SDM center All-hands breakout session notes March 2002 Gatlinburg TN

SDM center Summary l What is our “product”  Web based service geared towards biologists  Workflow based interface  Not providing a toolkit  Long-term / community support a real issue to be resolved in the future  Targeting small number of users in DOE & collab institutions  After 1 year (prior to review)  Focused on single workflow for Matt’s scenario  Workflow interface hosted at NCSU  After 3 years  More general workflow capabilities

SDM center Summary l Demo details  Chip data (download initiated by Matt)  ClusFavor => list of genes  Wrapped (by NCSA?)  User selection of genes => gene accession #s  NCBI keyword search => gene sequences  Eventually need user input here  Blast search against HTGS => alignments  User selection of sequences => 2000bp seq  Transfac / MatInspector => ???? (ask matt)  User input  What do we need to do with final output ??  Alternative scenarios working through this workflow & others

SDM center Summary l Schedule for Demo Sept 9 (all hands meeting)  data / reports through mail list to be archived  Know if we will be ready by all-hands  Plenty of time for Matt to use it before DOE review l NCSU  WSDL description of wrappers and composite w/f  June 15  Workflow interface  Aug 15  Requires obtaining input / output / flow for all wrappers and composite w/f (in XML format) no later than April 15  Will provide links to existing demos in near future

SDM center Summary l SDSC  Workflow scenario  August 15  Will use XWrap generated wrappers to access all sources if wrappers delivered by June 1  Interface  July 15  Specific interface to obtain required user inputs and adjustments in a reasonable fasion  Need intensive interaction with Matt  Additional queries should highlight aspects of semantic integration

SDM center Summary l GT  Wrappers  June 1  5 or 6 wrappers needed depending on Matt’s req for output  Expected to be hand coded using scripting language (which is then fed to wrapper generation code) l Matt  Get example input data sets to us ASAP  Describe how he needs the output of the workflow  Intensive meeting with SDSC (& others?)  Bridge funding? Travel funding?  Sooner the meeting the better  2-3 days ~ 3 hours a day (more or less)

SDM center Summary l Implementation details  Wrappers deployed on server side  Return results in XML  Object code linked in to integration component  Currently hidden by SDSC interface  Agent interfaces developed by NCSU  WSDL / SOAP  Used to connect agents (wrappers) located on distributed sites

SDM center Summary l Repositories  Wrapper repository at GT  Currently in place  Not password protected for now (may change in the future) l Code locations  Wrapper generator at GT  Wrappers transferred to SDSC (via repository)  Query engine at SDSC  Interfaces  SDSC will host “poor mans” interface to workflow scenario  NCSU will host workflow based interface and connect to SDSC service using agent technology  Password protected ( SDM / 1SDM)