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
- Number of models in this archive: 68
- Number of models currently runnable under JSim: 61
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.
- JSim version not yet available
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.
- JSim version not yet available
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.
- JSim version not yet available
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
- JSim version not yet available
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.
- JSim version not yet available
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
- JSim version not yet available
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
- JSim version not yet available
valero: A kinetic study of a ternary cycle between adenine nucleotides
westermark: A Model of Phosphofructokinase and Glycolytic Oscillations in the Pancreatic ß-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/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.
