Nathan Sheffield (12:19:03) (in thread): > try reloading the page

Levi Waldron (12:19:15) (in thread): > Try a VPN? I turn on Tunnelbear whenever a university firewall blocks me…

Levi Waldron (12:19:32) (in thread): > too bad because these poster rooms are super cool

Federico Marini (12:24:15) (in thread): > same here.

Federico Marini (12:24:37) (in thread): > no clue about that

Federico Marini (12:24:42) (in thread): > I’ll check it out

Levi Waldron (12:24:58) (in thread): > Any VPN with a free trial

Sonali (12:28:19): > I had some issues with chrome , it kept on crashing on me when I tried sharing my screen.. It started working after a few mins . Thanks@Levi Waldronand@Federico Marinifor stopping by.

Erica Feick (12:30:15) (in thread): > that is good feedback and I will pass it on to Pathable!

Federico Marini (12:30:28) (in thread): > THE HELL:stuck_out_tongue:The VPN of my own uniunblocks it

Levi Waldron (12:30:45) (in thread): > :joy:

Jeroen Gilis (12:41:24) (in thread): > I moved from work address to home address; still not functioning! (unexpected)

Nathan Sheffield (12:46:09) (in thread): > Does it work for you athttps://meet.jit.si/? - Attachment (meet.jit.si): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Federico Marini (12:49:26) (in thread): > wish I could let you use my POWERFUL UNI VPN:stuck_out_tongue:

Michael Love (13:00:07): > poster session worked well i think

Michael Love (13:00:14): > thanks to those who set it up

Nick Owen (13:01:04): > @Nick Owen has joined the channel

Charlotte Soneson (13:01:38) (in thread): > The identity of the nominator was not used or revealed at any stage in the evaluation process, except as a form of verification that the nomination came from an actual person.

Levi Waldron (13:02:16): > The poster session was so cool!

Levi Waldron (13:02:38): > That was all@Nathan SheffieldSheffield’s work!

Nathan Sheffield (13:16:13) (in thread): > I had to open port 10,000 UDP on the AWS instance, so it could be that if the firewall blocks that port, it would prevent it from working…

Nathan Sheffield (13:16:33) (in thread): > Also it uses TCP 4443

Levi Waldron (13:17:04) (in thread): > I can see the paranoid sysadmin shaking their head…

Freeman Wang (13:24:33): > @Freeman Wang has joined the channel

Leonardo Collado Torres (13:27:05): > Hi! FYI For those of you presenting posters later in the conf, make sure that you copy the chat before you close the window. I can’t see it anymore after rejoining.@Ameek Bhallahad sent me some links that I lost (luckily I remembered Ameek’s name). > > Also, I wasn’t sure if we were supposed to record the poster sessions. I did hit the record button once on the platform but I got an error message and forgot about it after that.

Leonardo Collado Torres (13:27:34) (in thread): > Ameek, can you resend me the links again please? Thanks!

Nathan Sheffield (13:27:42) (in thread): > Not all my work! Lots of input and suggestions and testing from many members of the organizing committee

CristinaChe (13:49:15): > The poster session has been super-interesting! Thanks to all the presenters!

Lluís Revilla (13:49:41) (in thread): > I think the question is not if it was used, but to thank people that nominated others

Leonardo Collado Torres (14:29:27): > I kind of wished we had some pre-scheduled breaks:stuck_out_tongue:I know that videos will be available and I can always catch up later, but well, my brain just spaces out here and there. > > Also, I don’t know if the webinars can be shown using HD (it’s a Zoom setting).

Aaron Lun (14:30:01): > I wish we had catered uber eats delivered to my door.

Leonardo Collado Torres (14:30:07): > hehe, at least some cookies:stuck_out_tongue:

Aaron Lun (14:30:44): > I can’t eat my award, leo!

Leonardo Collado Torres (14:31:01): > well, we wanted it to last haha (says so without having being involved in choosing the award: that was all Simone and Charlotte, great job too!)

Sonali (14:36:23) (in thread): > @Leonardo Collado TorresMe too! Also, number of coffee’s go up post lunch break .. That said, its really great that I can attend all talks this time, and dont have to choose..

Leonardo Collado Torres (14:56:15) (in thread): > aye, not having to choose is great! But my attention span takes a hit later in the day

Leonardo Collado Torres (14:56:41) (in thread): > coffee, now that’s something I hadn’t though about and that I likely need now:stuck_out_tongue:

Tania Guerrero (15:09:15) (in thread): > If it wasn’t for my issue sharing the screen which I kinda solved too late. Thanks for your patience and interest:grin:

Charlotte Soneson (15:18:08) (in thread): > Right. This is not a trivial topic (given power differentials, various types of potential associations between nominator and nominee, privacy, …), and thus we decided to not share this information, but rather leave it up to the individual nominator if they want to reveal their identity to the nominee. (Note that in particular, the privacy statement in the nomination form says that the provided personal information will not be shared outside the committee).

Aaron Lun (15:35:20): > aaah the soothing sounds of the best accent ever

Matthew McCall (15:36:00) (in thread): > Have a feeling this comment isn’t about the moderator

Leonardo Collado Torres (15:54:33) (in thread): > hehe, nor about the CDSB BoF speakers:stuck_out_tongue:

Aedin Culhane (16:34:11) (in thread): > You could try but you might have a dentist bill !

Ellis Patrick (16:46:24) (in thread): > as soothing as a chainsaw….

Aedin Culhane (17:26:31): > Great to see you here. I know the Boston Bioc meetups are are hold. How are things. Did you post yours positions in the#jobs#bioc2020board - Attachment: Attachment > Hello all. I’m Matt Brauer, head of Data Science at Maze Therapeutics. Maze is a startup biotech founded by such luminaries in the fields of functional genomics and genetics as Steve Elledge, Jonathan Weissman, Mark Daly, Sek Kathiresan and Aaron Gitler. We’re reducing a lot of their labs’ advances to practice, in the service of discovering meaningful medical advancements in difficult diseases. My group is looking for an accomplished computational biologist/bioinformatics scientist to join our team, and have a job posted on the job board. Please check it out!

Aedin Culhane (17:32:54) (in thread): > Nathan,@Aaron Lunpresented a talk bout basilisk in the#developers-forummaybe 5 months back. The session was recorded and should be on the bioconductor youtube channel.https://www.youtube.com/user/bioconductor/videos@Mike Smithwill know which one - Attachment (YouTube): Bioconductor > Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and…

Riyue Sunny Bao (17:36:24): > @Riyue Sunny Bao has joined the channel

Randall Johnson (18:01:29): > @Randall Johnson has joined the channel

Yoichiro Ohne (18:20:25): > @Yoichiro Ohne has joined the channel

Lambda Moses (22:15:12): > @Matthew McCallEarlier you asked me what surprised me the most from my “sociological” study of spatial transcriptomics literature. Now I recall a few more things and can give you a better answer. > 1. I thought single cell + transcriptome wide was the way to go and was surprised that non-single-cells methods, such as array and microdissection methods were more popular. I was also surprised when I realized that laser capture microdissection (LCM) and Tomo-seq are still used in quite recent preprints while I thought the single cell resolution methods reaching 10000 genes and array based methods with higher resolution rendered those methods with lower resolution obsolete. Nor do I see any sign of LCM dying. > 2. Most R packages (or packages that involve R) dedicated to spatial transcriptomics data analysis are not (yet?) on CRAN or Bioconductor, some of which aren’t new. > 3. Only a few spatial transcriptomics technologies spread beyond their institutions of origin.

Matthew McCall (23:00:08) (in thread): > Thank you so much for the thoughtful follow-up! Those are really interesting and important insights. Points 2 & 3 are definitely areas to seek improvement.

Lambda Moses (23:03:58) (in thread): > I’m still working on the paper for this; I’ll elaborate more in the paper.

Lambda Moses (23:18:35) (in thread): > For point 3, here are my speculative reasons: a possible reason why ST and Visium spread far and wide (though Lundeberg himself is still involved in most ST studies) is commercialization. I also think a probably top reason why LCM is so widespread is that many institutions have LCM core facilities that use commercial LCM equipment so doing LCM isn’t difficult. It’s just like while I can make tortilla chips at home, I still prefer to buy tortilla chips, because making tortilla chips takes specialized equipment (tortilla press), a lot of work, and some trial and error to get it right, but nevertheless, commercial tortilla chips taste just fine. Another reason is probably collaboration within institutions and that it’s easier to get help and training from the lab that developed the technology when that lab is only walking distance away; in person interaction is very helpful for wet lab.

2020-07-30

Sachendra Kumar (01:37:05): > @Sachendra Kumar has joined the channel

Hervé Pagès (02:41:49) (in thread): > also please save a Diablo III tablecloth for me Kevin! Thx

Kevin Rue-Albrecht (03:10:15) (in thread): > Hahaha, I love that game! in the rush of the moment this time I didn’t « blank » the photo area, leading to shameless advertising:yum:

Nastasja (03:28:13): > @Nastasja has joined the channel

Hervé Pagès (03:33:44) (in thread): > I’d say good you didn’t blank it, the picture looks better like that.:yum:

Ameek Bhalla (07:20:27) (in thread): > Sending you a direct reply.

Matthew McCall (07:50:07) (in thread): > Do you think you could confirm / disprove your speculations through a survey? Another reason for 3 could simply be: “The person I know that knows the most about this subject told me I should use XXX.” Where XXX is often the technology the responder developed. I’m reminded of an analysis I saw years ago where they looked at citations within and between universities. If I recall correctly, there were a few places that had a strong bias to cite work from their own institution.

Leonardo Collado Torres (08:56:07) (in thread): > ahh, it’s closed now, oops:sweat_smile:

Nitesh Turaga (12:13:56): > Lunch with core team link:https://pathable.zoom.us/j/95005217841?pwd=UmdSWU5sMzBCQmFORVZSSHJlRVhCQT09

Tim Howes (12:30:08): > @Tim Howes has joined the channel

lu wang (12:43:52): > @lu wang has joined the channel

Sidharth Sen (13:09:06): > @Sidharth Sen has joined the channel

Selvi G (13:18:34): > @Selvi G has joined the channel

Selvi Guharaj (13:18:51): > @Selvi Guharaj has joined the channel

Aedin Culhane (15:00:32): > Resources from Shirley Liu’s talk - File (PNG): Screen Shot 2020-07-30 at 2.54.16 PM.png

Lambda Moses (16:15:07) (in thread): > I think a survey can help

Antonio Colaprico (16:28:00): > @Antonio Colaprico has joined the channel

Dan Bunis (17:03:37): > Thanks for another great discussion in on improving accessibility of visualizations at the followup BOF session just now! To help push our ideas along and continue discussions further, I’ve just created a#accessible-vischannel.

Vivek Das (17:41:29): > I missed this one@Dan Bunis:disappointed:

Aedin Culhane (17:41:38): > Anyone want to hang out/chat.  Pop intohttps://meet.bioconductor.org/yEoLukjsyI - Attachment (meet.bioconductor.org): Jitsi Meet > Join a WebRTC video conference powered by the Jitsi Videobridge

Dan Bunis (17:46:02) (in thread): > It was recorded! But you can also join in on the discussion in the new channel.

Aedin Culhane (18:17:11): > Everyone welcome

Levi Waldron (18:31:21): > Happy hour athttps://meet.bioconductor.org/yEoLukjsyI!

Connie Li Wai Suen (20:27:11): > @Connie Li Wai Suen has joined the channel

Aaron Lun (23:55:01): > listening to Shirley’s keynote as my BGM while writing unit tests

2020-07-31

Marko Zecevic (03:55:48): > @Marko Zecevic has joined the channel

Michael Love (07:39:45): > @Federico Mariniand@Charlotte Soneson- watching the sessions i missed yesterday and seeing that you looked if i were there:scream:i had kid duty at the time. glad everything is recorded tho:laughing:this is a great session

Charlotte Soneson (07:41:26): > Ah yes, we were talking about prolific contributors to the F1000 Bioc workflows:star-struck:

Michael Love (07:41:59): > yeah I’m a big fan of the workflows… honestly i have no idea how they will be viewed wrt promotion

Michael Love (07:43:36): > i think what really helps is when main contributors to the field are agreeing to be peer reviewers, which seems to be the case now

Michael Love (07:45:05): > but if you can’t get more than 1-2 reviewers, or if the only reviewers who accept are somewhat outside of the field, then the value of the workflow pub may be lessened

Kevin Rue-Albrecht (07:50:32): > Getting ready for happy hour! - File (JPEG): Image from iOS

Michael Love (07:51:20) (in thread): > is this a brand new grill? or you just keep it super clean?:smile:

Kevin Rue-Albrecht (07:51:44) (in thread): > 4 bbq’s so far - it’s unit tested each time

Federico Marini (08:09:02) (in thread): > mine did not look like that after 4 rounds

Federico Marini (08:09:13) (in thread): > guess it is the 1st-bump-in-the-car principle

Kevin Rue-Albrecht (08:09:40) (in thread): > exactly - cleaning time already got halved after a couple of uses

Emma Jablonski (09:04:54): > @Emma Jablonski has joined the channel

Zachary Brehm (10:07:12): > @Zachary Brehm has joined the channel

Shian Su (11:00:01): > Thanks whoever pointed out the error in my errors.

Matthew McCall (11:03:34) (in thread): > I really liked the thoughtful way you handled that question in the moment.

Shian Su (11:05:24) (in thread): > I secretly looked at the polls when question time started.:shushing_face:

Matthew McCall (11:05:41) (in thread): > Very saavy!

Hector Climente (13:14:24): > @Hector Climente has joined the channel

bogdan tanasa (13:55:01): > @bogdan tanasa has joined the channel

Kirk Reardon (14:04:10): > @Kirk Reardon has joined the channel

Aedin Culhane (14:04:33): > Questions for Matt from the lightning talk session: Matt, how does your workflow work with R scripts + Rmd? How do you determine run order?

Aedin Culhane (14:05:15): > Questions for Robert from the lightning talks sesssion > * does converting a tool that wasn’t previously present in R/Bioconductor with some additional functionality count as a package? > * could you talk about the strategy of moving Imports to Suggests for special functionality (I have used this myself a number of times -Mike L) > * breaking up a package into the computation and visualization portions, feels to me like saying that the computational part is the more important one and takes priority in fixing over the visualization side. Since if an upstream graphical dependency break, you are supposed to fix your downstream package (whether it’s one big one or two small ones). Or what do you think? (Q by LCT)

Robert Castelo (14:11:16): > Here are my answers to the pending questions about my talk on today’s lightning session: > > does converting a tool that wasn’t previously present in R/Bioconductor with some additional functionality count as a package? > I would say YES! Sometimes there may be useful methods or algorithms that for whatever reason are not well implemented or maintained, or implemented outside the R/Bioconductor ecosystem and it would be useful to have them in this ecosystem as an R/Bioconductor package. > > could you talk about the strategy of moving Imports to Suggests for special functionality (I have used this myself a number of times -Mike L) > In my opinion this is a good strategy for functionality that is used not that often. At the moment that the user calls that functionality, the package issues an error saying that the user should install A, B, C to be able to call that functionality. The earliest account that I have from such an strategy is theduplicateCorrelation()function in thelimmapackage that asks you to install the packagestatmod. > > breaking up a package into the computation and visualization portions, feels to me like saying that the computational part is the more important one and takes priority in fixing over the visualization side. Since if an upstream graphical dependency break, you are supposed to fix your downstream package (whether it’s one big one or two small ones). Or what do you think? (Q by LCT) > I don’t agree with the statement that splitting the functionality of a package into two with different purposes, makes one of the packages more important than the other. This is about increasing software robustness and increasing modularity contributes to that goal.

Nitesh Turaga (14:12:50): > I’m having some trouble watching the video on pathable for@Aaron Lun’s talk. Is there a video for it on youtube?

Erick Cuevas (14:12:56): > @Erick Cuevas has joined the channel

Nitesh Turaga (14:12:59): > <!here>

Charlotte Soneson (14:13:28): > I don’t think so. Is this in the browser or in Zoom?

Nathan Sheffield (14:13:32): > @Nitesh TuragaI don’t believe videos have been posted to youtube.

Nitesh Turaga (14:14:31): > Zoom, and it insists my email isn’t recognized. And browser doesn’t give me audio. I’ve restarted / refreshed chrome a few times

Nitesh Turaga (14:14:44): > Maybe i’ll just restart my computer

Nitesh Turaga (14:17:06): > Ok, restarting my computer let’s me watch it in zoom. Not in the browser though:stuck_out_tongue:All good.

Matthew Carlucci (14:21:51) (in thread): > > Matt, how does your workflow work with R scripts + Rmd? > Scikick runs knitr to render both .R and .Rmd into markdown pages, then into the final HTML website. > > How do you determine run order? > Astep1.Rmdthat must run beforestep2.Rmdis specified with the command (sk add step2.Rmd -d step1.Rmd). Onsk run, the snakemake backend will choose an appropriate run order based on these definitions.

Shijie C. Zheng (14:54:56): > @Shijie C. Zheng has joined the channel

Pierre-Luc Germain (14:59:33): > @Pierre-Luc Germain has joined the channel

Lambda Moses (15:04:53): > When will the videos be posted on YouTube?

Erica Feick (15:08:03): > We are working on that, but they will be available on this platform until everything is uploaded to YouTube.

Leonardo Collado Torres (16:16:44): > August 14 is what the website says, but I bet that they’ll be out before that thx to Erica, Levi & others:wink:

CristinaChe (16:17:17): > A huge thank to the organizers and all the speakers for a truly wonderful conference. I learned a lot in a nice, open and constructive atmosphere. I would just like to add that I understand a virtual conference loses something in terms of personal interactions, but I want to highlight that in my opinion it gains a lot in terms of accessibility and inclusivity. So it would be wonderful to find a way to combine the two formulas once the world is back to normal. Thanks again :)

Ameek Bhalla (16:23:56) (in thread): > I edited the question to add my name to it. An advantage of the anonymous questions is that it helps shy people come out of their shell, but a disadvantage is that it prevents followup between the interested parties. So I wish the anonymous questioning were optional. > > Also, as they say, “it’s a feature not a bug” that presenters can look at and ponder questions. It allows questioners to hear the best possible version of the answer (as was the answer here:slightly_smiling_face:).

Ameek Bhalla (16:28:39) (in thread): > They are indeed unhidden now. Thank you for it and for organizing conference:slightly_smiling_face:

Dr Awala Fortune O. (16:32:59): > Thank you everyone it’s indeed a wonderful experience, being part of the conference, I’m super elated and challenged to move on in this career path.

Simina Boca (16:45:04): > Folks, don’t forget to join the Happy Hour!

Simina Boca (16:45:21): > Poster session table 1!

Leonardo Collado Torres (16:45:32): > https://posters.bioconductor.org/Bt7b1YCXccGupnIjMgF80EXuxo9coP9oXKW98GnH

Simina Boca (17:00:25): > Some people are at Table 2 as well I think

Lambda Moses (17:21:23): > Is it just me? - File (PNG): Screen Shot 2020-07-31 at 2.20.42 PM.png

Marcel Ramos Pérez (17:22:06): > https://bit.ly/bioc2020

Nitesh Turaga (17:36:00): > Thanks for the great conference to all the organizers!

Charlotte Soneson (17:44:11): > And to all the participants!:smiley:

Levi Waldron (17:57:14) (in thread): > Good, thank you!

Aedin Culhane (18:11:59): > post conference chat onbit.ly/bioc2020.. is still going on if you want to join

Federico Marini (18:32:27): > I got the feeling I was being stalked in the last minutes of the call

Federico Marini (18:32:38): - File (JPEG): Photo on 01.08.20 at 00.25.jpg

Federico Marini (18:33:20): > Photo is very low Q, but it is one of the most massive hedgehogs I ever met

Daniela Cassol (18:42:42): > Will the closing remarks talk be available?https://bioc2020.pathable.co/meetings/virtual/Zzu3PQw3XctNvW5rf - Attachment (bioc2020.pathable.co): BioC 2020 > BioC 2020

2020-08-01

Kevin Rue-Albrecht (10:11:46): > interesting trend: might timezones and long days at the screen have taken their toll over time? - File (PNG): image.png

Kevin Rue-Albrecht (10:11:53) (in thread): > https://kevinrue.github.io/twitter-stats/Bioc2020.html

Aaron Lun (12:35:20): > go to sleep, albrecht!

Federico Marini (13:13:42): > Where’s your recording@Aaron Lun? I missed that yesterday but can’t find it on the platform:disappointed:

Aaron Lun (13:13:52): > ¯*(ツ)*/¯

Charlotte Soneson (13:22:51): > it’s not lost, don’t worry:slightly_smiling_face:somehow it hasn’t made it to the platform meeting page.

Aaron Lun (13:30:03): > worst case I still have the video here. Won’t have the intro and the questions though.

Charlotte Soneson (13:32:02): > it’s all there. I have emailed the platform

Spencer Nystrom (19:07:58): > You have a choice of with or without ASMR mouth sounds.

2020-08-02

Shraddha Pai (11:13:46): > Hi all, tried and failed three times to upload my slides to F1000 on Friday. Has anyone else had this problem? I emailed F1000 on Friday, haven’t heard back yet. Thanks!

Levi Waldron (12:39:01) (in thread): > Argh, keep us posted! Thanks for your persistence.@Qian Liuhas been our point person for F1000 and can follow up if needed.

Levi Waldron (12:40:48) (in thread): > In the meantime, here’s the pre-recording (https://drive.google.com/file/d/1H1XAqbR6BsKnXx8kp907D8XXbOMXWXB8/view?usp=sharing) and the unedited conference version with Q&A etc (https://www.dropbox.com/s/l15htvpwzfz0rna/Day%205%201400h%20-%20Making%20the%20infrastructure%20sausage-%20tales%20of%20Bioconductor%20package%20development.mp4?dl=0) of@Aaron Lun’s talk

Levi Waldron (12:41:39) (in thread): > Could’ve been - I haven’t seen any data yet but I felt like I noticed lesser live attendance as the week went on. thanks for the plot@Kevin Rue-Albrecht! Maybe 5 days is too much?

Qian Liu (12:42:56) (in thread): > Hi@Shraddha Pai, if you don’t get a response from F1000 by Monday, please send me an email atqian.liu@roswellpark.org, include your issue for submission, and I can forward to F1000 and hopefully get it solved soon. Thanks!

Kevin Rue-Albrecht (12:44:19) (in thread): > i’m also trying to keep in mind that this is only tweeting, i know i’ve tweeted less this year, partly due to a lack of screen estate for all the windows, and a struggle to multi-task

Levi Waldron (12:46:37) (in thread): > Here’s the pathable visits data & line plot for the past 7 days - File (PNG): image.png - File (CSV): Metrics Visits-export-8-2-2020-04_45–vFL8OejTSzxBaLKv.csv

Kevin Rue-Albrecht (12:47:09) (in thread): > oh wow, that’s a drop

Levi Waldron (12:47:18) (in thread): > Although there must be something wrong, there certainly were more than 85 visits on Thursday and Friday

Levi Waldron (12:47:58) (in thread): > Also this: - File (PNG): image.png

Kevin Rue-Albrecht (12:48:36) (in thread): > not to nitpick: does that mean that 9 users never logged in of the entire week?

Levi Waldron (12:48:58) (in thread): > Apparently so:laughing:

Kevin Rue-Albrecht (12:49:06) (in thread): > (sad face, though it’s a pretty good success ratio)

Shraddha Pai (16:05:04) (in thread): > Thanks@Qian Liuwill do.

Federico Marini (16:05:18) (in thread): > Oh perfect:slightly_smiling_face:

2020-08-03

Levi Waldron (03:20:58) (in thread): > Dear Deaniela, I’m sorry, we didn’t record the closing remarks, they seemed too informal and personal to record. But the slides are available here, and these do have the information content:https://docs.google.com/presentation/d/1bui4R_JFA_VfxsLvNBdl3d9_RjO6Pxwteq5DrOpHMes/edit?usp=sharing

Sunil Nahata (04:08:39): > @Sunil Nahata has joined the channel

NABISUBI PATRICIA (05:22:38): > How can I solve that error - File (JPEG): Image from iOS

Federico Marini (06:07:58): > I can’t trace this back to any workshop as of now, but from the error message it looks like theurlSupportis not defined in the session.

Charlotte Soneson (10:43:44) (in thread): > The recording is also up in the platform now

Daniela Cassol (11:00:55) (in thread): > Thank you!

Federico Marini (11:28:48) (in thread): > Yeeehaaaa

Federico Marini (11:28:54) (in thread): > Plan for ther night:white_check_mark:

Steve Brooks (12:02:27): > @Steve Brooks has joined the channel

Steve Brooks (12:03:47): > Hi is Rafael Irizarry’s keynote available online? I’d like to share it with a collaborator who didn’t attend#bioc2020.

Kevin Rue-Albrecht (12:11:47): > I’ll check to make sure this is OK with the code of conduct after this message, buttechnicallyyou can go to the page of Rafa’s talk (https://bioc2020.pathable.co/meetings/virtual/aJQ9Be2LSFcBZRFGC), launch the video, and in the bottom right you’ll see 3 dots offering a “Download” button - File (PNG): image.png

Kevin Rue-Albrecht (12:12:54): > My understanding is that all the recordings will be made available on the Bioconductor YouTube channel at some point, so Ithinkthat it’s OK to download and share the video.

Kevin Rue-Albrecht (12:13:38): > > SOCIAL MEDIA POLICY Images and content from talks, workshops, and posters may be shared publicly through social media unless the presenter asks for it not to be. To avoid confusion, presentations not to be shared should be labeled “Do Not Share” on each slide, as should be posters. > https://bioc2020.pathable.co/code-of-conduct

Kevin Rue-Albrecht (12:16:04) (in thread): - File (PNG): image.png

Junyan Xu (12:53:44): > @Junyan Xu has joined the channel

Sean Davis (13:30:18) (in thread): > By August 14: - File (PNG): image.png

Sean Davis (13:30:35) (in thread): > May be sooner….

Kevin Rue-Albrecht (17:28:45): > @Peter Hickeytabrworkshop next year?https://leonawicz.github.io/tabr/:grimacing: - Attachment (leonawicz.github.io): Music Notation Syntax, Manipulation, Analysis and Transcription in R

2020-08-04

Kylie Bemis (12:32:23) (in thread): > If it is possible to do as a delayed op (without creating the result), then nothing is created. Any realized/subsetted results will be created and returned in-memory. Temporary files are only created on user demand via usual R temp files. In future months, we will submit a DelayedArray-matter integration package with realization backend so writing results can then be controlled via DelayedArray options.

rohitsatyam102 (14:40:27): > @James MacDonaldI am using mapIDS function to get unique gene names for a vector containing sever gene names. However, I stumbled upon a few genes which were mapped wrong I think. Eg:SCYL3maps toCCL15. However, these genes lie on different chromosomes when checked on Ensembl. Similar is with LAP3 being mapped to CXCR4. How should I fix this? - File (PNG): image.png

James MacDonald (14:46:46) (in thread): > @rohitsatyam102When you say the keytype is “ALIAS”, you are asking for the current gene symbol for any previous aliases. In other words, > > > select(org.Hs.eg.db, "SCYL3", c("SYMBOL","ALIAS","ENTREZID"), "ALIAS") > 'select()' returned 1:many mapping between keys and columns > ALIAS SYMBOL ENTREZID > 1 SCYL3 CCL15 6359 > 2 SCYL3 SCYL3 57147 > > So SCYL3 is a deprecated alias for CCL15, which you can confirm here:https://www.ncbi.nlm.nih.gov/gene/?term=6359%5BUID%5DIf instead you wanted any aliases for a given symbol, you would do it differently: > > > select(org.Hs.eg.db, "SCYL3", c("SYMBOL","ALIAS","ENTREZID"), "SYMBOL") > 'select()' returned 1:many mapping between keys and columns > SYMBOL ALIAS ENTREZID > 1 SCYL3 PACE-1 57147 > 2 SCYL3 PACE1 57147 > 3 SCYL3 SCYL3 57147 >

James MacDonald (14:50:28) (in thread): > This is why you shouldn’t really rely on gene symbols to identify genes. They aren’t unique, and depending on the age of the paper you might be reading, SCYL3 may refer to CCL15, or it could refer to SCYL3. > > This is also true for NCBI Gene IDs as well as Ensembl Gene IDs. But those IDs get deprecated, and if you have some old Gene ID and you try to look it up you won’t find the match (in an OrgDb package), but if you go to NCBI it will tell you that the ID has been deprecated, and also what the new ID is.

rohitsatyam102 (14:58:07) (in thread): > I have two gene lists obtained from two different datasets. One dataset used UCSC hg19 (Gene names with NCBI Accession Number) and other I took from Human Proteome Atlas (RNA FANTOM brain region gene data) (Gene Names with Ensemble IDs) which saysThe data was obtained from FANTOM5 and is based on The Human Protein Atlas version 19.3 and Ensembl version 92.38. Now for an apple to apple comparison, I need to first convert both the genesets to similar nomenclature. I am completely confused as to how should I achieve this.

James MacDonald (16:00:13) (in thread): > Probably you should use the Gene IDs and Ensembl IDs. Although that won’t likely be as satisfactory as one might like. You could use theorg.Hs.eg.dbpackage to map from Ensembl to Gene ID, or get the Ensembl 92 EnsDb from Annotation hub and use that to map the other way. But as a simple example, whereensdbis the Ensembl 92 EnsDb from Annotation hub: > > > select(org.Hs.eg.db, "5430", "ENSEMBL") > 'select()' returned 1:many mapping between keys and columns > ENTREZID ENSEMBL > 1 5430 ENSG00000181222 > 2 5430 ENSG00000284832 > > select(ensdb, "5430", "GENEID", "ENTREZID") > ENTREZID GENEID > 1 5430 ENSG00000284832 > > There will be any number of disagreements, that you will have to sort out yourself.

James MacDonald (17:10:58) (in thread): > Or to put it another way, > > > select(ensdb, c("ENSG00000181222","ENSG00000284832"), "ENTREZID","GENEID") > GENEID ENTREZID > 1 ENSG00000181222 NA > 2 ENSG00000284832 5430 >

Leonardo Collado Torres (17:53:43) (in thread): > I would really wait for the video to be available online instead of downloading and sharing. That paragraph is talking about images, not video

Kevin Rue-Albrecht (18:16:42) (in thread): > Agreed. Perhaps worth an edit to the CoC for the next time around. I noticed that some recordings had the option for download while other didn’t, weirdly enough

2020-08-05

Shraddha Pai (11:37:30) (in thread): > Hi@Levi Waldron@Qian LiuF1000 got back to me. After yet another failed attempt on Chrome, I was able to successfully upload the slides using Firefox. FWIW I was using Chrome 84.0.4147.89 (which didn’t work).

Qian Liu (12:24:17) (in thread): > Thanks so much for the update!@Shraddha Pai

2020-08-07

Jack Zhu (10:03:54): > @Jack Zhu has joined the channel

Jack Zhu (10:05:41): > Hi, good morning! I would like to have confirmation from someone that the default keytype in TxDb.Hsapiens.UCSC.hg19.knownGene is GENEID, which is actuallyENTREZID, thanks.

Jack Zhu (10:06:09): > > head(keys(TxDb.Hsapiens.UCSC.hg19.knownGene)) > [1] “1” “10” “100” “1000” “10000” “100008586”

Vince Carey (10:16:03): > This question should probably go tosupport.bioconductor.org, but perhaps this is sufficient resolution: > > > TxDb.Hsapiens.UCSC.hg19.knownGene > TxDb object: > # Db type: TxDb > # Supporting package: GenomicFeatures > # Data source: UCSC > # Genome: hg19 > # Organism: Homo sapiens > # Taxonomy ID: 9606 > # UCSC Table: knownGene > # Resource URL:[http://genome.ucsc.edu/](http://genome.ucsc.edu/)# Type of Gene ID: Entrez Gene ID > # Full dataset: yes > # miRBase build ID: GRCh37 > # transcript_nrow: 82960 > # exon_nrow: 289969 > # cds_nrow: 237533 > # Db created by: GenomicFeatures package from Bioconductor > # Creation time: 2015-10-07 18:11:28 +0000 (Wed, 07 Oct 2015) > # GenomicFeatures version at creation time: 1.21.30 > # RSQLite version at creation time: 1.0.0 > # DBSCHEMAVERSION: 1.1 >

Vince Carey (10:16:35): > Note the entry ‘Type of Gene ID’ above.

Lukas Weber (10:32:34): > Hi all, I was wondering about the availability of workshop materials. I think it was mentioned that workshop materials will be available for one week after the conference, and talks/presentations for a year. For the workshops, will the videos/presentations also be available for a year? (so the one week only applies to the online computational materials)? Thanks

Jack Zhu (11:01:19) (in thread): > Thanks, Vince.

Sean Davis (11:09:35) (in thread): > The “runnable” workshops will be up through this week. The workshop materials athttps://bioc2020.bioconductor.org/workshopsare available publicly and indefinitely. All talks/presentations will be available on youtube by about August 14 and once on Youtube will be available indefinitely. - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 27 - 31, Boston, USA.

Lukas Weber (11:10:02) (in thread): > great, thank you!

Sean Davis (11:11:21) (in thread): > And for more details: - File (PNG): image.png

Sean Davis (11:11:28) (in thread): > https://bioc2020.bioconductor.org/index - Attachment (bioc2020.bioconductor.org): BioC 2020 > Where Software and Biology Connect. July 27 - 31, Boston, USA.

2020-08-13

Devika Agarwal (09:25:26) (in thread): > ahh great! thanks! Also received some GeneTonic stickers in the mail :D

2020-08-14

Roye Rozov (15:00:00): > @Roye Rozov has joined the channel

Dirk Eddelbuettel (16:55:21) (in thread): > Hi@Sean Davisany update on the ‘by Aug 14 videos will be live’ issue? I tried to look yesterday but found nothing recent (but could well have looked in the wrong corner of these intertubes).

Sean Davis (16:59:27): - Attachment: Attachment > Hi @Sean Davis any update on the ‘by Aug 14 videos will be live’ issue? I try to look yesterday but found nothing recent (but could well have looked in the wrong corner of these intertubes).

Sean Davis (16:59:50) (in thread): > I’ll check into it. Sorry if that slipped….

2020-08-15

Sean Davis (13:13:49) (in thread): > As it is the 15th, things are a bit delayed. The videos are being edited. The first dozen or so are nearly complete and will be showing up on the Bioconductor Youtube channel. Rough edits of the first few will be up today.

Sean Davis (13:19:39) (in thread): > https://www.youtube.com/playlist?list=PLdl4u5ZRDMQSENJBo6k_wcA27gtydm-bz - Attachment (YouTube): Bioc2020 > https://bioc2020.bioconductor.org/

2020-08-18

Daniel Baker (09:00:43): > @Daniel Baker has joined the channel

2020-08-19

Adrija Kalvisa (04:32:30): > @Adrija Kalvisa has joined the channel

2020-08-20

Daniel Baker (11:53:16): > @Daniel Baker has left the channel

2020-08-24

Evgeniy Rumynskiy (05:38:18): > @Evgeniy Rumynskiy has joined the channel

Evgeniy Rumynskiy (05:39:58): > @Evgeniy Rumynskiy has left the channel

CristinaChe (12:53:12): > It’s arrived:heart_eyes:Thanks so much! - File (JPEG): Image from iOS

Levi Waldron (12:56:48) (in thread): > Cool!!!

2020-08-26

Iwona Belczacka (03:54:38): > @Iwona Belczacka has joined the channel

2020-08-31

Lluís Revilla (15:24:48): > Hi all, thanks for uploading the videos:star-struck:!! But as I was watching them I noticed a video that some videos missing are missing, I’m particularly interested on the CAB session:wink:, are there any update on this?

Mikhail Dozmorov (15:40:13): > @Lluís Revilla, edits and uploads are still in process, we are at day 3. The CAB video has just been uploaded and already availablehttps://youtu.be/noHn5fEbBwA - Attachment (YouTube): Meet and Talk with the BioC Community Advisory Board and BioC Awards Ceremony

Lluís Revilla (15:52:38): > Thanks!

2020-09-01

Pratima Chennuri (23:29:04) (in thread): > Still waiting for mine….

2020-09-02

Ying Xu (22:03:53): > @Ying Xu has joined the channel

2020-09-06

Tyrone Chen (22:32:07): > @Tyrone Chen has joined the channel

2020-09-08

Qian Liu (10:36:51): > https://support.bioconductor.org/p/133771/

Qian Liu (10:37:19): > BioCAsiais coming to a screen near you thisOctober (15-18). This will be the sixth Bioconductor Asia meeting that aims to bring together researchers with an interest in Bioconductor and R to exchange ideas and expertise. > We’re planning a fun and welcoming virtual meeting with talks and workshops to suit beginners through to more experienced users. > To learn about the amazing line-up of speakers, register for the event****(it’s free!) ****or submit an abstract (short and lightning talk slots are available) please visithttps://biocasia2020.bioconductor.org/. Abstracts are due Friday September 25. > We hope to e-see you there! - Attachment (biocasia2020.bioconductor.org): BioC Asia 2020 > Oct 15 - 18

Qian Liu (11:06:02): > https://twitter.com/mritchieau/status/1302755994435375104?s=20 - Attachment (twitter): Attachment > Calling all Bioconductors in Asia! #BioCAsia is coming to a screen near you in 2020 (Oct 15-18). Amazing line-up of speakers, including #rstats #bioconductor co-founder Robert Gentleman. Abstract submission open until Sept 25. Learn more by visiting https://biocasia2020.bioconductor.org/ 1/2

Qian Liu (11:06:31): > https://twitter.com/mritchieau/status/1302756174232653824?s=20 - Attachment (twitter): Attachment > #BioCAsia will have hands-on workshops in English and Mandarin and registration is free thanks to the support of our generous sponsors @CSL Chinese Anti-Cancer Association @F1000Research @RConsortium #rstats #bioconductor. Please help spread the word https://biocasia2020.bioconductor.org/ 2/2

Qian Liu (11:07:08): > Please feel free to RT and spread the word!:party_parrot:

Qian Liu (11:08:59): > Please also join the#biocasia2020channel if you are interested!

Ruizhu HUANG (12:53:53): > @Ruizhu HUANG has joined the channel

2020-09-11

Assa (07:26:37): > @Assa has joined the channel

2020-09-12

Kevin Rue-Albrecht (05:55:14): > I hate to be the needy sticker guy, but I still haven’t received my bioc2020 sticker. Anyone else? Is there a plan B?

Lucy (06:24:37): > Me neither! Waiting to decorate my laptop :)

Lambda Moses (19:11:34): > Me neither, though my laptop is already full

2020-09-13

Lucy (04:38:37): > Mine would be my first sticker!:slightly_smiling_face:

2020-09-14

Ilir Sheraj (06:24:04): > @Ilir Sheraj has joined the channel

2020-09-15

Thomas Gade Koefoed (10:30:14): > @Thomas Gade Koefoed has joined the channel

2020-09-20

Pratima Chennuri (15:06:57) (in thread): > I am also waiting……

2020-09-21

Chris Cheshire (03:38:10): > @Chris Cheshire has joined the channel

2020-09-22

Mike Smith (11:25:35): > Simone has been on vacation for a couple of weeks, but she mentioned yesterday that sending out remaining stickers was on her todo list for this week.

2020-09-30

Robin Zhou (16:45:48): > @Robin Zhou has joined the channel

2020-10-01

Aedin Culhane (10:14:27): > Sending out last lot of stickers the end of this week,,, If anyone forgot to fill up the form or need a Bioc2020 sticker. let me know

Joselyn Chávez (12:13:05) (in thread): > Hi@Aedin Culhane! I forgot to fill the form, is it possible to send stickers to México?

Pratima Chennuri (13:13:22) (in thread): > I’d very much like one please, I did fill the form, thank you.

2020-10-02

Robert Castelo (09:25:21): > Got miiiiiineeeeeeeee!!!!!:tada::party_parrot:Thanks to the organizers for making this happen and@Simone Bellfor the post!! In the era of electronic communication, a physical letter that it’s not advertisement and doesn’t come come from the tax office feels very special. - File (JPEG): 20201002_151804.jpg

Lukas Weber (09:31:15) (in thread): > Thanks@Aedin Culhane! I might have forgotten to fill out the form. I’ll send you my address if you still have some left - thanks!

Kevin Rue-Albrecht (12:37:41) (in thread): > Same here, mine arrived yesterday

2020-10-07

ravindra raut (02:40:48): > @ravindra raut has joined the channel

Anjali Silva (09:07:51): > @Anjali Silva has joined the channel

Nathan (23:23:46): > @Nathan has joined the channel

2020-10-08

rohitsatyam102 (18:10:43) (in thread): > Sorry to ask this but I got an email regarding the stickers that I will receive them (in India). Does that mean I filled that form Aedin is pointing towards or is there a new one?

2020-10-09

Aedin Culhane (16:01:28): > Folks in the Americas… I am late mailing the stickers.. sorry its late. Very very very final call on stickers.https://docs.google.com/forms/d/e/1FAIpQLSdZp1vxJGP61XgKPc8P8XwXbZ9Kv-yFyJ1YWZ4Y-R7-5hiTsg/viewform

Stephanie Hicks (16:38:46): > @Aedin CulhaneI’m 95% sure I filled out the form, but now unsure…. Is there anyway to verify if someone has already filled out the form? I don’t want to add extra work, but also don’t want to miss out on a sticker:upside_down_face:

Aaron Lun (16:39:35): > Do speakers get them automatically?

Dan Bunis (18:41:46) (in thread): > on this note… I’m actually 95% sure I already did fill out the form twice, sorry!, so I very much hope it’s easy for you to identify and remove duplicates!

Pratima Chennuri (18:57:55) (in thread): > Will be worth the wait, filled in the form again, just in case. Cheers!

2020-10-10

Davide Corso (10:50:59): > @Davide Corso has joined the channel

2020-10-11

Yuyao Song (23:41:52): > @Yuyao Song has joined the channel

2020-10-12

Ellora Chua (22:21:06): > @Ellora Chua has joined the channel

2020-10-13

Amarinder Singh Thind (19:17:42): > @Amarinder Singh Thind has joined the channel

2020-10-14

Hyun-Hwan Jeong (02:29:22) (in thread): > I also got it today! - File (High Efficiency Image File): B41AFBBC-87AB-43C6-B881-0AAC06A1D2E0.heic

Emi Tanaka (02:40:02): > @Emi Tanaka has joined the channel

Simina Boca (08:08:42): > I got mine yesterday!

rohitsatyam102 (08:10:48): > I am still waiting for mine!

Pratima Chennuri (19:03:19): > Very delighted to pick this up from my mailbox today. Thank you. - File (JPEG): PXL_20201014_230127256.MP.jpg

2020-10-15

Pol Castellano (04:43:24): > @Pol Castellano has joined the channel

2020-10-17

Leo Lahti (17:27:01) (in thread): > yes

2020-10-18

Noah Pieta (00:22:58): > @Noah Pieta has joined the channel

hiro (02:52:18): > @hiro has joined the channel

2020-10-19

brian capaldo (14:09:20): > @brian capaldo has left the channel

2020-10-20

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2020-10-23

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2020-10-26

Jeffrey O’Brien (14:02:45): > @Jeffrey O’Brien has joined the channel

2020-10-29

Jordan L. (13:51:04): > @Jordan L. has joined the channel

2020-10-30

Kevin Rue-Albrecht (08:16:14): > Hello community! > > The#eurobioc2020submission deadline is extended toMonday, November 16th! > > The organising committee welcomes submissions for: > * talks > * workshops > * posters > * birds-of-a-feather session topics > The scope for submissions is far from limited to Bioconductor packages; we welcome contributions as workflows, live demonstrations, interactive Shiny applications, data visualisations, new concepts, packages in development, calls for feedback and collaborations, … and all the many more hidden gems produced by the community; surprise us! > > Submit your contribution hereWe look forward to seeing you all online for this stimulating and community-driven conference! - Attachment (OpenReview): EuroBioC 2020 Conference > Welcome to the OpenReview homepage for EuroBioC 2020 Conference

2020-11-05

Aedin Culhane (11:56:01) (in thread): > Dan Did you get the stickers. I sent them to you

Dan Bunis (12:32:03) (in thread): > yes yes!!! weeks ago =)

Dan Bunis (12:33:12) (in thread): > :smiley: - File (JPEG): 20201015_095516.jpg

2020-11-10

Aedin Culhane (17:50:03) (in thread): > Did you see the Nature article on graphics for color deficiencies during the week

2020-11-11

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

2020-11-17

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2020-11-18

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2020-11-19

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2020-11-23

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2020-12-01

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2020-12-02

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2020-12-03

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2020-12-08

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2020-12-10

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2020-12-11

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2020-12-12

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2020-12-14

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2020-12-15

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2020-12-16

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2020-12-18

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2020-12-21

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2020-12-25

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2021-01-15

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2021-01-21

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2021-01-22

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2021-01-26

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2021-02-05

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2021-02-07

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2021-02-19

abdullah hanta (01:27:14): > @abdullah hanta has joined the channel

Shraddha Pai (10:02:20) (in thread): > Oooh, I don’t think I ever got mine. Is the sticker for BioC2020 still available?

2021-02-27

Hervé Pagès (16:07:25): > @Hervé Pagès has left the channel

2021-03-01

Diana Hendrickx (03:18:08): > @Diana Hendrickx has joined the channel

2021-04-20

Levi Waldron (11:51:59): > archived the channel