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Stoltzfus_EvoIO_2010

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Presentation on the EvoIO collaborative (evoio.org) given by Arlin Stoltzfus June 29, 2010, at the iEvoBio conference in Portland, OR (USA).

Presentation on the EvoIO collaborative (evoio.org) given by Arlin Stoltzfus June 29, 2010, at the iEvoBio conference in Portland, OR (USA).

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  • 1. June 29, 2010 iEvoBio
    EvoIO
    Community-driven standards for sustainable interoperability
    www.evoio.org
    Arlin Stoltzfus
    National Institute of Standards and Technology, Gaithersburg, MD arlin@umd.edu
    Karen Cranston
    Field Museum of Natural History, Chicago, IL 50506
    Hilmar Lapp
    National Evolutionary Synthesis Center (NESCent), Durham, NC 27705
    Sheldon McKay
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
    Enrico Pontelli
    Department of Computer Science, New Mexico State University, Las Cruces, NM 88003
    Rutger Vos
    University of Reading, Reading, RG6 6BX, United Kingdom
    Nico Cellinese
    University of Florida, Florida Museum of Natural History, Gainesville, FL 32611
  • 2. June 29, 2010 iEvoBio
    Outline
    • an interop disaster story
    • 3. the EvoIO “stack”
    • 4. neXML (data format)
    • 5. phyloWS (web services)
    • 6. CDAO (ontology)
    • 7. process (organization, strategy, hackathons)
    • 8. implementations
    • 9. how to get involved
  • June 29, 2010 iEvoBio
    Fireplug conforming to NFPA Standard (1905)
    An interop disaster story
    Seck & Evans, 2004. NISTIR 7158
    The Great Baltimore Fire of 1904
  • 10. June 29, 2010 iEvoBio
    The Oakland Firestorm of 1991
    Image: wikipedia
    standards are voluntary
    Seck & Evans, 2004. NISTIR 7158
    Oakland conforms to standard
  • 11. June 29, 2010 iEvoBio
    Lessons
    Interoperability standards are developed by stakeholders
    • organize in response to problem
    • 12. collectively develop the solution
    Standards are voluntary
    • compliance is a business decision
    To further the goal of interoperability
    • mitigate costs of compliance
    • 13. enhance benefits of compliance
  • June 29, 2010 iEvoBio
    EvoIO “stack”
  • 14. June 29, 2010 iEvoBio
    Character-state data model
    (widely used model underlying CDAO and neXML)
  • 15. June 29, 2010 iEvoBio
    Specification:
    Study use-cases to clarify scope
    Choice of representation:
    Choose language and development tools
    Ontology refinement
    Conceptualization:
    • Identify terms from use cases, artefacts
    • 16. Build concept glossary
    • 17. Classify key concepts and relations
    Implementation:
    Formalize the concepts and relations using the chosen language and tools
    Evaluation:
    Test the ontology for its ability to represent data called for in the use cases, and to support reasoning
    CDAO development
    Some CDAO concepts and relations in regard to trees
  • 18. June 29, 2010 iEvoBio
    neXML
    • formally defined syntax
    • 19. OTS tools to validate
    • 20. extensible
    • 21. versioned
  • June 29, 2010 iEvoBio
    PhyloWS URL API
    Subdomain for
    any phylogenetic
    resource
    Subdomain for
    PhyloWS API
    http://purl.org/phylo/treebase/phylows/study/TB2:S1787
    Permanent URL
    resolver domain
    Subdomain
    for TreeBASE
    Object ID
  • 22. June 29, 2010 iEvoBio
    2007
    2008
    2009
    2010
    2011
    Process
    Planning meeting (Philly)
    Phylohackathon (Durham)
    WG1
    neXML
    WG2
    DB interop hackathon (Durham)
    CDAO (Durham)
    WG3
    PhyloWS (Tokyo)
    Google Summer-of-Code
    WG4
    Google Summer-of-Code
    Evolutionary Informatics Working Group
    Phyloinformatics VoCamp (Montpellier, Fr)
    Google Summer-of-Code
  • 23. June 29, 2010 iEvoBio
    2009 Data resource interop hackathon
    Image: Hilmar Lapp
  • 24. June 29, 2010 iEvoBio
    Jim Balhoff
    National Evolutionary Synthesis Center, Durham, NC
    Rutger Vos
    University of Reading, Reading, RG6 6BX, United Kingdom
    Vivek Gopalan
    Bioinformatics and Computational Biosciences Branch (BCBB), NIAID
    Brandon Chisham
    New Mexico State University, Las Cruces, NM
    Implementations
    Nexml IO implementations
    • Bio::Phylo, BioPerl, HIVQuery (Perl)
    • 25. DAMBE (C)
    • 26. Mesquite, TreeBase (Java) *
    • 27. Phenex (Java via XMLbeans)
    • 28. DendroPy (Python)
    • 29. NCL (C++)
    • 30. BioRuby (Ruby)
    PhyloWS
    • Phylr
    • 31. TreeBase2
    • 32. Bio::Phylo (ToLWeb and TimeTree via screen-scraping)
    CDAO
  • June 29, 2010 iEvoBio
    Stack development
    Arlin
    Karen
    Interop targets
    Hilmar
    Sheldon
    Enrico
    Rutger
    Nico
    How to get involved
    www.evoio.org
  • 35. June 29, 2010 iEvoBio
    Extra slides
    Not used, due to time limitations
  • 36. June 29, 2010 iEvoBio
    Organizational values
    Flexible task-specific groups
    Heavy use of electronic collaboration tools
    Open-source code
    Open development teams
    Consensus decision-making
    Flexible leadership
    Coffee
  • 37. June 29, 2010 iEvoBio
    The hackathon model
    Before the event
    Organizers develop theme
    Organizers recruit participants
    At the event, day 1
    Initial presentations, group discussion
    Participants self-organize around “pitches”
    At the event, after day 1
    Participants work on project goals
    After the event . . .