Org:Database Interop Hackathon/Agenda

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Planning and preparation for meeting

This is for the organizers

Teleconference, Dec 4, 2008

calling in: Hilmar, Todd, Rutger, Arlin (absent: Katja)

Agenda items in order

  1. Confirmation emails Send confirmation emails that will confirm the invitation. Do we need any response to those or information from people other than whether or not they confirm to attend? Are we all in agreement that everyone who has responded positively at this point can be confirmed?
    • yes, for the ones we have discussed and accepted.
  2. Outstanding responses Outstanding responses. I'm not clear on the status of Matt Kosnik, Valentin Ruano-Rubio, Vivek Gopalan, Lucie Chan / Mark Miller (nominated by O'Leary), participant from EOL (Cranston?), and participant from ITIS. Martin Wu needs follow-up (from myself).
    • Kosnik: Todd will follow up
    • Arlin: clarify with Julie that she can nominate herself in preference, otherwise get someone else (Valentin Ruano-Rubio)
    • Arlin: add Vivek's response to response page
    • preference for Lucie Chan
    • Karen Cranston for EOL & TOL
    • ITIS: Hilmar to check with Katja
    • UPDATE: status for PhyloFacts also not clear. Latest nomination: Meredith Patterson. Todd to follow up.
  3. More nominations Action on nominations.
    • Albert Vilella (EBI): yes (Hilmar)
    • Karen Cranston (EOL, ToL): already addressed (yes)
    • Reed Beaman (TOLKIN): yes (Rutger)
    • Sam Donnelly (pPOD): add to open call (pPOD has some products, but has tech focus, not a data provider)
    • Paul Thomas (Panther): send PI invitation (Arlin)
    • someone from Kepler: yes to Ilkay Altintas (Hilmar)
    • Sheldon McKay (iPlant integrated discovery environment): yes (Todd)

Teleconference, Dec 8, 2008

Agenda items in order

  1. More nominations -- Matthew Yoder (of MX fame, nominated by Katja Seltmann)
    • add him to open call list
  2. Open Call for Participation.
    • not many seats available, just a few
    • venues: evoldir, TDWG, bioperl-announce, biojava announce, bioinformatics.org bulletin board, Syst Biol bulletin
    • specific names & projects to target: Yoder, phylopedia (Martin Wu), Donelly, TimeTree, others
    • text: concise and much shorter than the one in the invitations
    • Rutger volunteers to write text; will set up google spreadsheet for invitation data (see below)
    • shall we allow feedback
    • inconclusive discussion about whether to solicit feedback
  3. Hackathon mailing list, participants will be subscribed upon confirmation.
    • dbhack1@nescent.org
  4. Advance participant preparation - Data and information to gather from participants
    • survey drafted by Rutger, with comments from Hilmar
    • wiki page, use email list, everyone participates
    • email list could help to get people motivated; will have to do some prodding
    • continue the data-gathering with the teleconference
  5. (not on original agenda) Organizing wiki Hackathon docs will be in current area, which is nescent.org/wg/evoinfo. Participants will be given accounts with access to evoinfo wiki space. Arlin and Rutger are OK with that. Separate email list as described above.

Teleconference, Dec 11, 2008, 2:00pm

  1. update on response
    • Julie, Valentin
  2. do we need a face-to-face meeting to prepare (discussion)
    • tentative agreement-- yes, late jan or early feb; cancel later if needed
  3. what demonstration projects?
    • kinds of projects
      • services, e.g., taxonomic querying service implementation to allow users to access data taxonomically
      • data interop, e.g., view treebase content in treefam interface following data translation
    • preparation
      • phenoscape project lesson: building out ontology should not be underestimated
    • pick an easy target (treebase) and a hard target (morphbank)
    • best carrots are services
      • phylomatic - use to get species tree for tree reconciliation
      • tree visualization
      • tree reconciliation
    • reconcile tree example (arlin), imagine: in treefam, user clicks on "show reconcile tree" button-- the question is: how do we make this happen?
      1. calling script sucks out OTU names from this sequence family, gets unique list of species
      2. calling script invokes external service to get species tree from list of species names
      3. phylomatic-like service processes names (translate as needed to another taxonomy, then get species tree)
      4. phylomatic-like service returns species tree in standard (newick, nhx, phyloxml, nexml) format
      5. calling script receives species tree
      6. calling script gets gene tree from this family
      7. calling script invokes external tree-reconciling service, sends species tree and gene tree
      8. tree-reconciliation service processes inputs and returns reconcile tree (nhx, nexml, phyloxml format)
      9. calling script receives reconciled tree
      10. calling script sends tree to ATV viewer for user to see
    • visual editor or viewer (phenex, mx mc whatever?)


agenda items in order

  1. Coordinating preparatory work
    1. standards Coordinating preparatory work for the participating standards (NeXML, CDAO, PhyloWS). What needs to be done, who to engage, any milestones.
      • _
    2. data providers Coordinating preparatory work by the participating data providers. What can they do in advance, who will coordinate, cajole, and pester.
      • _
    3. demo projects Coordinating preparatory work by demonstration project programmers. What could they do, who will coordinate.
      • _
    4. end users Coordinating preparatory work by end users.
      • _
    5. minimum reporting standards Coordinating preparatory work for minimum reporting standards involvement.
      • _