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JSim CellML Models Page

This page allows users to run models from the CellML model archive 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 CellML models do not specify simulation time length or delta, these must be set by the user before running the model.

Users are strongly advised to read Running CellML Models under JSim before running CellML models under JSim. The warning icon indicates that a unit conversion has been turned off because the model does not satisfy JSim unit balance.

Terms of use

Currently available models

adrian_chandler_hodgkin_1970
Voltage Clamp Experiments in Striated Muscle Fibres

albrecht_colegrove_friel_2002
Differential Regulation of ER Ca2+ Uptake and Release Rates Accounts for Multiple Modes of Ca2+-induced Ca2+ Release

albrecht_colegrove_hongpaisan_pivovarova_andrews_friel_2001
Multiple Modes of Calcium-induced Calcium Release in Sympathetic Neurons

aon_cortassa_2002
Modulation of a Metabolic Network by Cytoskeletal Organisation and Dynamics

asthagiri_lauffenburger_2001
Feedback Effects On Signal Dynamics In A Mitogen-Activated Protein Kinase (MAPK) Cascade

bakker_mensonides_teusink_vanhoek_michels_westerhoff_2000
Glycosomes Protect Trypanosomes from Glycolysis

bakker_michels_opperdoes_westerhoff_1997
Modelling Glycolysis in Trypanosoma brucei, Bakker et al, 1997

baylor_hollingworth_chandler_2002
Calcium Sparks in Skeletal Muscle Fibers

beard_2005
A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation, Beard, 2005

beeler_reuter_1977
Beeler-Reuter Mammalian Ventricular Model 1977

ben-tal_2005
Simplified Models For Gas Exchange In The Human Lungs

bernus_wilders_zemlin_verschelde_panfilov_2002
A Computationally Efficient Electrophysiological Model of Human Ventricular Cells

bertram_arnot_zamponi_2002
G-Protein Specificity In Synaptic Signalling

bertram_previte_sherman_kinard_satin_2000
The Phantom Burster Model For Pancreatic Beta-Cells

bertram_satin_zhang_smolen_sherman_2004
Modelling Multiple Bursting Models in Pancreatic Islets

bertram_sherman_2004
A Calcium-based Phantom Bursting Model for Pancreatic Islets

bertram_smolen_sherman_mears_atwater_martin_soria_1995
Modulatory Role for CRAC in Pancreatic Beta-Cell Electrical Activity

bhalla_iyengar_1999
The Phospholipase 2A (PLA2) Pathway Model from Bhalla and Iyengar

bindschadler_sneyd_2001
A Bifurcation Analysis of Two Coupled Calcium Oscillators

bondarenko_szigeti_bett_kim_rasmusson_2004
Modelling the Action Potential of Mouse Ventricular Myocytes

bonhoeffer_rembiszewski_ortiz_nixon_2000
Modelling the Population Dynamics of Virus Infected Cells

boyett_zhang_garny_holden_2001
Modelling The Effect Of Intracellular Ca2+ On Sinoatrial Node Action Potentials, 2001

butera_rinzel_smith_1999
Models Of Respiratory Rhythm Generation In The Pre-Botzinger Complex. I. Bursting Pacemaker Neurons

chang_fujita_1999
A Kinetic Model of the Thiazide-Sensitive Na-Cl Cotransporter

chang_fujita_2001
Mathematical Models of Ionic Transport in the Distal Tubule of the Rat

chassagnole_rais_quentin_fell_mazat_2001
The Threonine-Synthesis Pathway In Escherichia coli

chay_1997
Extracellular And Intracellular Calcium Effects On Pancreatic Beta-Cells

chay_lee_fan_1995
Intracellular Ca2+ Spikes in Non-excitable Cell Models

chen_calzone_csikasz-nagy_cross_novak_tyson_2004
An Integrative Analysis of Cell Cycle Control in Budding Yeast

chen_csikasz-nagy_gyorffy_val_novak_tyson_2000
Modelling the Budding Yeast Cell Cycle

ciliberto_novak_tyson_2003
Modelling the Morphogenesis Checkpoint in the Budding Yeast Cell Cycle

ciliberto_petrus_tyson_sible_2003
A Kinetic Model of the Cyclin E/Cdk2 Developmental Timer in Xenopus laevis embryos

ciliberto_tyson_2000
Mathematical Model for the Early Development of the Sea Urchin Embryo

clancy_rudy_2001
Clancy-Rudy Markovian Model of Ion Channels 2001

clancy_rudy_2002
A Single Mutation Underlies Brugada and LQT

colegrove_albrecht_friel_2000
Quantitative Analysis Of Mitochondrial Ca2+ Uptake And Release Pathways In Sympathetic Neurons

condorelli_george_2001
A Kinetic Analysis of the Activation of Soluble Guanylate Cyclase by Nitric Oxide

cortassa_aon_marban_winslow_orourke_2003
Modelling Mitochondrial Energy Metabolism

cortassa_aon_winslow_orourke_2004
Modelling Mitochondria As Biological Oscillators

courtemanche_ramirez_nattel_1998
Mathematical Model Of A Human Atrial Action Potential, 1998

cronwright_rohwer_prior_2002
Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae

curien_ravanel_dumas_2003
A Kinetic Model of the Branch-Point between the Methionine and Threonine Biosynthesis Pathways in Arabidopsis thaliana

dawson_lea_irvine_2003
Kinetic Model of the Inositol Trisphosphate Receptor

demir_clark_giles_1999
A Model Of Parasympathetic Modulation Of Pacemaker Rate, 1999

demir_clark_giles_murphey_1994
A Mathematical Model Of A Rabbit Sinoatrial Node Cell, 1994

demiray_1981
Exponential Constitutive Material Law

devries_sherman_2000
Enhancement Of Emergent Bursting In Pancreatic Beta-Cells

devries_sherman_2001
From Spikers To Bursters Via Heterogeneity

deyoung_keizer_1992
IP3-Mediated Ca2+ Release

difrancesco_noble_1985
Di Francesco-Noble Purkinje Fibre Model 1985

dixit_perelson_2004
Modelling the Complex Patterns of Viral Load Decay under Antiretroviral Therapy

dokos_celler_lovell_1996
A Single Cell Mathematical Model of the Ion Currents Underlying Sinoatrial Node Pacemaker Activity

drouhard_roberge_1987
The Drouhard-Roberge Sodium Current Model (1987)

dumaine_towbin_brugada_vatta_nesterenko_nesterenko_brugada_brugada_antzelevitch_1999
Modelling the Ionic Mechanisms Underlying Brugada Syndrome

earm_noble_1990
Model Status

ebihara_johnson_1980
The Ebihara-Johnson Sodium Current Model (1980)

evans_errington_shelly_feeney_chapman_godfrey_smith_chappell_2004
Modelling The In Vitro Kinetics Of The Anti-Cancer Agent Topotecan

faber_rudy_2000
Updated Luo-Rudy Mammalian Ventricular Model II

fall_keizer_2001
Mitochondria And Ca2+ Signalling

fallon_lauffenburger_2000
Binding, Internalisation and Postendocytotic Sorting of Interleukin-2 and Its Receptor

fenton_karma_1998
A Simplified Ventricular Myocyte Model

fink_slepchenko_loew_1999
Intracellular IP3 and Calcium Release in a Smooth Muscle Cell

fink_slepchenko_moraru_watras_schaff_loew_2000
Calcium Waves in Differentiated Neuroblastoma Cells

fitzhugh_1961
The FitzHugh-Nagumo Simplified Cardiac Myocyte Model

fitzhugh_arimoto_yoshizawa_1961
The FitzHugh-Nagumo Simplified Cardiac Myocyte Model

flynn_green_pedley_boxer_dearling_watson_boden_begent_2002
A Model-Based Approach for Assessing the Efficacy of Radioimmunotherapy

fohlmeister_miller_1997
Modelling the Impulse Encoding Mechanisms of Ganglion Cells in the Tiger Salamander Retina

fridlyand_tamarina_philipson_2003
Modelling Ca2+ Flux in Pancreatic Beta-cells

friel_1995
[Ca2+]i Oscillations in Sympathetic Neurons

gall_susa_1999
Na/Ca Exchange in Models for Pancreatic Beta-Cells

gardner_dolnik_collins_1998
Controlling Cell Cycle Dynamics Using a Reversibly Binding Inhibitor

garny_kohl_hunter_boyett_noble_varghese_boyett_2003

goforth_bertram_khan_zhang_sherman_satin_2002
Calcium-activated K+ Channels in Pancreatic Beta-Cells

goldbeter_1991
A Minimal Cascade Model for the Mitotic Oscillator Involving Cyclin and cdc2 Kinase

goldbeter_1995
A Model For Circadian PER Oscillations In Drosophila

greenstein_wu_po_tomaselli_winslow_2000
Role of Ito1 in Shaping Action Potential Morphology and Duration

grossman_feinberg_kuznetsov_dimitrov_paul_1998
Modelling the Kinetics of Plasma Virus Following the Initiation of Therapy

guccione_mcculloch_waldman_1991
The Guccione Constitutive Material Law

halloy_bernard_loussouarn_goldbeter_2002
The Follicular Automaton Model for Hair Cycles

hatzimanikatis_lee_bailey_1999
Regulation of the G1-S Transition of the Mammalian Cell Cycle

haugh_wells_lauffenburger_2000
Epidermal Growth Factor Receptor Signaling Through The Phospholipase C Pathway

hefti_harder_eppenberger_schaub_1997
Fibroblast Growth Factor Signalling in Cardiac Myocyte Hypertrophy

herz_bonhoeffer_anderson_may_nowak_1996
Modelling Viral Dynamics In Vivo

heyd_drew_2003
A Mathematical Model for the Elongation of a Peptide Chain

hilemann_noble_1987
Hilemann-Noble Atrial Cell Model 1987

hilgemann_noble_1987
Hilemann-Noble Atrial Cell Model 1987

hodgkin_huxley_1952
Hodgkin Huxley Squid Axon Model 1952

hoefnagel_starrenburg_martens_hugenholtz_kleerebezem_vanswam_bongers_westerhoff_snoep_2002
Metabolic Engineering of Lactococcus lactis

huang_ferrell_1996
The Mitogen-Activated Protein Kinase (MAPK) Cascade

hunter_mcculloch_terkeurs_1998
The Mechanical Properties of Cardiac Muscle, 1998

hunter_mcnaughton_noble_1975
The Polynomial Model

hynne_dano_sorensen_2001
Full-scale model of glycolysis in Saccharomyces cerevisiae

iber_maini_2002
A Mathematical Model for Germinal Centre Kinetics and Affinity Maturation

itskov_ehret_mavrilas_2005

iyer_mazhari_winslow_2004
A Computational Model of the Human Left-Ventricular Epicardial Myocyte

jafri_rice_winslow_1998
Jafri-Rice-Winslow Ventricular Model 1998

joseph_zavros_merchant_kirschner_2003
Modelling Human Gastric Acid Secretion

kamp_hell_2000
cAMP/PKA Signalling Cascade Regulation of Cardiac L-type Calcium Channel Activity

keener_2001
Diffusion Induced Oscillatory Insulin Secretion

keizer_levine_1996
RyR Adaptation and Ca2+ Oscillations

kesmir_deboer_1999
Modelling the Kinetics of Germinal Centre Reactions

kholodenko_demin_moehren_hoek_1999
Quantification of EGF Receptor Signalling

kirschner_panetta_1998
Modelling Immunotherapy of the Tumour-Immune Interaction

kirschner_webb_1996
A Model for Treatment Strategy in the Chemotherapy of AIDS

kneller_ramirez_chartier_courtemanche_nattel_2002
Mathematical Model of a Canine Atrial Action Potential, 2002

kodama_2000
The Role of Insulin-like Growth Factor I as a Cardiac Hormone

komarova_wodarz_2003
Modelling the Evolutionary Dynamics of Mutator Phenotypes in Cancer

korzeniewski_zoladz_2001
Oxidative Phosphorylation

kurata_hisatome_imanishi_shibamoto_2002
Improved Mathematical Model for the Primary Pacemaker Cell

lambeth_kushmerick_2002
Modelling Glycogenolysis in Skeletal Muscle