i5K Coordinating Group

Conference Call Notes

July 12, 2022

11:00-12:00 (EDT

The focus of this meeting will be de-briefing from the AGS at Notre Dame, particularly with respect to re-visioning i5K.

Attending: Duane McKenna, Brian Scheffler, Anna Childers, Amanda Stahlke, Kevin Hackett, Monica Poelchau, Mike Pfrender, Jay Evans, Marian Goldsmith, Rob Waterhouse, Brad Coates, Glenn Hanes

  • Upcoming Meetings [brief updates, if any]
    • ICE-Helsinki, July 2022 (Rob). Arthropod session is going ahead - 8 speakers. May organize a lunch afterwards for those who are interested in further discussion. Could include additional i5k visioning. https://ice2020helsinki.fi/ Advertised on Slack, and ArthropodNews mailing list - to encourage people attending ICE to connect with our i5k/genomes session (July 21st 08:00-10:00 Room 218).
    • Lep Workshop-Crete, 21-27 August 2022 (Marian). Going ahead, smaller than usual.
    • Biodiversity Genomics-Hinxton, 3-7 October 2022 (Mark, Rob, Anna).
      • Do we want an i5k session? Decision is due ~July 16th.
      • What would the goal of the session be?
      • There will be insects discussed, not sure how to have the best impact/most meaningful meetings to give the best ‘lessons learned’.
      • ERGA, GIGA, VGP, EBP are running sessions.
      • Are there specific talks for major projects scheduled? No.
      • Do we approach Erich Jarvis about the EBP slot - can i5k have an 8-minute window so that we can showcase what is happening, or is this session already full? Could also highlight insects coming other out of other projects (e.g. ERGA, Dtol). And add all species being sequenced to Goat. **Rob will reach out to Erich**.
    • ESA-Vancouver, 13-16 November 2022 (Brad, Catherine): symposia. Hybrid meeting, speakers will be a mix of in-person and virtual.
    • Mosquito/vector meeting, 24-29 July 2022. Crete, same venue as lep workshop.
  • Publications
    • Any reports? H. zea paper will be re-submitted soon, minor revisions
  • EBP Update (Kevin, Anna)
    • Talk on B10k birds project - Guojie Zhang. 1400 bird species are being assembled. BGI version of Illumina sequencing. Erich Jarvis is collaborating with them on long read sequencing as well.
    • John Kress gave an update on convention for biological diversity/DSI. There will be a meeting on this in Montreal later in the year (December?). Not much progress.
    • EBP is creating a Governance document. i5k is a member, but not all groups are signatory members on the MOU. We could do this (if a non-US and/or non-USDA person signs this). Do we need separate affiliations for Ag100Pest and Beenome? All groups are expected to sign the governance doc, eventually. There will be elections and committees. Official structure is intended to signal stability and formality that funders need. Also issues of patenting - push towards no patenting of DNA sequences, but not all countries agree. No resolution on a Ukraine statement - preserving collections for use in genomics; this was too difficult to word, so it was dropped. This means that EBP will stay out of politics.
    • Planning a frontiers workshop and associated publications. Invitation only, May 2023, Lausanne, 25 participants. If you’re interested in participating, contact Harris Lewin.
  • Brainstorming 2022: De-brief from AGS Visioning (Monica, Brad)
    • Different insights came from the different sessions.
    • They like what we’re doing, and they want more of it - impression of ‘they’ vs. ‘us’.

    • Virtual session proposed more significant tasks and changes.
    • Next steps:
      • list of tasks to choose among, prioritize
      • choose champions for tasks. Will likely require more people engaged. Several volunteers, but they need direction
      • call for updates to the website to more clearly indicate who we are and what we do, as well as better link-outs to existing resources and where to go for help
      • e.g. are there resources we can point to that explain how people can deal with also submitting their non-arthropod metagenomes?
    • Virtual session: smaller session, but some unique insights from non-cc members. There was a bit of a disconnect on what i5k is and does, who can be a member. Training, community building, networking were key. Going beyond genome assemblies now - hurdles are smaller. Pan-genomes, MGAs, etc. Problems with metagenomics due to filtering problems (although this might be an education thing - can submit as an environmental sample - could be a new webinar with NCBI!).
    • Marian - how do other larger groups handle these questions? We don’t want to re-invent the wheel. Are larger groups equivalent to i5k?
    • Possibility to apply for an RCN.
      • A new research coordination network? academic partner to champion some big NSF grants
      • An NSF program https://beta.nsf.gov/funding/opportunities/research-coordination-networks
      • https://www.nifa.usda.gov/grants/programs/data-science-food-agricultural-systems-dsfas
    • Has i5k resulted in collaborations that led to new/better genome sequencing?
    • Working groups help provide an ‘in’ for outsiders to participate in i5k
    • Duane - hard to know how to approach the group because we’re spread thin. it’s hard to know what we can offer for collaborations, even within this group. It may help to articulate specifically how people can collaborate.
  • i5k cc timing: should we change the meeting time earlier, to get more European participation? We could send out a doodle poll for 10 am vs. 11 am Wednesdays Eastern.

NEXT MEETING: August 17, 2022

Ideas for How to Re-vision i5K Coordinating Group

  • What is i5K role in light of new mass sequencing efforts?
  • How does i5K CG relate to the greater i5K community?
  • Open up meetings to all i5K=AGS members? If so, what are the responsibilities of i5K CG members?

Get Input:

- i5K CG Brainstorming
- AGS Lunch Brainstorming: In-person or Hybrid
- Series of Informative i5K-associated Group Presentations with Feedback from the i5K SC members

- Ag100Pest (Anna)
- Beenome100 (Jay)
- Beetle (Duane)
- Cornome (Brad, Jay, Jon)
- DToL (Mark)
- GEvol-Germany (Kristen)
- i5K@NAL (Monica, Chris)
- Leps (Marian)
- Others, e.g., GIGA, GAGA, ERGA

I5K Activities/Roles for i5K Coordinating Group

  • Technical Seminar Series, e.g., PacBio, Nanopore; topics such as pangenomes (e.g., Justin Vaughn)
  • Topical Seminar Series, e.g., AGSX
  • Comparative Genomics: new models for making the best of core resources
  • Share datasets (within and between taxa)
  • Training: work
  • Maintain databases, or share them: e.g., GOAT, NCBI
  • Set/elevate standards
  • Free resources: i5K Workspace
  • Partnerships
  • Funding: joint funding initiatives; build gravitas to funding agencies; uniting bug folks across countries/organizations