celldesigner tutorial

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

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

3、resentingmodelsofbiochemicalreactionnetworksOver100softwarepackagessupportSBMLBioPAX(BiologicalPAthwayeXchange)formatforstoringbiologicalpathwaydata;ontologyfordescribingbiochemicalprocessesandtheirhierarchiesSBGN(SystemsBiologyGraphicalNotation)formatforrepresentinggraphicallybiologicalinte

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

5、athematicalsimulationsDatabaseconnectionExporttoPDF,PNG,…FreelyavailableSupportedEnvironmentWindows(2000orlater)MacOSXLinuxWhatisCellDesignergoodfor?CellDesigner:Offersan« easy-to-use »graphicalrepresentationofanetworkFacilitatesexchangeofmodelsdevelopedbydifferentgroups,usingastandardlanguag

6、e(SBML:SystemsBiologyMarkupLanguage)Allowstoannotatethereactions,proteins,genes,etc.Proposeslinkstootherdatabases(PubMed,IHOP,BioModels,KEGG,etc.)OrganizesalotofinformationinauniquediagramAllowsanexchangewithothermodelingtoolsInstallandStartCellDesignerDownloadCellDesignerversion4.0βfromhttp:

7、//celldesigner.orgDownload:Setup:Launch:StartCellDesignerCellDesignerscreenGeneralviewTREEAREAdisplaysallthelistofthecomponentsinatreestructure.DRAWAREAistheareawherethemodelisbuiltfromthetoolbaritems.LISTAREAdisplaysandeditsthelistofthecompo