celldesigner tutorial

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1、CellDesignerTutorialLaurenceCalzone,AndreiZinovyevUMRU900INSERM/InstitutCurie/EcoledesMinesdeParisWednesday,April30thOutlineCellDesignerTutorial-PracticeExampleVarietyofmodels:exampleofNFkBAmodelcanberepresentedinmanydifferentways:Manyrepresentationsforthesamemodel.=>Eachmodelerusesitsownreprese

2、ntation=>Needtoreadthepapertounderstandthemodel=>Beforebeingabletouseortranslatemodelsintomathematics,needtounderstandthemodeler’ssymbols=>Needforastandardformattobeableto-usemodels-exchangemodels-comparemodels-composemodels-etc.StandardformatsSBML(SystemsBiologyMarkupLanguage)formatforrepresent

3、ingmodelsofbiochemicalreactionnetworksOver100softwarepackagessupportSBMLBioPAX(BiologicalPAthwayeXchange)formatforstoringbiologicalpathwaydata;ontologyfordescribingbiochemicalprocessesandtheirhierarchiesSBGN(SystemsBiologyGraphicalNotation)formatforrepresentinggraphicallybiologicalinteractionse

4、.g.protein-proteininteraction,generegulatorynetworks,etc.CellDesigner:ashortoverviewWhatisCellDesigner?CellDesignerisastructureddiagrameditorfordrawinggene-regulatoryandbiochemicalnetworksthatusesstandardformats.CellDesignercontentFullSBMLsupportGraphicalnotation(SBGN)Possibilityformathematicals

5、imulationsDatabaseconnectionExporttoPDF,PNG,…FreelyavailableSupportedEnvironmentWindows(2000orlater)MacOSXLinuxWhatisCellDesignergoodfor?CellDesigner:Offersan« easy-to-use »graphicalrepresentationofanetworkFacilitatesexchangeofmodelsdevelopedbydifferentgroups,usingastandardlanguage(SBML:SystemsB

6、iologyMarkupLanguage)Allowstoannotatethereactions,proteins,genes,etc.Proposeslinkstootherdatabases(PubMed,IHOP,BioModels,KEGG,etc.)OrganizesalotofinformationinauniquediagramAllowsanexchangewithothermodelingtoolsInstallandStartCellDesignerDownloadCellDesignerversion4.0βfromhttp://celldesigner.org

7、Download:Setup:Launch:StartCellDesignerCellDesignerscreenGeneralviewTREEAREAdisplaysallthelistofthecomponentsinatreestructure.DRAWAREAistheareawherethemodelisbuiltfromthetoolbaritems.LISTAREAdisplaysandeditsthelistofthecompo