From Evolutionary Informatics Working Group
Revision as of 15:50, 10 March 2009 by Dpc13 (talk) (Original proposal (June 2006))
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Documents in progress (or links to completed versions)

Reports to NESCent

Third Report to NESCent (May, 2008 meeting)

Second Report to NESCent (Nov, 2007 meeting)

First Report to NESCent (Jun, 2007 meeting)

Current planning notes (projects, goals)

Next meeting in Fall of 2008

Deliverables and goals


NeXML implementation is starting to appear in a number of toolkits and programs. This provides potential for growth but does not drive growth, hence, further implementation drives during the meeting is perhaps not the best thing to do. The next step now is to make it attractive by providing "carrots" for adoption. For example:

These services include a lot of unconstrained metadata, for example:

  • attachments that refer to publications
  • attachments that indicate what data type a tree was based on
  • whether species in a ToLweb subtree are extinct
  • want to integrate with ontology; bind terms to ontology, projects that create carrots
    • NeXML interface to TimeTree as a test case for tying metadata to ontology
      • how many estimates are tied to nuclear DNA data
    • Tree of Life services, refers to publications, good to have consistent ref to publications
    • exercise: get estimates on primate divergences to rate-smooth trees
    • NeXML output for Phenote program to infer character-state matrices
  • CarrotBase
    • requires identifying strategic partners
    • Arlin needs to work on this to see if they are willing
    • biomoby-mygrid good crowd to work with
  1. date
  2. goals
  3. guests

Outreach, dissemination, partnering

To do:

  1. evoinfo web presence enhancements
    • blog
      • set up (hilmar)
      • recruit group members to post at combined rate of 1 per week or more
    • CDAO web site at
      • contact NESCent IT to set up project space with accounts for principals
      • implement new design from Francisco
      • contact other projects to share domain name
  2. MIAPA
    • consider knowledge capture project
      • assemble resources
      • consider white paper
      • consider how to adapt phenote code
      • try getting code from project described by Good, et al
  3. Phenoscape
    • follow up on C. elegans project with Phenote (arlin)
      • need to convert OWL ontos to OBO (see
      • seems like I can only do one type of character per phenote config file. how about a hierarchy? make a feature request.
  4. Dryad - nothing in particular?


  1. MIAPA
    • add Jim Leebens-Mack to group list (arlin, 5/28/08)
    • consider knowledge capture project
      • follow up with Brian O'Meara (arlin, 5/26/08)
        • add Brian to email list, include in follow-ups (arlin, 5/28/08)

Adjunct projects and collaborations

MIAPA, CarrotBase

Ongoing projects

Future data exchange standard

To do:

  1. NeXML manuscript
    • venue
    • outline
    • authors
    • deadlines
  2. implementation target strategy
    • see notes from day 4
    • need to develop plan
    • consider recruiting leaders in addition to Hilmar

Comparative Data Analysis Ontology

To do:

  1. mapping with NeXML (Enrico)
    • formalize
    • write description for wiki
  2. miscellaneous
    • consider starting a mailing list for discussion?
    • see web site issues under "Outreach" (Francisco)


  1. manuscript (Arlin, Julie, Enrico)
  2. miscellaneous
    • add rutger to access list for cdao (arlin, 5/28/08)

Substitution (transition) model language

  1. initial straw-man version from working group meeting
    • tangible outcome-- a version of code linked somewhere! (hilmar, xuhua)
  2. plan for moving forward
    • consider term list from TreeTapper project
    • MIAPA compliance could be a target

Historical Archive

Meeting Notes, Third Meeting (19-23 May, 2008)

Please see the separate Meeting_3_notes page.

Meeting Notes, Second Meeting (12-14 November, 2007)

Please see the separate Meeting_2_notes page.

Meeting Notes, First Meeting (20-23 May, 2007)

Please see the separate Meeting_1_notes page.

Identifying top-priority challenges (March, 2007)

As its first activity, the working group completed a prioritization task. Each participant was asked to identify the top 3 goals from a set of 10 possibilities. Supporting current standards was the only clear winner in our prioritization exercise-- 8 out of 13 respondents put it in the top 3, and 5 chose it as the #1 priority.

However, we also need to develop a strategy for the remaining goals, each of which was assigned a high priority by two or more participants. The organizers have de-prioritized the Database Archive goal because there is already a consortium of scientists addressing this issue (see pPOD). We are working on a strategy to prioritize and order the remaining goals. For a graphical presentation, see the attached document, File:Goals strategy.pdf.

Goals of high priority

  1. Supporting current file format standards
  2. description language for state-transition models
  3. A library of examples (canonical uses)
  4. Developing a next-generation data exchange standard
  5. Analysis Templates to allow a novice user to carry out an analysis designed by an expert.
  6. The future: identifying new demands from new types of data and analyses
  7. support for validation and comparative assessment of methods

Goals of low priority

We have no plan to address these goals as a group. Nevertheless, they are important. The Database Archive goal is being addressed by another group. For the remaining goals, the organizers strongly encourage group members to assess needs and develop strategies to address the goals (use the wiki pages below), with a view toward writing a white paper or proposing a future working group.

Original proposal (June 2006)

Rutger Vos and Arlin Stoltzfus wrote the original proposal for a NESCent working group in evolutionary informatics. The proposal stressed supporting current standards, particularly NEXUS, but defined the problem of support very broadly to include support for creation, validation, editing, visualization, storage, and conversion of NEXUS files.