JSim Biomodels Page
This page allows users to run models from the Biomodels Database under JSim. To run these models online, you must have a Java plugin installed in your WWW browser. To run them in JSim on your own computer, download the model code and the JSim application. Either way, see Running JSim for instructions on how to use JSim. Since these models do not specify simulation time length or delta, these must be set by the user before running the model.
Notes:
- Models on this page require JSim version 1.6.84 or higher.
- JSim does not yet support SBML events. Those models containing SBML events will show warnings in the translated MML source code.
Return to complete JSim model archives.
Currently available models
- Number of models in this archive: 172
- Number of models currently runnable under JSim: 171
- Number of runnable models containing unsupported events: 46
BIOMD0000000001: Edelstein1996 EPSP AChEvent
BIOMD0000000002: Edelstein1996 EPSP AChSpecies
BIOMD0000000003: Goldbeter1991 MinMitOscil
BIOMD0000000004: Goldbeter1991 MinMitOscil ExplInact
BIOMD0000000005: Tyson1991 CellCycle 6var
BIOMD0000000006: Tyson1991 CellCycle 2var
BIOMD0000000007: Novak1997 CellCycle
BIOMD0000000008: No description available
BIOMD0000000009: No description available
BIOMD0000000010: No description available
BIOMD0000000011: Levchenko2000 MAPK noScaffold
BIOMD0000000012: Elowitz2000 Repressilator
BIOMD0000000013: Poolman2004 CalvinCycle
BIOMD0000000014: Levchenko2000 MAPK Scaffold
BIOMD0000000015: Curto1998 purineMetabol
BIOMD0000000016: Goldbeter1995 CircClock
BIOMD0000000017: No description available
BIOMD0000000018: Morrison1989 FolateCycle
BIOMD0000000020: hodgkin-huxley squid-axon 1952
BIOMD0000000021: Leloup1999 CircClock
BIOMD0000000022: No description available
BIOMD0000000023: Rohwer2001 Sucrose
BIOMD0000000024: Scheper1999 CircClock
BIOMD0000000025: Smolen2002 CircClock
BIOMD0000000026: Markevich2004 MAPK orderedElementary
BIOMD0000000027: Markevich2004 MAPK orderedMM
BIOMD0000000028: Markevich2004 MAPK phosphoRandomElementary
BIOMD0000000029: Markevich2004 MAPK phosphoRandomMM
BIOMD0000000030: Markevich2005 MAPK AllRandomElementary
BIOMD0000000031: Markevich2004 MAPK orderedMM2kinases
BIOMD0000000032: Kofahl2004 pheromone
BIOMD0000000033: No description available
BIOMD0000000034: Smolen2004 CircClock
BIOMD0000000035: Vilar2002 Oscillator
BIOMD0000000036: Tyson1999 CircClock
BIOMD0000000037: No description available
BIOMD0000000038: Rohwer2000 Phosphotransferase System
BIOMD0000000039: Marhl2000 CaOscillations
BIOMD0000000040: Field1974 Oregonator
BIOMD0000000041: Kongas2001 creatine
BIOMD0000000042: Nielsen1998 Glycolysis
BIOMD0000000043: Borghans1997 CaOscillation model1
BIOMD0000000044: Borghans1997 CaOscillation model2
BIOMD0000000045: Borghans1997 CaOscillation model3
BIOMD0000000046: Olsen2003 peroxidase
BIOMD0000000047: Oxhamre2005 Ca oscillation
BIOMD0000000048: Kholodenko1999 EGFRsignaling
BIOMD0000000049: Sasagawa2005 MAPK
BIOMD0000000050: Martins2003 AmadoriDegradation
BIOMD0000000051: Chassagnole2002 Carbon Metabolism
BIOMD0000000052: Brands2002 MonosaccharideCasein
BIOMD0000000053: Ferreira2003 CML generation2
BIOMD0000000054: Ataullahkhanov1996 Adenylate
BIOMD0000000055: Locke2005 CircClock
BIOMD0000000056: Chen2004 CellCycle
- JSim version not yet available
BIOMD0000000057: Sneyd2002 IP3 Receptor
BIOMD0000000058: Bindschadler2001 coupled Ca oscillators
BIOMD0000000059: Fridlyand2003 Calcium flux
BIOMD0000000060: No description available
BIOMD0000000061: Hynne2001 Glycolysis
BIOMD0000000062: bhartiya2003 tryptophan operon
BIOMD0000000063: Galazzo1990 pathway kinetics
BIOMD0000000064: Teusink2000 Glycolysis
BIOMD0000000065: Yildirim2003 Lac Operon
BIOMD0000000066: Chassagnole2001 Threonine Synthesis
BIOMD0000000067: Fung2005 Metabolic Oscillator
BIOMD0000000068: Curien2003 MetThr synthesis
BIOMD0000000069: Fuss2006 MitoticActivation
BIOMD0000000070: Holzhutter2004 Erythrocyte Metabolism
BIOMD0000000071: Bakker2001 Glycolysis
BIOMD0000000072: Yi2003 GproteinCycle
BIOMD0000000073: Leloup2003 CircClock DD
BIOMD0000000074: Leloup2003 CircClock DD REV-ERBalpha
BIOMD0000000075: Xu2003 Phosphoinositide turnover
BIOMD0000000076: Cronwright2002 Glycerol Synthesis
BIOMD0000000077: Blum2000 LHsecretion 1
BIOMD0000000078: Leloup2003 CircClock LD
BIOMD0000000079: Goldbeter2006 weightCycling
BIOMD0000000080: Thomsen1989 AdenylateCyclase
BIOMD0000000081: Suh2004 KCNQ Regulation
BIOMD0000000082: Thomsen1988 AdenylateCyclase Inhibition
BIOMD0000000083: Leloup2003 CircClock LD REV-ERBalpha
BIOMD0000000084: Hornberg2005 ERKcascade
BIOMD0000000085: Maurya2005 GTPaseCycle reducedOrder
BIOMD0000000086: Bornheimer2004 GTPaseCycle
BIOMD0000000087: Proctor2006 telomere
BIOMD0000000088: Maeda2006 MyosinPhosphorylation
BIOMD0000000089: Locke2006 CircClock LL
BIOMD0000000090: Wolf2001 respiratory oscillations
BIOMD0000000091: Hsp90model basis510
BIOMD0000000092: Fuentes2005 ZymogenActivation
BIOMD0000000093: Yamada2003 JAK STAT pathway
BIOMD0000000094: Yamada2003 JAK STAT SOCS1 knockout
BIOMD0000000095: Zeilinger2006 PRR7-PRR9-Y
BIOMD0000000096: Zeilinger2006 PRR7-PRR9light-Y
BIOMD0000000097: Zeilinger2006 PRR7-PRR9light-Yprime
BIOMD0000000098: Goldbeter1990 Ca Oscillations
BIOMD0000000099: Laub1998 SpontaneousOscillations
BIOMD0000000100: Rozi2003 GlycogenPhosphorylase Activation
BIOMD0000000101: Vilar2006 TGFbeta
BIOMD0000000102: Legewie2006 apoptosis WT
BIOMD0000000103: Legewie2006 apoptosis NC
BIOMD0000000104: Klipp2002 MetabolicOptimization linearPathway(n=2)
BIOMD0000000105: No description available
BIOMD0000000106: Yang2007 ArachidonicAcid
BIOMD0000000107: Novak1993 M phase control
BIOMD0000000108: Kowald2006 SOD
BIOMD0000000109: Haberichter2007 cellcycle
BIOMD0000000110: Qu2003 CellCycle
BIOMD0000000111: Novak2001 FissionYeast CellCycle
BIOMD0000000112: Clarke2006 Smad signalling
BIOMD0000000113: Dupont1992 Ca dpt protein phospho
BIOMD0000000114: Somogyi1990 CaOscillations
BIOMD0000000115: Somogyi1990 CaOscillations SingleCaSpike
BIOMD0000000116: McClean2007 CrossTalk
BIOMD0000000117: Dupont1991 CaOscillation
BIOMD0000000118: Golomb2006 SomaticBursting
BIOMD0000000119: Golomb2006 SomaticBursting nonzero[Ca]
BIOMD0000000120: Chan2004 TCell receptor activation
BIOMD0000000121: Clancy2001 Kchannel
BIOMD0000000122: Fisher2006 Ca Oscillation dpdnt NFAT dynamics
BIOMD0000000123: Fisher2006 NFAT Activation
BIOMD0000000124: Wu2006 K+Channel
BIOMD0000000125: Komarova2005 TheoreticalFramework BasicArchitecture
BIOMD0000000126: Clancy2002 CardiacSodiumChannel WT
BIOMD0000000127: Izhikevich2003 SpikingNeuron
BIOMD0000000128: Bertram2006 Endothelin
BIOMD0000000129: Izhikevich2004 SpikingNeurons inhibitionInducedSpiking
BIOMD0000000130: Izhikevich2004 SpikingNeurons integrator
BIOMD0000000131: Izhikevich2004 SpikingNeurons reboundBurst
BIOMD0000000132: Izhikevich2004 SpikingNeurons reboundSpike
BIOMD0000000133: Izhikevich2004 SpikingNeurons resonator
BIOMD0000000134: Izhikevich2004 SpikingNeurons SpikeLatency
BIOMD0000000135: Izhikevich2004 SpikingNeurons subthresholdOscillations
BIOMD0000000136: Izhikevich2004 SpikingNeurons thresholdVariability
BIOMD0000000137: Sedaghat2002 InsulinSignalling noFeedback
BIOMD0000000138: Tabak2007 dopamine
BIOMD0000000139: Hoffmann2002 KnockOut IkBNFkB Signaling
BIOMD0000000140: Hoffmann2002 WT IkBNFkB Signaling
BIOMD0000000141: Izhikevich2004 SpikingNeurons Class1Excitable
BIOMD0000000142: Izhikevich2004 SpikingNeurons Class2Excitable
BIOMD0000000143: Olsen2003 neutrophil oscillatory metabolism
BIOMD0000000144: Calzone2007 CellCycle
BIOMD0000000145: Wang2007 ATP induced Ca Oscillation
BIOMD0000000146: Hatakeyama2003 MAPK
BIOMD0000000147: ODea2007 IkappaB
BIOMD0000000148: Komarova2003 BoneRemodeling
BIOMD0000000149: Kim2007 Wnt ERK Crosstalk
BIOMD0000000150: Morris2002 CellCycle CDK2Cyclin
BIOMD0000000151: Singh2006 IL6 Signal Transduction
BIOMD0000000152: Fernandez2006 ModelA
BIOMD0000000153: Fernandez2006 ModelB
BIOMD0000000154: Zatorsky2006 p53 Model3
BIOMD0000000155: Zatorsky2006 p53 Model6
BIOMD0000000156: Zatorsky2006 p53 Model5
BIOMD0000000157: Zatorsky2006 p53 Model4
BIOMD0000000158: Zatorsky2006 p53 Model2
BIOMD0000000159: Zatorsky2006 p53 Model1
BIOMD0000000160: Xie2007 CircClock
BIOMD0000000161: Eungdamrong2007 Ras Activation
BIOMD0000000162: Hernjak2005 Calcium Signaling
BIOMD0000000163: Zi2007 TGFbeta signaling
BIOMD0000000164: SmithAE2002 RanTransport
BIOMD0000000165: Saucerman2006 PKA
BIOMD0000000166: Zhu2007 TF modulated by Calcium
BIOMD0000000167: Mayya2005 STATmodule
BIOMD0000000168: Obeyesekere1999 CellCycle
BIOMD0000000169: Aguda1999 CellCycle