i5K Coordinating Group

Conference Call Agenda

September 18, 2019

10:00-11:00 (EDT)

The focus will be on determining how to move ahead post EBP NYC Workshop.

Attending : Monica Poelchau, Kevin Hackett, Stephen Richards, Mike Pfrender, Surya Saha, Chris Childers, Glenn Hanes, Meg Allen, Anna Childers, Mara Lawnicziak, Mark Blaxter

  • EBP Workshop Take-aways (Sue, Monica, Anna, fringy, Gene, Kevin)
    • Need for Ag100Pest repository/database standards (where to store different data types)
    • Fringy needs a list of Ag100Pest species – can Anna provide?
      • Need in order to coordinate with other groups (e.g. Wellcome Trust)
      • Ag100Pest + Sanger could also coordinate different sequencing types (e.g. Sanger could provide Illumina from British samples)
    • Chromosome issue – i5k likely can't meet the 'chromosome' standard. Better if insect people use Hi-C (best scaffolding technique atm) and not completely meet the chromosome standard, since we don't necessarily know how many chromosomes a species has. Assigning chromosomes is more of a product rather than a standard.
    • Who will determine if a project is 'done'? Who is in charge of this? (Standards should help, but standards are changing)
    • Access + benefits sharing – there is a need for standards on that front
    • Need a monthly conference call for technical issues (e.g. VGP is doing successful 'deep dive' calls). E.g. what will be the i5k standard for assembly quality?
      • VGP is talking about day-to-day work to keep the project going
      • Ag100Pest could consider opening up their calls, since Ag100Pest calls have similar scope. It's okay for it to 'be real'.
      • Also the need for broader topical discussions, e.g. vouchering, database, assembly standards for all insects
    • Manual curation of assemblies
    • Industry money will need to come in to carry the project out (conservation goals aren't enough).
    • Next EBP meeting is in Hinxton (UK), Oct 5-9 2020
    • AAAS meeting in Seattle in February
  • Funding
    • NSF Proposal (June 25) (Sue, fringy, Mike)
      • No updates so far – supposed to get news in October
    • Fringy/EBP: NSF AccelNet. Coordination grant for a network of networks. Funds to run meetings, websites, project coordination. Due end of January (likely). Fringy will be in touch with us (among other groups)
  • I5K Webinar: Top Issues (Anna)
    • Olga Petterson and Mara L regarding sample prep – do we need an arthropod group, or should we join the VGP sample prep group?
    • Surya: assembly standards. Adam Philippy's group is developing tools/standards for assembly quality assessment at the nucleotide level. Would be nice to hear about that. It would be useful to get input from other people from the arthropod community on this.
    • Standards for i5k assembly quality, resulting in a publication? Low input discussion.
    • Arima genomics?
    • Dovetail?
    • Panel discussion – Dovetail, Arima etc – how do their methods compare? Scaffolding is one of the most expensive steps.
    • Surya will help!
  • Standards for i5K Assembly (Anna)
  • Selected Future Meeting Issues/Updates, time permitting
    • Should we think about setting up an i5k session similar to the VGP session in 2021?
    • AAAs.
    • Rob Waterhouse is co-organizing an insect session. Does i5k/Ag100Pest/AGC want to have some participation? Focus should be biology rather than organization.
      • Ag100Pest will think about contributing
      • Denis Tagu? Duane McKenna
    • ESA – early registration is due September 23
  • Other Ag100Pest news:
    • Some level of sequencing on at least 35 species
    • A number of failures, as well
  • EBP coordination:
    • Tracking what has been done and whether it meets a standard
    • Will there be a spreadsheet? Fringy has volunteered for EBP
    • Problem is to define what the columns of the spreadsheet are – e.g. are you thinking about sequencing it, or actually sequencing it?
      • Mark Blaxter's suggestion:
        • Register BioProjects for projects that we are actually going to do (=serious intent)
        • Register BioSample when it's actually started (where we should define what metadata to include)
        • Register vouchers?
        • SRA
        • Assembly submission
      • I5k webinar for figuring out standards for reporting?
      • Do we need a different software solution? Just NCBI search interface? Need another software solution?

NEXT MEETING: Oct 16, 2019

10:00-11:00 am EDT