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System BiologyYeremiah R. TjaminFrom -logy To -omicsParadigm of modern world: every thing is connectedso is scienceWe should shift from compartmentalized science, teaching and learning to system science, teaching and learningGenetics GenomicsProtein Biochemistry ProteomicsMetabolism MetabolomicsSBMLSystem Biology Markup LanguageProgramming language use in system processes modelingImplemented in many system modeling softwares: CellDesignerInfobiotics WorkbenchSBML Toolbox For MatlabPortability and interoperability

Implementation In CellDesignerCellDesigner: a graphical interface for drawing process diagram of biochemical reaction or gene regulationStore in sbmlRun in simulation workbench:SBW: System Biology WorkbenchInfobiotics WorkbenchModeling A Simple Gene RegulationA gene G produced a protein PProtein P is also degradedExpression of G can be repressed by the negative transcription factor R, which binds with G to form a complex R.G. This prevents G from producing PThe action of R is itself inhibited by protein I, which binds to R to form a complex R.I; so prevents the binding of R to G

Representation In P System ReactionG G + PP R + G R.GR.G R + GR + I R.IR.I R + I

k1k2k3k4k5k6Reaction Constantsk1 = 0,1k2 = 0,01k3 = 1k4 = 1k5 = 1k6 = 1

Initial ConditionsG0 = 1R0 = 1I0 = 1P0 = 0R.G0 = 0R.I0 = 0

Model Specification In CellDesigner

Run In Infobiotics WorkbenchNumber of P molecules:

What Is The System Response Time?

Model Specification In JDesigner

Run In SBW Simulation Tool