Plan B: hackseqRNA: COVID-19 Ultra-hackathon

[jenjaelin]

hackseqRNA: COVID19 Ultra-hackathon

Core Objectives

• We are in the midst of pandemic. The general sentiment is of fear and uncertainty. Bioinformaticians and RNA-biologists are at a unique position understanding the biology of SARS-CoV-2 and COVID-19, and it’s our responsibility to do this to the best of our ability

1. Establish a collaborative and interdisciplinary network of bioinformaticians and coders with diverse skills to assist research labs working on SARS-CoV-2 to analyze data at no cost.
2. Accept community-led projects on SARS-CoV-2 and RNA-biology
3. Organize immediate scientific efforts (via hackathon projects)

Logistics Outline [German]

• Target Size: 25 projects; 500 participants. >24h of work per participant.
• Orient hackathon around remote-participants with a decentralized structure.
• Have ‘cores’ of 4-6 people working together during the hackathon all across the world. Does not have to be the same project.
• Projects go online March 23rd / March 30th as fallback, allow immediate ‘trickle in’ work to happen
• Final project submissions open until Friday May 15th
• Sprint 1: April 4th 8AM PST to 8 PM PST *tentative
• Sprint 2: May 2nd 8AM PST to 8 PM PST *tentative
• Hackathon: May 22 8AM PST to May 24 8PM PST

Team Leaders / Projects [ Stephen + David ]

• Re-open Project applications on a rolling basis upto May 15th.

Project Recruitment

• Create "Onboarding" document. Gather all necessary information to get a project online rapidly. See Interview questions / project requirements.
• Create rubric to assess project submissions in quality.
• Interviews may be optional? Will discuss further
• Define Deliverables: Scientific abstract, lay abstract and a 5 minute presentation / youtube video which we will share to select the winner via voting. Use comment section for Q+A etc...

Bioinformatics Reservers [ Emre + Lisa ]

• “Bioinformatician Reserves”: Create a detailed “Skills Inventory” for interested participants that we can share with any research teams that reach out for additional bioinformatics help. Focus on highly specialized skills such as “single cell RNA-seq analysis”, “Ribo-seq analysis”, etc...
• Interface for COVID-19 reserachers to query available skills and/or request a particular analysis.

Participant Recruitment

• Allow for ‘promiscuous’ participation amongst projects in trickle-phase. You can contribute to multiple projects and ‘try them out’.
• Dedicated participation in ‘hackathon phase’ with participants ranking 2-3 choices closer to the date and we sort.

Sponsors [Justin is the man]

• Re-contact sponsors to confirm they can swittch to this event
• Re-contact all previou ssponros to see if they wnat to help contribute to this event

Issues which may arise

• If we change the name then current project leads feel left out
• Risk of losing interest if 2 month phase is slow
• Use milestones to keep goals going and constant reward
• Add people to projects on a rolling basis. How do we do final sign-ups
• HPC capacity limits. ORCA is not sufficient
• We would need additional sponsors
• Larger time commitment from organizers

Invite to Slack channel for non-essential comms

[ababaian]

Hey @hackseq/hackseqrna_org Can we have a virtual meeting / conference call next Monday or Tuesday after work? We don't have to physically meet but we need to all have a good chat about what we want to do next.

I thought about it quite a bit and I think we may have a very good opportunity in the next few weeks to run a remote hackathon focusing on RNA/COVID. Lots of people are feeling like they can't contribute and if we can get a bunch of projects up and running then this will be something productive people can focus on and maybe even something productive that can be generated with this collective work-effort. I feel like we (as scientists) have a responsibility to try and understand this thing, it's just hard to figure out where to start. Let's find a few good jumping off points for people and go down the rabbit hole together.

[jenjaelin]

I’m down with that. Maybe use some of our extra funds from not having to book location and food to fund remote things J

…

On Mar 13, 2020, at 11:16, Artem Babaian ***@***.***> wrote:  Hey @hackseq/hackseqrna_org Can we have a virtual meeting / conference call next Monday or Tuesday after work? We don't have to physically meet but we need to all have a good chat about what we want to do next. I thought about it quite a bit and I think we may have a very good opportunity in the next few weeks to run a remote hackathon focusing on RNA/COVID. Lots of people are feeling like they can't contribute and if we can get a bunch of projects up and running then this will be something productive people can focus on and maybe even something productive that can be generated with this collective work-effort. I feel like we (as scientists) have a responsibility to try and understand this thing, it's just hard to figure out where to start. Let's find a few good jumping off points for people and go down the rabbit hole together. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[ababaian]

hackseqRNA CoV-2 Contingency Plan

Hey all, I outlined some thoughts I've had on the contingency plan. We're in uncharted territory but I think if we can discuss how to majorly re-think how a hackathon happens then I think we can create a lot of good with this.

The feeling I want us to project moving forward is that we as bioinformaticians are not helpless and can fight back and contribute to the pandemic effort.

[ababaian]

@hackseq/hackseqrna_org See you all tonight at 5:30!

[emreerhan]

What platform will we be using for the meeting?

[ababaian]

Google hangouts? Unless someone has another suggestion

[bfjia]

Skype? Hangout has a 10ppl limit that we might hit if everyone joins. Or we could jump on the zoom bandwagon. J

…

-------- Original message -------- From: Artem Babaian <notifications@github.com> Date: 2020-03-16 10:11 (GMT-08:00) To: hackseq/hackseqRNA <hackseqRNA@noreply.github.com> Cc: Justin Jia <justin_jia2006+git@hotmail.com>, Team mention <team_mention@noreply.github.com> Subject: Re: [hackseq/hackseqRNA] 6th Organizational Meeting - Next week: When? vote inside (#23) Google hangouts? Unless someone has another suggestion — You are receiving this because you are on a team that was mentioned. Reply to this email directly, view it on GitHub<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fhackseq%2FhackseqRNA%2Fissues%2F23%23issuecomment-599657310&data=02%7C01%7C%7C6d484f3da2fd415fd1f808d7c9cd1dbe%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637199755107859509&sdata=vvTcVjWEV3KATJpsPQwwTlE3JPtVBYLMrRqKhRXjjao%3D&reserved=0>, or unsubscribe<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABQMASS5I3GAZGTQTTRMFPDRHZMVLANCNFSM4LFGD7EQ&data=02%7C01%7C%7C6d484f3da2fd415fd1f808d7c9cd1dbe%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637199755107872600&sdata=iOOzOgWAcAgpj3tvKTmCGzpGmBHEVvpEkd%2BoW0KIqNE%3D&reserved=0>.

[ababaian]

Can someone sort out the best option?

[emreerhan]

Emre Erhan is inviting you to a scheduled Zoom meeting.

Topic: HackseqRNA Meeting 6
Time: Mar 16, 2020 05:30 PM Pacific Time (US and Canada)

Join Zoom Meeting
https://zoom.us/j/456691280

Meeting ID: 456 691 280

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Meeting ID: 456 691 280
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[emreerhan]

The biggest issue is a 40min limit on meetings with more than 3 people. If it takes longer than that we can just create another meeting.

[alexsweeten]

Might catch the first 15 minutes or so on Zoom, but need to leave rather soon today.

[jenjaelin]

Oh man, my apologies. It somehow went from 5:00 to 7:00 before I realized it -.-

Our lab has been drowning in COVID logistical nightmares and research planning

[ababaian]

No worries @jenjaelin! This is secondary for everyone until we get some stability in our lives. Join the slack and we can chat, I'll get you up to speed.