Stoltzfus_EvoIO_2010

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Arlin Stoltzfus

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

Technology Education

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

June 29, 2010 iEvoBio Outline ,[object Object]

the EvoIO “stack”

neXML (data format)

phyloWS (web services)

CDAO (ontology)

process (organization, strategy, hackathons)

implementations

how to get involved,[object Object]

June 29, 2010 iEvoBio The Oakland Firestorm of 1991 Image: wikipedia standards are voluntary Seck & Evans, 2004. NISTIR 7158 Oakland conforms to standard

June 29, 2010 iEvoBio Lessons Interoperability standards are developed by stakeholders ,[object Object]

collectively develop the solution Standards are voluntary ,[object Object],To further the goal of interoperability ,[object Object]

enhance benefits of compliance,[object Object]

June 29, 2010 iEvoBio Character-state data model (widely used model underlying CDAO and neXML)

June 29, 2010 iEvoBio Specification: Study use-cases to clarify scope Choice of representation: Choose language and development tools Ontology refinement Conceptualization: ,[object Object]

Build concept glossary

Classify key concepts and relationsImplementation: 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

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Stoltzfus_EvoIO_2010

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.

3. the EvoIO “stack”

4. neXML (data format)

5. phyloWS (web services)

6. CDAO (ontology)

7. process (organization, strategy, hackathons)

8. implementations

9.

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.

12.

13.

14. June 29, 2010 iEvoBio Character-state data model (widely used model underlying CDAO and neXML)

15.

16. Build concept glossary

17. Classify key concepts and relationsImplementation: 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.

19. OTS tools to validate

21.

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.

26. Mesquite, TreeBase (Java) *

27. Phenex (Java via XMLbeans)

28. DendroPy (Python)

30.

32.

34.

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 . . .