RecentDevelopmentsandFutureDirectionsinPathway

1、Recent Developments andFuture DirectionsinPathway ToolsPeter D. KarpSRI InternationalRecent DevelopmentsTwo Pathway Tools releases per year: May and NovemberRelease notes are at Note which software component, and whether change applies to desktop, Web, or bothUpgrades recommended at least once per y

2、earRecent Developments Version 9.5New Interfaces to Oracle and MySQL New ontology of cellular components NavigatorMore interactivity in OverviewDisplay of Omics data on individual pathways Save Omics viewer displaysComparative genomicsAlign orthologous genesSummary tablesCross-species comparison of

3、reactions and pathwaysRecent Developments 9.5NavigatorGenome browser improvements Pseudogenes, center gene by clicking on tick mark, TU grey backgroundShow frame in all databasesPromoters and TF binding sites with low quality evidence are drawn using dashed linesEditorsMarvin chemical editor availab

4、leEmbed hyperlinks to PGDB objects within commentsReaction mergingRecent Developments 9.5PathoLogicInference of transport reactionsInferred from free-text descriptions of protein functions in Common-Name slotGUI permits review and editing of inferred reactionsExample: L-lysine periplasm + ATP = L-ly

5、sine + ADP + Pi Pseudogenes handled correctlyOther PGDBs can be used as reference DBs for pathway predictionWindows portRecent Developments Version 9.0NavigatorNew genome browserMore compact pathway diagramsImproved operon depiction in gene pages Recent Developments Version 8.5Cellular Overview and

6、Omics Viewer ImprovedUsers can create combined displays of gene expression, proteomics, metabolomics, and reaction flux measurements on the Omics Viewer Drawing speed is improved Metabolic pathways in the Overview are now grouped by pathway classZooming of the diagram is supported (desktop version o

7、nly) The periplasm and outer membrane have been added to the diagram, as have those proteins present in the periplasm and outer membrane The layout of the Cellular Overview can be computed completely automatically by PathoLogic in a new PGDBCompound stereochemistry supportedSupport for JME chemical

8、editor, molBug ReportsComprehensive bug reports are critical to allowing fast solutionsPlatform and Pathway Tools versionError messageWhat operation was in progress when error occurredBacktrace :zoom :count :allComing in Version 10.0 and LaterSupport for GORepresentation of GO, but no inferenceSeman

9、tic zooming in OverviewWorking on display of names in OverviewImprovements to pathway graphicsExpand comparative genomicsNew advanced query web interfaceDetect dead-end metabolitesWhat Other Features are Needed?Contributions from other groups can accelerate development of Pathway ToolsPast contribut

10、ionsSBML Export (J. Zucker)Import/Export tool (L. Goldovsky)How to Stimulate Software ContributionsDistribution modelsSRI distributesDeveloper distributesSRI runs 3rd-party inference tools during BioCyc generationHow to accelerate development?Tutorials on Pathway Tools internals?Hackathons?Tutorials on Lisp?Tools NeededInference of GO ter