(精选)Scientific Workflow教学课件.pptVIP

* * * * * * * * * * * * * * * * * * * Scientific Workflow, LifeDB andVizBuilder Shahriyar Hossain, Hasan Jamil jamil@ / Backdrop BioFlow (IEEE SWF 2009, 2008) VizBuilder (DILS 2009) Integra (IEEE ICSC 2009, IEEE CIS 2009) SmartBase (FQAS, 2009) LifeDB (DEXA 2009, SWAT4LS 2008) FastWrap (IEEE IRI 2009) OntoMatch (IEEE IRI 2009, FQAS 2009) OntoBuilder (CoopIS 2001, ICDE 2004, AI Mag 2005) What is Scientific Workflow? “A model of the way a scientist works with their data and tools – coordinated data export, import and analysis via software systems” - Bertram Lud?scher Kepler – UC Davis, UC SB, and UC SD Taverna – EMBL-EBI Microsoft VPL …. Differences with Business workflow Scientific workflow deals with larger and more complex data Business workflow is more control oriented Business workflows have to be secure Real-World example The query, or work flow, the user wants to submit is the hypothesis: ”the human p63 transcription factor indirectly regulates certain target mRNAs via direct regulation of miRNAs”. If positive, the user also wants to know the list of miRNAs that indirectly regulate other target mRNAs with high enough confidence score (i.e., pV alue = 0:0006 and targetSites = 2), and so he proceeds as follows. (IEEE SWF 2009) microRNA gene.txt Web-tool (1) - microRNA / microRNA mRNA Why not Python/Perl/Java? Difficult for a domain scientist to - Define - Modify, as the web-links, as well as, the flow might change - Reuse a Python/Perl or Java program. Kepler Predefined component Library which can be extended Drawing Pane LifeDB Web BioFlow Engine Wrapper VizBuilder instruction I/O VizBuilder A web based Visual Programming Environment (Not coupled with BioFlow) No need to learn BioFlow syntax BioFlow define function getMiRNASanger extract microRNA varchar(200), geneName varchar(200), pvalue varchar(30) using wrapper mirnaWrapper in ontology mirnaOntology from http://microrna.sanger.ac.uk/cgi-bin/targets/v5/hit_list.pl/ submit( mirna_id v