ezBioNet: A Modeling and Simulation System for Analyzing Biological Reaction Networks

Abstract

Toachieverobustnessagainstlivingenvironments,alivingorganismiscomposedofcomplicated regulatorymechanismsrangingfromgeneregulationstosignaltransduction.Ifsuchlifephenomena aretobeunderstand,anintegratedanalysistoolthatshouldhavemodelingandsimulation functionsforbiologicalreactions,aswellasnewexperimentalmethodsformeasuringbiologicalphenomena, isfundamentallyrequired.Wehavedesignedandimplementedmodelingandsimulation software(ezBioNet)foranalyzingbiologicalreactionnetworks.Thesoftwarecansimultaneously performanintegratedmodelingofvariousresponsesoccurringincells,rangingfromgeneexpressions tosignalingprocesses.Tosupportmassiveanalysisofbiologicalnetworks,wehaveconstructed aserver-sidesimulationsystem(VCellSim)thatcanperformordinarydifferentialequations(ODE) analysis,sensitivityanalysis,andparameterestimates.ezBioNetintegratestheBioModeldatabase byconnectingtheeuropeanbioinformaticsinstitute(EBI)serversthroughWebservicesAPIsand supportsthehandlingofsystemsbiologymarkuplanguage(SBML)files.Inaddition,weemployed eclipseRCP(richclientplatform)whichisapowerfulmodularityframeworkallowingvariousfunctional expansions.ezBioNetisintendedtobeaneasy-to-usemodelingtool,aswellasasimulation system,tounderstandthecontrolmechanismbymonitoringthechangeofeachcomponentina biologicalnetwork.Aresearchermayperformthekineticmodelingandexecutethesimulation. ThesimulationresultcanbemanagedandvisualizedonezBioNet,whichisfreelyavailableat http://ezbionet.cbnu.ac.kr.