Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Plan B: hackseqRNA: COVID-19 Ultra-hackathon #23

Open
7 tasks
jenjaelin opened this issue Mar 10, 2020 · 25 comments
Open
7 tasks

Plan B: hackseqRNA: COVID-19 Ultra-hackathon #23

jenjaelin opened this issue Mar 10, 2020 · 25 comments

Comments

@jenjaelin
Copy link

jenjaelin commented Mar 10, 2020

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
Copy link
Collaborator

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
Copy link
Author

jenjaelin commented Mar 13, 2020 via email

@ababaian
Copy link
Collaborator

ababaian commented Mar 16, 2020

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.

hackseq_rosie

@ababaian
Copy link
Collaborator

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

@emreerhan
Copy link

What platform will we be using for the meeting?

@ababaian
Copy link
Collaborator

Google hangouts? Unless someone has another suggestion

@bfjia
Copy link

bfjia commented Mar 16, 2020 via email

@ababaian
Copy link
Collaborator

Can someone sort out the best option?

@emreerhan
Copy link

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

One tap mobile
,,456691280# US Toll

Dial by your location
US Toll

Meeting ID: 456 691 280
Find your local number: https://zoom.us/u/actDrYpAfo

@emreerhan
Copy link

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
Copy link

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

@jenjaelin
Copy link
Author

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
Copy link
Collaborator

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.

@ababaian ababaian changed the title 6th Organizational Meeting - Next week: When? vote inside Plan B: hackseqRNA: COVID-19 Ultra-hackathon Mar 17, 2020
@ababaian
Copy link
Collaborator

@hackseq/steering_committee_2016 @hackseq/steering_committee @hackseq/hs18_org @hackseq/hs19_organizers If you have a free moment please see the above contingency plan we're enacting for hackseqRNA. Please leave your comments/thoughts, we're going to take hackseq to some new and exciting places!

@NoushinN
Copy link
Contributor

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.

hackseq_rosie

Love the banner, can I share on social media?
First name: hackseqRNA; nickname: ULTRA COVID19

@ababaian
Copy link
Collaborator

ababaian commented Mar 17, 2020

Not yet @NoushinN! We're holding off all promotion until we get the first steps sorted out.

I think for the tag I'm leaning towards "hackseqRNA: COVID-19 Ultra-hackathon"

@NoushinN
Copy link
Contributor

btw, the website doesn't reflect team lead time extension, the last one was March 13

@ababaian
Copy link
Collaborator

We haven't updated any of the website yet, we just laid out the plan last night.

@bfjia
Copy link

bfjia commented Mar 17, 2020

@ababaian should we reach our to Dr. colijn at SFU since we are making this COVID19 focused. maybe we can pull her onto the planning committee somehow.
She recently had a hackathon in feburary focusing on COVID19

@ababaian
Copy link
Collaborator

ababaian commented Mar 17, 2020

Correct, Stephen is on this : )

Pop on the slack for minor chat

@DCGenomics
Copy link

I'd suggest talking with Pete Kane from SVAI/Research to the People, the Japanese Biohackathon folks, Nick Loman, and Russ Altman about their COVID efforts as well! We'll all get more done if this is a united front.

Also, LMK when you're ready to go live and Ill advertise at biohackathons.github.io

@lisancao
Copy link
Contributor

lisancao commented Mar 17, 2020

Okay, based on the above this is my current tasklist, if anyone knows any interested webdevs that would help a lot:

  • design interface for task submission and viewing, seek out team that can complete it (modeled after mechanical turk, kaggle)
  • design task criterion, tracking for completed/in progress tasks and reward token system
  • Work with bioFreelancers to create index of Bioinformatician reserves, includes a dedicated README, based on Emre's Bioinformatics Reserves above
  • Create open dataset/curated COVID19 resources README for HackseqRNA, *almost completed
  • Outreach to similar organizations once we get things up and running

@NoushinN
Copy link
Contributor

@lisancao: I can help with the COVID19 resources, ping me on the readme

@NoushinN
Copy link
Contributor

We haven't updated any of the website yet, we just laid out the plan last night.

Great, I would like to change mine to lead if possible...will look out for it

@lisancao
Copy link
Contributor

@NoushinN thanks for the help! You can find it here: https://github.com/hackseq/hackseqRNA/blob/master/COVID-19_Data.md

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

8 participants