Published on

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

Published in: Technology, Education
  • Be the first to comment

  • Be the first to like this

No Downloads
Total views
On SlideShare
From Embeds
Number of Embeds
Embeds 0
No embeds

No notes for slide


  1. 1. June 29, 2010 iEvoBio<br />EvoIO<br /> Community-driven standards for sustainable interoperability<br /><br />Arlin Stoltzfus<br />National Institute of Standards and Technology, Gaithersburg, MD<br />Karen Cranston<br />Field Museum of Natural History, Chicago, IL 50506<br />Hilmar Lapp<br />National Evolutionary Synthesis Center (NESCent), Durham, NC 27705<br />Sheldon McKay<br />Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724<br />Enrico Pontelli<br />Department of Computer Science, New Mexico State University, Las Cruces, NM 88003<br />Rutger Vos<br />University of Reading, Reading, RG6 6BX, United Kingdom<br />Nico Cellinese<br />University of Florida, Florida Museum of Natural History, Gainesville, FL 32611<br />
  2. 2. June 29, 2010 iEvoBio<br />Outline <br /><ul><li> an interop disaster story
  3. 3. the EvoIO “stack”
  4. 4. neXML (data format)
  5. 5. phyloWS (web services)
  6. 6. CDAO (ontology)
  7. 7. process (organization, strategy, hackathons)
  8. 8. implementations
  9. 9. how to get involved</li></li></ul><li>June 29, 2010 iEvoBio<br />Fireplug conforming to NFPA Standard (1905)<br />An interop disaster story<br />Seck & Evans, 2004. NISTIR 7158<br />The Great Baltimore Fire of 1904<br />
  10. 10. June 29, 2010 iEvoBio<br />The Oakland Firestorm of 1991<br />Image: wikipedia<br />standards are voluntary<br />Seck & Evans, 2004. NISTIR 7158<br />Oakland conforms to standard<br />
  11. 11. June 29, 2010 iEvoBio<br />Lessons<br />Interoperability standards are developed by stakeholders<br /><ul><li> organize in response to problem
  12. 12. collectively develop the solution </li></ul>Standards are voluntary<br /><ul><li> compliance is a business decision </li></ul>To further the goal of interoperability<br /><ul><li> mitigate costs of compliance
  13. 13. enhance benefits of compliance</li></li></ul><li>June 29, 2010 iEvoBio<br />EvoIO “stack”<br />
  14. 14. June 29, 2010 iEvoBio<br />Character-state data model<br />(widely used model underlying CDAO and neXML) <br />
  15. 15. June 29, 2010 iEvoBio<br />Specification: <br />Study use-cases to clarify scope<br />Choice of representation: <br />Choose language and development tools<br />Ontology refinement<br />Conceptualization: <br /><ul><li>Identify terms from use cases, artefacts
  16. 16. Build concept glossary
  17. 17. Classify key concepts and relations</li></ul>Implementation: <br />Formalize the concepts and relations using the chosen language and tools<br />Evaluation: <br />Test the ontology for its ability to represent data called for in the use cases, and to support reasoning<br />CDAO development<br />Some CDAO concepts and relations in regard to trees<br />
  18. 18. June 29, 2010 iEvoBio<br />neXML<br /><ul><li> formally defined syntax
  19. 19. OTS tools to validate
  20. 20. extensible
  21. 21. versioned </li></li></ul><li>June 29, 2010 iEvoBio<br />PhyloWS URL API<br />Subdomain for<br />any phylogenetic<br />resource<br />Subdomain for<br />PhyloWS API<br /><br />Permanent URL <br />resolver domain<br />Subdomain<br />for TreeBASE<br />Object ID<br />
  22. 22. June 29, 2010 iEvoBio<br />2007<br />2008<br />2009<br />2010<br />2011<br />Process<br />Planning meeting (Philly)<br />Phylohackathon (Durham)<br />WG1<br />neXML<br />WG2<br />DB interop hackathon (Durham)<br />CDAO (Durham)<br />WG3<br />PhyloWS (Tokyo)<br />Google Summer-of-Code<br />WG4<br />Google Summer-of-Code<br />Evolutionary Informatics Working Group<br />Phyloinformatics VoCamp (Montpellier, Fr)<br />Google Summer-of-Code<br />
  23. 23. June 29, 2010 iEvoBio<br />2009 Data resource interop hackathon<br />Image: Hilmar Lapp<br />
  24. 24. June 29, 2010 iEvoBio<br />Jim Balhoff<br />National Evolutionary Synthesis Center, Durham, NC<br />Rutger Vos<br />University of Reading, Reading, RG6 6BX, United Kingdom<br />Vivek Gopalan<br />Bioinformatics and Computational Biosciences Branch (BCBB), NIAID<br />Brandon Chisham<br />New Mexico State University, Las Cruces, NM<br />Implementations<br />Nexml IO implementations<br /><ul><li> Bio::Phylo, BioPerl, HIVQuery (Perl)
  25. 25. DAMBE (C)
  26. 26. Mesquite, TreeBase (Java) *
  27. 27. Phenex (Java via XMLbeans)
  28. 28. DendroPy (Python)
  29. 29. NCL (C++)
  30. 30. BioRuby (Ruby)</li></ul>PhyloWS<br /><ul><li> Phylr
  31. 31. TreeBase2
  32. 32. Bio::Phylo (ToLWeb and TimeTree via screen-scraping)</li></ul>CDAO<br /><ul><li>Nexplorer3
  33. 33. CDAO-store
  34. 34. translations</li></li></ul><li>June 29, 2010 iEvoBio<br />Stack development<br />Arlin<br />Karen<br />Interop targets <br />Hilmar<br />Sheldon<br />Enrico<br />Rutger<br />Nico<br />How to get involved<br /><br />
  35. 35. June 29, 2010 iEvoBio<br />Extra slides<br />Not used, due to time limitations<br />
  36. 36. June 29, 2010 iEvoBio<br />Organizational values<br />Flexible task-specific groups<br />Heavy use of electronic collaboration tools<br />Open-source code<br />Open development teams<br />Consensus decision-making <br />Flexible leadership<br />Coffee<br />
  37. 37. June 29, 2010 iEvoBio<br />The hackathon model<br />Before the event <br />Organizers develop theme<br />Organizers recruit participants <br />At the event, day 1<br />Initial presentations, group discussion<br />Participants self-organize around “pitches”<br />At the event, after day 1<br />Participants work on project goals<br />After the event . . .<br />