i5K Coordinating Group

Conference Call Meeting notes

July 15, 2020

11:00-12:00 (EDT)

The focus will be organizing July's AGS virtual meeting. Updates only as needed. If there is time, we will begin a discussion of i5K goals vis-à-vis EBP.

Attending: Kevin Hackett, Monica Poelchau, Dorith Rotenberg, Michael Pfrender, Duane McKenna, Surya Saha, Brad Coates, Kristen Panfilio, Susan Brown, Stephen Richards, Meg Allen, Marian Goldsmith, Rob Waterhouse, Chris Childers, Glen Scoles, Anna Childers, Robert Miller, Jay Evans

  • Meetings
    • AGS July 20-24, 2020 (Rob, Sue)
      • There is a series of very detailed guides on Slack on how to participate in the meeting - search for 'guide' on Slack and filter by 'files'. Play around with it before the meeting.
      • Things are going as planned
      • 939 registrants!!! In-person meetings were deliberately capped at 300; last attendance was 275
      • 750 Slack invitees so far (rolling, batch invites)
      • Sue: What about next year - do we need to start doing hybrid meetings, part in person and part virtual? Concern about hybrid model - people might not come. We shall see.
      • Testing on Monday (including with speakers from China in the US am); sessions Tuesday-Thursday; workshops on Friday and Monday. Workshops are being run by Gloria and Mary-Ann (VeupathDB). There is now a cap at about 200 for the workshops. Good advertisement for regular webinars run by VeupathDB and i5k workspace
      • Post-conference survey - would be good to set this up
      • China session might help build community for an 'i5k East' branch
      • Overflow topics - were there any? No (so no new topics for i5k webinar). Perhaps put out a request for i5k webinar speakers during the meeting? Ideally talks that address a particular problem/research question. Perhaps add this to the post-meeting survey? Could also look through the V-posters for ideas (e.g. Redfly)
      • Please register if you haven't yet, and use Slack for interaction!
      • Twitter-slack interaction - no need to set anything up on your own. If you tweet and include @arthropod_i5k, it gets sent to the twitter Slack channel
    • EBP Oct 5-9, 2020 (Kevin, fringy)
      • Assembly group standards have now been posted to the EBP website
        • There will be some discussion/sign-off on this at the EBP meeting in October.
        • Aspiration to make all genomes good enough so we don't have to redo them
        • Hi-fi reads will often reach the standards set by the committee (contig N50 has to be \> 1 Mb, there needs to be some Hi-C for scaffolding, sequence quality \> Q40). This makes the EBP goals attainable.
        • Now VGP standards can be met by 'the people' that don't have the same data/infrastructure/resources as the vertebrate genomics community
        • Continued push to understand why it's important to strive for as good an assembly as possible. Right now, quality is cheaper than dealing with a poor assembly
        • Assembly standards are Technology-free (agnostic)- focuses more on the results rather than the methods
        • ONT recipes are not ready so looking forward to that - Fringy
      • There's been good cross-talk between committees during the recent calls
      • Annotation group: more of a discussion
      • IT/informatics group: more of a discussion
      • Analysis discussion tomorrow 7/16/2020 at 6 am Pacific
      • Australia has funding for 50 species
      • EBP workshop in October - needs volunteers to organize i5k/arthropods session. Talk about this after AGS… They will do pre-recorded talks. New member interested in plant-insect interactions, might try to get him to join i5k
    • ESA Nov 15-18, 2020 (Monica, Brad)
      • All abstracts submitted. Waiting to hear about format - livestream vs. pre-recorded.
    • PAG-San Diego: Ag100Pests Talks Jan 9-11, 2021 (Anna, Surya)
      • No updates, too much going on plus covid-19 uncertainty
  • Project Updates
    • EBP Update (fringy): Assembly Standard
    • DToL (Mark, Mara)
    • Ag100Pests, include Desert Locust (Anna)
      • things are moving along. Working on getting the first genomes out in public.
      • Some changes in assembly committee to differentiate jobs/workload
      • USAID money for Desert locust.
    • Beetles (Duane)
      • postdoc advert - thanks for passing along!
      • Ag100Pest will almost double the representation of beetle genomes in NCBI at the moment
      • Sue and Erin Scully are coordinating with Anna and Ag100Pest to ensure non-redundancy on additional Tribolium-related beetles
    • Cornome (Brad, Jay, Dave)
      • no updates
    • Bees (Brian)
    • France (Denis)
    • California Ecosystem (fringy)
      • meetings are starting. Very vertebrate-focused (great white shark subspecies; "charismatic megafauna" = good for marketing, also via Hollywood!). Arthropods have a marketing problem. Perhaps take advantage of new high-quality imaging to make people excited about insects outside of bees and monarchs? Need to emphasize wider entomological conservation/ biodiversity angles.
  • I5K into the Future (Kevin) - we should discuss this durin** g our next meeting**
    • started i5k in November of 2010 (we have a ten-year anniversary coming up!)
    • Science blurb in March 2011
    • i5k pilot; i5k Workspace
    • What do we consider i5k's goal now, 10 years after our start? Who are our members (need more geographic diversity?)? We're supporting the EBP project, so moving towards sequence ALL arthropod genomes. Funding mostly successful in concert with others. Training has been a success, but could have more involvement. Webinars have focused on technology so far. What are the roles within the group?
    • Time for a commentary paper?
  • Other - new database(s) in China that are not part of the INSDC. What will happen to data sharing? Commercial databases can't be part of the INSDC. We need to learn more about the databases and their connections.