SBML Models

These models in the table below are SBML models from SBML model repository. You can link to a page containing a summary of the model when you click a model name, and publications describing the model when you click publications. A link to SBML page, a publication, E-Cell and SBML models, the name of the software used to generate the SBML and the person who created the SBML model are shown in a page containing a summary of the model. This page also provides links for downloading the model's definition in E-Cell and SBML models.

Model	Reference	File & Simulation
CellCycle-1991Gol (Goldbeter, 1991) [ DESCRIPTION ]	Goldbeter, A. A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. Proc. Natl. Acad. Sci. USA 88: 9107-1101 (1991)
		[ Simulation ]
CellCycle-1991Tys (Tyson, 1991) [ DESCRIPTION ]	Tyson JJ. Modeling the cell division cycle: cdc2 and cyclin interactions. PNAS, 88: 7328-7332 (1991).
		[ Simulation ]
CellCycle-1991Tys-2 (Tyson, 1991) [ DESCRIPTION ]	Tyson JJ. Modeling the cell division cycle: cdc2 and cyclin interactions. PNAS, 88: 7328-7332 (1991).
		[ Simulation ]
CellCycle-1997Nov (Novak & Tyson, 1997) [ DESCRIPTION ]	Novak B, Tyson JJ. Modeling the control of DNA replication in fission yeast, PNAS, USA, 94:9147-9152 (1997).
		[ Simulation ]
CellCycle-1998Gar (Gardner et al., 1998) [ DESCRIPTION ]	Gardner TS, Dolnik M, Collins JJ. A theory for controlling cell cycle dynamics using a reversibly binding inhibitor. PNAS 95: 14190-14195 (1998).
		[ Simulation ]
CircClock-1999Lel (Leloup & Goldbeter, 1999) [ DESCRIPTION ]	Leloup J-C, Goldbeter A. Chaos and birhythmicity in a model of circadian oscillations of the PER and TIM proteins in Drosophila. J Theor Biol 198: 445 - 459 (1999).
		birhythmic [ Simulation ] chaotic [ Simulation ] periodic [ Simulation ]
CircClock-2001Ued (Ueda et al, 2001) [ DESCRIPTION ]	Ueda HR, Hagiwara M, Kitano H. Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm. J theor Biol 210: 401-406 (2001).
		[ Simulation ]
CircClock-2002Vil (Vilar et al, 2002) [ DESCRIPTION ]	Vilar JMG, Kueh HY, Barkai N, Leibler S. Mechanisms of noise resistance in genetic oscillators, PNAS, 99(9):5988-5992 (2002).
		[ Simulation ]
ElectroPhys-1952Hod (Hodgkin & Huxley, 1952) [ DESCRIPTION ]	Hodgkin A L & Huxley A F. A quantitative description of membrane current and its application to conduction and excitation in nerve. A quantitative description of membrane current and its application to conduction and excitation in nerve.
		[ Simulation ]
Genetic-2000Elo (Elowitz & Leibler, 2000) [ DESCRIPTION ]	Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 403: 335 - 338 (2000).
		[ Simulation ]
Genetic-2003Mar (Marwan, 2003) [ DESCRIPTION ]	Marwan W. Theory of time-resolved somatic complementation and its use to explore the sporulation control network in Physarum polycephalum. Genetics 164: 105-115 (2003).
		[ Simulation ]
MAPKcasc-2000Kho (Kholodenko, 2000) [ DESCRIPTION ]	Kholodenko BN. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267: 1583-1588 (2000).
		[ Simulation ]
MAPKcasc-2000Lev (Levchenko et al, 2000) [ DESCRIPTION ]	Levchenko A, Bruck J, Sternberg PW. Scaffold proteins may biphasically affect the levels of mitogen- activated protein kinase signaling and reduce its threshold properties. Proc. Natl. Acad. Sci. USA 97( 11):5818-5823 (2000).
		[ Simulation ]
MAPKcasc-2000Lev-2 (Levchenko et al, 2000) [ DESCRIPTION ]	Levchenko A, Bruck J, Sternberg PW. Scaffold proteins may biphasically affect the levels of mitogen- activated protein kinase signaling and reduce its threshold properties. Proc. Natl. Acad. Sci. USA 97(11):5818-5823 (2000).
		[ Simulation ]
Metabolism-2000Teu (Teusink et al, 2000) [ DESCRIPTION ]	Teusink, B, Passarge, J, Reijenga, CA, Esgalhado, E, van der Weijden, CC, Schepper, M, Walsh, MC, Bakker, BM, van Dam, K, Westerhoff, HV and Snoep, JL. "Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry" Eur J Biochem 267, 5313-5329 (2000).
		[ Simulation ]
Metabolism-2002Hoe (Hoefnagel et al., 2002) [ DESCRIPTION ]	Hoefnagel, MHN, Starrenburg, MJC, Martens, DE, Hugenholtz, J, Kleerebezem, M, Van Swam, II, Bongers, R, Westerhoff, HV and Snoep, JL. Metabolic engineering of lactic acid bacteria, the combined approach: Kinetic modelling, metabolic control and experimental analysis. Microbiology. 148: 1003-1013 (2002).
		[ Simulation ]
Metabolism-2002Hoe-2 (Hoefnagel et al., 2002) [ DESCRIPTION ]	Hoefnagel, MHN, Starrenburg, MJC, Martens, DE, Hugenholtz, J, Kleerebezem, M, Van Swam, II, Bongers, R, Westerhoff, HV and Snoep, JL. Metabolic engineering of lactic acid bacteria, the combined approach: Kinetic modelling, metabolic control and experimental analysis. Microbiology. 148: 1003-1013 (2002).
		[ Simulation ]
Metabolism-2002Lam (Lambeth & Kushmeric, 2002) [ DESCRIPTION ]	Lambeth, MJ and Kushmeric, MJ (2002) "A computational model for glycogenolysis in skeletal muscle", Annals of Biomedical Engineering 30, 808?827. PDF
		[ Simulation ]
Miscellaneous-1963Lor (Lorenz, 1963) [ DESCRIPTION ]	Lorenz EN. Deterministic nonperiodic flow. Journal of the Atmospheric Sciences, 20:130-141 (1963).
		[ Simulation ]
MolMotors-2003Kol (Kolomeisky & Fisher, 2003) [ DESCRIPTION ]	Kolomeisky AB, Fisher ME. A simple kinetic model describes the processivity of Myosin-V. Biophys. J. 84: 1642-1650 (2003).
		[ Simulation ]
Receptor-1992DeY (DeYoung & Keizer, 2000) [ DESCRIPTION ]	DeYoung GW,Keizer J. A single pool IP3- receptor based model for agonist simulated Ca2+ oscillations, PNAS 89:9895-9899 (1992).
		[ Simulation ]
Receptor-1996Ede (Edelstein et al, 1996) [ DESCRIPTION ]	Edelstein S., Schaad O., Henry E., Bertrand D. Changeux J.-P. A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions. Biol. Cybern. 75: 361-379 (1996).
		[ Simulation ]