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1、SYSTEMSBIOLOGY:SIMULATIONOFDYNAMICNETWORKSTATESBiophysicalmodelshavebeenusedinbiologyfordecades,buttheyhavebeenlimitedinscopeandsize.Inthisbook,BernhardØ.Palssonshowshownetworkreconstructionsthatarebasedongenomicandbibliomicdata,andtaketheformofestablishedstoichiometricma
2、trices,canbeconvertedintodynamicmodelsusingmetabolomicandfluxomicdata.TheMassActionSto-ichiometricSimulation(MASS)procedurecanbeusedforanycellularprocessforwhichdataisavailableandallowsascalablestep-by-stepapproachtothepracticalconstructionofnetworkmodels.Specifically,itcan
3、treatintegratedprocessesthatneedexplicitaccountingofsmallmoleculesandproteins,whichallowssimulationatthemolecularlevel.Thematerialhasbeenclass-testedbytheauthoratboththeundergraduateandgraduatelevel.AllcomputationsinthetextareavailableonlineinMATLABRandMATHEMATICARworkb
4、ooks,allowinghands-onpracticewiththematerial.BernhardØ.PalssonisTheGallettiProfessorofBioengineeringandAdjunctProfessorofMedicineattheUniversityofCalifornia,SanDiego.SystemsBiologySIMULATIONOFDYNAMICNETWORKSTATESBernhardØ.PalssonUniversityofCalifornia,SanDiegoCAMBRIDGEUNI
5、VERSITYPRESSCambridge,NewYork,Melbourne,Madrid,CapeTown,Singapore,S˜aoPaulo,Delhi,Tokyo,MexicoCityCambridgeUniversityPressTheEdinburghBuilding,CambridgeCB28RU,UKPublishedintheUnitedStatesofAmericabyCambridgeUniversityPress,NewYorkwww.cambridge.orgInformationonthistitle:ww
6、w.cambridge.org/9781107001596CB.Ø.Palsson2011Thispublicationisincopyright.Subjecttostatutoryexceptionandtotheprovisionsofrelevantcollectivelicensingagreements,noreproductionofanypartmaytakeplacewithoutthewrittenpermissionofCambridgeUniversityPress.Firstpublished2011Print
7、edintheUnitedKingdomattheUniversityPress,CambridgeAcataloguerecordforthispublicationisavailablefromtheBritishLibraryISBN978-1-107-00159-6HardbackAdditionalresourcesforthispublicationathttp://systemsbiology.ucsd.eduCambridgeUniversityPresshasnoresponsibilityforthepersisten
8、ceoraccuracyofURLsforexternalorthird-partyinternetwebsitesreferredtointhispublication,anddoesnot
