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.
Return to complete JSim model archives.
Currently available models
BIOMD0000000077: Blum2000 LHsecretion 1
- JSim version not yet available
BIOMD0000000076: Cronwright2002 Glycerol Synthesis
BIOMD0000000065: Yildirim2003 Lac Operon
BIOMD0000000053: Ferreira2003 CML generation2
BIOMD0000000066: Chassagnole2001 Threonine Synthesis
BIOMD0000000081: Suh2004 KCNQ Regulation
- JSim version not yet available
BIOMD0000000087: Proctor2006 telomere
- JSim version not yet available
BIOMD0000000001: Edelstein1996 EPSP AChEvent
- JSim version not yet available
BIOMD0000000078: Leloup2003 CircClock LD
- JSim version not yet available
BIOMD0000000030: Markevich2005 MAPK AllRandomElementary
BIOMD0000000022: No description available
BIOMD0000000010: No description available
BIOMD0000000052: Brands2002 MonosaccharideCasein
BIOMD0000000071: Bakker2001 Glycolysis
BIOMD0000000004: Goldbeter1991 MinMitOscil ExplInact
BIOMD0000000084: Hornberg2005 ERKcascade
BIOMD0000000073: Leloup2003 CircClock DD
- JSim version not yet available
BIOMD0000000070: Holzhutter2004 Erythrocyte Metabolism
BIOMD0000000024: Scheper1999 CircClock
BIOMD0000000014: Levchenko2000 MAPK Scaffold
BIOMD0000000015: Curto1998 purineMetabol
BIOMD0000000083: Leloup2003 CircClock LD REV-ERBalpha
- JSim version not yet available
BIOMD0000000062: bhartiya2003 tryptophan operon
BIOMD0000000043: Borghans1997 CaOscillation model1
BIOMD0000000075: Xu2003 Phosphoinositide turnover
- JSim version not yet available
BIOMD0000000002: Edelstein1996 EPSP AChSpecies
BIOMD0000000058: Bindschadler2001 coupled Ca oscillators
BIOMD0000000085: Maurya2006 GTPaseCycle reducedOrder
- JSim version not yet available
BIOMD0000000063: Galazzo1990 pathway kinetics
BIOMD0000000031: Markevich2004 MAPK orderedMM2kinases
BIOMD0000000046: Olsen2003 peroxidase
BIOMD0000000027: Markevich2004 MAPK orderedMM
BIOMD0000000008: No description available
BIOMD0000000047: Oxhamre2005 Ca oscillation
BIOMD0000000061: Hynne2001 Glycolysis
BIOMD0000000026: Markevich2004 MAPK orderedElementary
BIOMD0000000011: Levchenko2000 MAPK noScaffold
BIOMD0000000055: Locke2005 CircClock
- JSim version not yet available
BIOMD0000000032: Kofahl2004 pheromone
BIOMD0000000041: Kongas2001 creatine
BIOMD0000000038: Rohwer2000 Phosphotransferase System
BIOMD0000000007: Novak1997 CellCycle
- JSim version not yet available
BIOMD0000000072: Yi2003 GproteinCycle
BIOMD0000000042: Nielsen1998 Glycolysis
BIOMD0000000054: Ataullahkhanov1996 Adenylate
BIOMD0000000021: Leloup1999 CircClock
BIOMD0000000051: Chassagnole2002 Carbon Metabolism
BIOMD0000000079: Goldbeter2006 weightCycling
- JSim version not yet available
BIOMD0000000036: Tyson1999 CircClock
BIOMD0000000082: Thomsen1988 AdenylateCyclase Inhibition
BIOMD0000000057: Sneyd2002 IP3 Receptor
BIOMD0000000017: No description available
BIOMD0000000064: Teusink2000 Glycolysis
BIOMD0000000045: Borghans1997 CaOscillation model3
BIOMD0000000035: Vilar2002 Oscillator
BIOMD0000000080: Thomsen1989 AdenylateCyclase
BIOMD0000000018: Morrison1989 FolateCycle
BIOMD0000000056: Chen2004 CellCycle
- JSim version not yet available
BIOMD0000000009: No description available
BIOMD0000000005: Tyson1991 CellCycle 6var
BIOMD0000000044: Borghans1997 CaOscillation model2
BIOMD0000000069: Fuss2006 MitoticActivation
BIOMD0000000039: Marhl2000 CaOscillations
BIOMD0000000016: Goldbeter1995 CircClock
BIOMD0000000003: Goldbeter1991 MinMitOscil
BIOMD0000000012: Elowitz2000 Repressilator
BIOMD0000000059: Fridlyand2003 Calcium flux
BIOMD0000000050: Martins2003 AmadoriDegradation
- JSim version not yet available
BIOMD0000000074: Leloup2003 CircClock DD REV-ERBalpha
- JSim version not yet available
BIOMD0000000029: Markevich2004 MAPK phosphoRandomMM
BIOMD0000000086: Bornheimer2004 GTPaseCycle
- JSim version not yet available
BIOMD0000000025: Smolen2002 CircClock
- JSim version not yet available
BIOMD0000000048: Kholodenko1999 EGFRsignaling
BIOMD0000000037: No description available
BIOMD0000000033: No description available
BIOMD0000000068: Curien2003 MetThr synthesis
- JSim version not yet available
BIOMD0000000013: Poolman2004 CalvinCycle
BIOMD0000000049: Sasagawa2005 MAPK
BIOMD0000000040: Field1974 Oregonator
BIOMD0000000020: hodgkin-huxley squid-axon 1952
BIOMD0000000060: No description available
BIOMD0000000023: Rohwer2001 Sucrose
BIOMD0000000028: Markevich2004 MAPK phosphoRandomElementary
BIOMD0000000067: Fung2005 Metabolic Oscillator
BIOMD0000000006: Tyson1991 CellCycle 2var
BIOMD0000000034: Smolen2004 CircClock
Model development and archiving support at physiome.org provided by the following grants: NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.
