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1、Downloadedfromhttp://rsif.royalsocietypublishing.org/onAugust5,2018J.R.Soc.Interface(2009)6,1027–1034doi:10.1098/rsif.2008.0489Publishedonline20January2009Modelvalidationofsimple-graphrepresentationsofmetabolism1,2,*PetterHolme1DepartmentofPhysics,Umea˚University
2、,90187Umea˚,Sweden2ComputationalBiology,RoyalInstituteofTechnology,10044Stockholm,SwedenThelarge-scalepropertiesofchemicalreactionsystems,suchasmetabolism,canbestudiedwithgraph-basedmethods.Todothis,oneneedstoreducetheinformation,listsofchemicalreactions,availabl
3、eindatabases.Evenforthesimplesttypeofgraphrepresentation,thisreductioncanbedoneinseveralways.Weinvestigatedifferentsimplenetworkrepresentationsbytestinghowwelltheyencodeinformationaboutonebiologicallyimportantnetworkstructure—networkmodularity(thepropensityforedg
4、estobeclusteredintodensegroupsthataresparselyconnectedbetweeneachother).Toachievethisgoal,wedesignamodelofreactionsystemswherenetworkmodularitycanbecontrolledandmeasurehowwellthereductiontosimplegraphscapturesthemodularstructureofthemodelreactionsystem.Wefindthatt
5、henetworktypesthatbestcapturethemodularstructureofthereactionsystemaresubstrate–productnetworks(wheresubstratesarelinkedtoproductsofareaction)andsubstancenetworks(withedgesbetweenallsubstancesparticipatinginareaction).Furthermore,wearguethattheproposedmodelforrea
6、ctionsystemswithtunableclusteringisageneralframeworkforstudiesofhowreactionsystemsareaffectedbymodularity.Tothisend,weinvestigatestatisticalpropertiesofthemodelandfind,amongotherthings,thatitrecreatescorrelationsbetweendegreeandmassofthemolecules.Keywords:chemical
7、networks;complexnetworks;chemicalreactionsystems;statisticalgraphmethods1.INTRODUCTIONtemperaturedependence,thesituationgetsevenmoreintricate.)Thecomplexityofmodellingalargemeta-Metabolism,thesetofchemicalprocessessustainingbolicsysteminsuchaframeworkisstaggering
8、.Thelifeinanorganism,isawell-studiedexampleofaapproachwetakedisregardsallthereactioncoefficientschemicalreactionsystem.Suchsystemsarefundamen-andreducesthesyste
