1. Postdoc Meeting 1/4/11

2. Round-Robin Introductions NameInstitutionRole Bindu JosephUC DavisPostdoc Lin WangCornellPostdoc Christos NoutsosCSHLPostdoc Lecong ZhouVirginia TechScientific Analyst Wacek KusnierczykKSUPostdoc Chunlao TangCSHLPostdoc Eric LyonsUA/iPlantScientific Developer Liya WangCSHLScientific Analyst Jerry LuCSHLScientific Analyst Cornel GhibanCSHLScientific Developer Martha NarroUA/iPlantProject Coordinator Karla GendlerUA/iPlantManager/Analyst

3. Objectives Why learn about the integration process? – You can assist in identifying and evaluating tools that can be integrated, as well as analyses than can be constructed using them – Your experiences can shape the design of the API and its associated toolkit – You can participate in bringing valuable tools into the iPlant CI – You can serve as a resource for other people interested in building content for iPlant – You can bring your own scientific workflows and analyses into the iPlant DE. This is your chance to be famous ;-)

4. Homework ToolAssigneeNotes RQtlChristos/LiyaStarting w/ QTL package is a little too ambitious GeneManiaBinduMix of file- and option based configuration. May require two steps to run a GM analysis. BismarckJerryStraighforward, simple command model ermineJLecongApp is easy to use but has data file dependencies RMAPJerryStraighforward, simple command model MUSCLEKarlaVery complex program. Seems to require decision tree support in configuration. Tuxedo SuiteMattLarge numbers of often conflicting parameters. Mix of command flag styles. TargetPWaclawSimple parameter set, straightforward application. ClustalWMarthaModerately complex parameters. May need decision tree support. GAGEChunlao TAULin

5. Lessons So Far Simple transactional applications are easiest to describe. R packages require special treatment, and so do some Java applications. Complex configuration (decision trees) models are required in some cases. Older applications (MUSCLE, ClustalW) can have odd configuration modes or are more like comprehensive software suites.

6. The iPlant Integration Model Programs installed on iPlant Linux nodes Job Execution Framework Job Submission Framework Tool and Analysis Metadata Manager Discovery Environment Analysis 1 Tool A Tool Z Analysis 2 Tool A Tool X JSON: JavaScript Object Notation

7. BOWTIE

8. Postdoc Update Christos Noutsos