MODEL CODE FOR BIO-SPICE USABILITY TESTING

Five models were used to test several Bio-SPICE tools, editors and simulators, in order to evaluate tool usability.

The five models used were:

• Circadian rhythm, mRNA transcription and protein phosphorylation

(Smolen P et al, J Neurosci, 21:6644-6656, 2001)

      14 ODEs; 20 mass action reactions.

•         Circadian rhythm II, mRNA transcription and protein phosphorylation
       (same as Circadian rhythm scaled to 95 ODEs; 100 mass action reactions.)

•         Cell division cycle, cdc2 and cyclin interactions
      (Tyson J, PNAS, 88:7328-7332, 1991)
         6 ODEs; 14 reaction equations.

•         Allosteric model for glycolytic oscillations
      (Goldbeter A & Lefever R, Biophys J, 12:1302-1315, 1972)
      2 ODEs (minimal model)

•         Memory induction
      (Pettigrew D et al, J Comp Neurosci, 18:163-181, 2005)
      16 ODEs; 39 reaction equations.

	Circadian Rhythm I		Circadian Rhythm II		Cell Division Cycle		Allosteric Glycolytic Oscillations		Memory Induction
	generic	SBML	generic	SBML	generic	SBML	generic	SBML	generic	SBML
BioSpreadSheet/ ESS	Circadian	Circadian	Circadian100		CellCyc
BioSketchPad/ Charon
Jarnac/ JDesigner	Circadian	Circadian	Circadian100		CellCyc	CellCyc	GlycoOsc		MemoryInd
Jigcell	Circadian	Circadian	Circadian100		CellCyc	CellCyc	GlycoOsc		MemoryInd	MemoryInd
Simpathica	Circadian	Circadian	Circadian100	Circadian100	CellCyc	CellCyc
BioNets	Circadian		Circadian100		CellCyc
PathwayBuilder	Circadian	Circadian			CellCyc	CellCyc

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