systems biology - dynamic pathway modeling - olaf waulkenhour

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1、OlafWolkenhauerwww.sbi.uni-rostock.deApril8,2005cCopyrightO.Wolkenhauer.Allrightsreserved.Thisworkmaynotbetranslatedorcopiedinwholeorinpartwithoutpermissionoftheauthor.Distributionoruseinconnectionwithanyformofelectronicstorage,computersoftwareorinternette

2、chnologyisonlyallowedwithpermissionoftheauthor.iiThisisadraftmanuscriptWhileinthepastitwasmorecommontomakepreprints,algorithmsandsoftwarefreelyavailable,authorshavebecomemoreprotectiveoftheirwork.Idonotknowwhetherthisisare ectionoftheincreasedcom-petitionf

3、orrecognitionorthepressuretocommercializeresearchresults.BymakingthesenotesavailableIhopetoreceiveinformationabouterrors,misconceptions,missingreferencesoracknowledgment,andsuggestionstoimprovethetext.Inthemodernworldofpublishingonealsofeelsaneedtoclarifyt

4、hattheauthormakesnonowarrantyofanykind,expressedorimplied,withregardtoprograms,algorithms,theoreticalconcepts,orthedocumentationcontainedinthismanuscript.Theauthorshallnotbeliableinanyeventforincidentalorconsequentialdamagesinconnectionwith,orarisingoutof,

5、theuseofthematerialprovidedhere.CONTENTSiiiContents1Prefacevi2ModellingNaturalSystems12.0.1DierentialEquations..........................32.0.2DynamicSystemsTheory........................62.0.3DealingwithUncertainty........................102.0.4TheSystems

6、BiologyApproach.....................142.1CellChemistry..................................172.2CellSignalling..................................192.3ExperimentalTechniques............................232.3.1GelElectrophoresis............................232.3.2

7、Blotting..................................232.3.3ScanningandLaserDensitometryofWesternBlots..........242.3.4QuanticationofWesternblots-GeneralConsiderations......252.4TheDynamicProteome.............................272.5ZoomingIn...........................

8、.........292.6Outlook......................................363BiochemicalReactions393.1TheODEApproach...............................393.1.1Dierentialvs.DierenceEquations..................423.1.2NumericalSim