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JSim JWS Models Page

This page allows users to run models from the JWS Online Models 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.

Note: Models on this page require JSim version 1.6.84 or above.

Return to complete JSim model archives.

Currently available models

assmus: Potato tuber

ataullakhanov: The Regulation of Glycolysis in Human Erythrocytes

attila: Analysis of a Generic Model of Eukaryotic Cell-Cycle Regulation

bali: A modelling study of feedforward activation in

bhartiya: Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design

bradshaw: A computational model of mitochondrial deoxynucleotide metabolism and DNA replication.

branch3: None

branch5: None

bruggeman: The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica

bruggeman2: Time-dependent hierarchical regulation analysis: deciphering cellular adaptation

chassagnole1: Dynamic Modeling of the Central Carbon Metabolism of Eschericia coli

chassagnole2: Control of the threonine-synthesis pathway in Escherichia coli :a theoretical and experimental approach

chen: Kinetic analysis of a molecular model of the budding yeast cell cycle.

chen2: Integrative analysis of cell cycle control in budding yeast.

ciliberto: Mathematical model of the morphogenesis checkpoint in budding yeast.

cronwright: Metabolic Control Analysis of Glycerol Synthesis inSaccharomyces cerevisiae

curien: A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana

dano1: Reduction of a biochemical model with preservation of its basic dynamic properties

dano2: Reduction of a biochemical model with preservation of its basic dynamic properties

dano3: Reduction of a biochemical model with preservation of its basic dynamic properties

eissing: Bistability Analyses of a caspase activation model for receptor-induced apoptosis.

feedbackmoi: None

fuentes: Kinetics of intra- and intermolecular zymogen activation with formation of an enzyme-zymogen complex

galazzo1: Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae

gomes: Protein glycation in Saccharomyces cerevisiae. Argpyrimidine formation and methylglyoxal catabolism

heinrich: Heinrich model

holzhutter: The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks

hornberg: Principles behind the multifarious control of signal transduction ERK phosphorylation and kinase/phosphatase control

ihekwaba: Sensitivity analysis of parameters controlling

jamshidi: Metabolic Dynamics in the Human Red Cell.

kholodenko: Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor

kim: Robustness analysis of biochemical network models

kintuta: None

kintutb: None

kintutc: None

kintutd: None

kofahl: Modelling the dynamics of the yeast pheromone pathway.

koster: Kinetics of Histone Gene Expression during Early Development of Xenopus laevis.

lambeth: A Computational Model for Glycogenolysis in Skeletal Muscle

laub: A Molecular Network That Produces Spontaneous Oscillations in Excitable Cells of Dictyostelium

lee: The Roles of APC and Axin Derived

lin3: None

lin3linkin: None

lin3moi: None

maher: Mathematical modelling of the urea cycle; a numerical investigation into substrate channeling.

martins: In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae

mayya: The STAT module can function as a biphasic amplitude filter.

nielsen: Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations

novak: A model for restriction point control of the mammalian cell cycle

obeyesekere: A mathematical model of the regulation of the G1 phase of Rb

olah: Triosephosphate isomerase deficiency: consequences of an inherited mutation at mRNA, protein and metabolic levels.

olivier: Comparing the regulatory behaviour of two cooperative, reversible enzyme mechanisms.

olsen: Mechanism of protection of peroxidase activity by oscillatory dynamics

ortega: Bistability from double phosphorylation in signal transduction

poolman: Modelling photosynthesis and its control

queralt: Downregulation of PP2ACdc55 Phosphatase by Separase Initiates Mitotic Exit in Budding Yeast

saavedra: Kinetic modeling can describe in vivo glycolysis in

schaber: A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast

schoeberl: Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors.

silva: Quantitative assessment of the glyoxalase pathway in Leishmania infantum as a therapeutic target by modelling and computer simulation.

snoep: Is there an optimal ribosome concentration for maximal protein production?

tyson2: Modeling the cell division cycle: cdc2 and cyclin interactions

tyson2001: Regulation of the Eukaryotic Cell Cycle: Molecular Antagonism, Hysteresis, and Irreversible Transitions

tyson3: Modeling the cell division cycle: cdc2 and cyclin interactions

uys: Sugar cane

valero: A kinetic study of a ternary cycle between adenine nucleotides

westermark: A Model of Phosphofructokinase and Glycolytic Oscillations in the Pancreatic -cell

wolf2: The impact of the regulatory design on the response of

Model development and archiving support at physiome.org provided by the following grants: NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; 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.