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Exposures
Generic mouse brainstem scaffold
Generic pig brainstem scaffold
Generic cat bladder scaffold
Pivonka, Zimak, Smith, Gardiner, Dunstan, Sims, Martin and Mundy, 2008
exposure
pivonka_2008.cellml
Human whole-body with embedded organs using automatic workflow for inserting the organs
Generic pig brainstem scaffold
ViewCreation-previous-docs
Cardiovascular model with the feedback loops
Generic human stomach scaffold
Generic rat stomach scaffold
rat flatmap
manifest.json
FCU_guanylylCyclase
FCU_guanylylCyclase.cellml
exposure
Generic mouse colon scaffold
Generic human stomach scaffold
ViewCreation-previous-docs
Generic mouse stomach scaffold
ViewCreation-previous-docs
Generic pig stomach scaffold
ViewCreation-previous-docs
Generic human colon scaffold
ViewCreation-previous-docs
The Heijman et al. 2011 model of the canince ventricular AP, with signalling
heijman-2011.cellml
Maleckar, Greenstein, Trayanova, Giles, 2009
Jafri, Rice, Winslow, 1998
jafri_rice_winslow_1998_a.cellml
Cardiac Ca2+ Dynamics: The Roles of Ryanodine Receptor Adaptation and Sarcoplasmic Reticulum Load
Wang, Sobie, 2008
wang_sobie_2008.cellml
Ten Tusscher, Noble, Noble, Panfilov, 2004
tentusscher_noble_noble_panfilov_2004_endo.cellml
tentusscher_noble_noble_panfilov_2004_epi.cellml
tentusscher_noble_noble_panfilov_2004_m.cellml
Generic Mouse Bladder Scaffold
Generic Pig Bladder Scaffold
NKE knowledge page
BG_NaK.cellml
exposure
NCX protein knowledge page
exposure
BG_NCX.cellml
Generic pig heart scaffold
ViewCreation-previous-docs
Generic human cecum scaffold
ViewCreation-previous-docs
Cervical Vertebra 1
generated.neon
Cervical Vertebra 3
generated.neon
Cervical Vertebra 4
generated.neon
Cervical Vertebra 5
generated.neon
Intervertebral Disc of C4
generated.neon
Intervertebral Disc of C5
generated.neon
Intervertebral Disc of C6
generated.neon
Intervertebral Disc of C7
generated.neon
Generic human bladder scaffold
Generic Pig Bladder Scaffold
SinglePASMC
Experiments
Na channel knowledge page
BG_fast_Na.cellml
exposure
Generic rat stomach scaffold
Bhalla, Iyengar, 1999
Complete network of the Bhalla-Iyengar model
Ca-IP3 component of the Bhalla-Iyengar model
EGFR pathway component of the Bhalla-Iyengar model
MAPK pathway component of the Bhalla-Iyengar model
Conversion of PIP to IP3 and DAG component of the Bhalla-Iyengar model
PKC pathway component of the Bhalla-Iyengar model
PLA2 pathway component of the Bhalla-Iyengar model
PLC-gamma pathway component of the Bhalla-Iyengar model
RAS pathway component of the Bhalla-Iyengar model
phospholipase C (PLC) pathway component of the Bhalla-Iyengar model
DISTAL_PHALANX_I
generated.neon
DISTAL_PHALANX_II
generated.neon
Lumbar Vertebrae 2
generated.neon
Lumbar Vertebrae 4
generated.neon
Lumbar Vertebrae 5
generated.neon
Intervertebral Disc of C2
generated.neon
Intervertebral disc of T1
generated.neon
Intervertebral disc of T6
generated.neon
Intervertebral disc of T10
generated.neon
Intervertebral disc of T11
generated.neon
Thoracic spine
test_file.json
Intervertebral disc of L2
generated.neon
Intervertebral disc of L4
generated.neon
Thoracic Vertebrae 6
generated.neon
Thoracic Vertebrae 7
generated.neon
Thoracic Vertebrae 8
generated.neon
Thoracic Vertebrae 9
generated.neon
Thoracic Vertebrae 10
generated.neon
Thoracic Vertebrae 11
generated.neon
Thoracic Vertebrae 12
generated.neon
KACh knowledge page
BG_KACh.cellml
Generic pig stomach scaffold
Generic mouse stomach scaffold
Kernik et al. 2019 hIPSC AP model
kernik-2019.cellml
Ni et al. 2017 Human Atrial model
Ni et al. 2017 Human Atrial model
Model of the human Purkinje cell by Sampson et al.
sampson-2010.cellml
Stewart, Aslanidi, Noble, Noble, Boyett, Zhang, 2009
ten Tusscher, Panfilov, 2006
ten_tusscher_model_2006_endo.cellml
ten_tusscher_model_2006_epi.cellml
ten_tusscher_model_2006_m.cellml
Voigt, Heijman et al. 2013 human atrial AP model
Voigt, Heijman et al. 2013 Human Atrial AP model
Improving in vitro to in vivo extrapolation by incorporating toxicokinetic measurements: A case study of lindane-induced neurotoxicity
Improving in vitro to in vivo extrapolation by incorporating toxicokinetic measurements: A case study of lindane-induced neurotoxicity
Lindane_rat_Units.cellml
BG_GPCR_B1AR_reduced
exposure
BG_GPCR_B1AR_reduced.cellml
AE1-BG
AE1-BG.cellml
Weinstein_2000_AE1_Fig3.cellml
Weinstein_2000_AE1.cellml
Parameters.cellml
Unit.cellml
Units.cellml
inverse03.py
Fig3A.py
Fig3B.py
Fig3C.py
Fig3D.py
The Physics of Physiology - Example 4: A simple biochemical reaction
FAIRDO BG example 3.4.cellml
The Physics of Physiology - Example 3: An electromechanical system
FAIRDO BG example 3.3.cellml
Mouse whole-body scaffold with embedded organs
Triceps brachii
generated.neon
Hip joint
joint_view.neon
Knee joint
joint_view.neon
Modeling the Recruitment and Synchronization of SMCs (Koenigsberger et al. 2004)
Experiments
Generic pig lung
Generic rat lung scaffold
Generic pig brainstem scaffold
Generic sheep brainstem
Generic human brainstem scaffold
Generic rat brainstem scaffold
Generic sheep brainstem
NaB protein knowledge page
BG_NaB.cellml
Thoracic Vertebrae 5
generated.neon
The Physics of Physiology - Example 1: An electrical circuit
FAIRDO BG example 3.1.cellml
Modeling the Recruitment and Synchronization of SMCs (Koenigsberger et al. 2004)
Experiments
Generic mouse heart scaffold
A 3D human whole-body model with integrated organs, vasculature, musculoskeletal and nervous systems for mapping nerves
mapclient workflow
Cervical spine
test_file.json
Thoracic Vertebrae 2
generated.neon
Thoracic Vertebrae 4
generated.neon
Generic mouse stomach scaffold
Generic rat stomach scaffold
Generic human lung scaffold
Generic rat lung scaffold
Generic human lung scaffold
Generic mouse lung scaffold
PROXIMAL_PHALANX_III
generated.neon
CAPITATE
generated.neon
Human whole-body scaffold with embedded organs
mapclient_workflow
BPS2020 model
Simulation of the Effects of Extracellular Calcium Changes Leads to a Novel Computational Model of Human Ventricular Action Potential With a Revised Calcium Handling
Generic human esophagus scaffold
Lumbar Vertebrae 1
generated.neon
Lumbar Vertebrae 3
generated.neon
Intervertebral disc of C3
generated.neon
Intervertebral disc of T2
generated.neon
Intervertebral disc of T3
generated.neon
Intervertebral disc of T4
generated.neon
Intervertebral disc of T5
generated.neon
Intervertebral disc of T7
generated.neon
Intervertebral disc of T8
generated.neon
Intervertebral disc of T12
generated.neon
Intervertebral disc of L1
generated.neon
Intervertebral disc of L3
generated.neon
Lumbar spine
test_file.json
Spine
test_file2.json
The Physics of Physiology - Example 5: A biochemical reaction with mixed stoichiometry
FAIRDO BG example 3.5.cellml
The Physics of Physiology - Example 8: Membrane ion channels
FAIRDO BG example 3.9.cellml
FEMUR
generated.neon
Pronator teres
generated.neon
Elbow joint
joint_view.neon
Generic human lung scaffold
Generic mouse lung scaffold
Generic human brainstem scaffold
Generic mouse brainstem scaffold
Generic rat brainstem scaffold
FCU_ExcitationContraction_Coupling
exposure
FCU_EC_coupling.cellml
Iyer, Mazhari, Winslow, 2004
A computational model of the human left-ventricular epicardial myocyte
Model of excitation-contraction in uterine myocytes from a pregnant rat
Model of Excitation-Contraction in a uterine SMC
Components
Experiments
Beeler, Reuter, 1977
Reconstruction of the action potential of ventricular myocardial fibres
Schmid, Nash, Young, Hunter, 2006
Myocardial Material Parameter Estimation - A Comparative Study for Simple Shear (Separated Fung Law)
Myocardial Material Parameter Estimation - A Comparative Study for Simple Shear (Taylor Series Expansion of the Tangent Law)
Reconstruction of the action potential of ventricular myocardial fibres, with modifications to demonstrate uncertainty.
Reconstruction of the action potential of ventricular myocardial fibres, with modifications to demonstrate uncertainty.
A Quantitative Model of Human Jejunal Smooth Muscle Cell Electrophysiology
A Quantitative Model of Human Jejunal Smooth Muscle Cell Electrophysiology
Workflows for analysis of valvular and aortic disease
Laminar structure of the Heart: A mathematical model.
Laminar structure of the Heart: A mathematical model.
Computational Mechanics of the Heart
Computational Mechanics of the Heart
Workflows for analysis of valvular and aortic disease
Aorta-Brown-Shi-et-al-2012.rdf
Laminar structure of the Heart: A mathematical model.
Laminar structure of the Heart: A mathematical model.
Laminar structure of the Heart: A mathematical model.
Laminar structure of the Heart: A mathematical model.
mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: A population-based simulation study
mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: A population-based simulation study
A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry
A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry
Bugenhagen 2010
Bugenhagen 2010
Library of metabolic components in CellML
reference
library
An updated computational model of rabbit sinoatrial action potential to investigate the mechanisms of heart rate modulation.
severi_fantini_charawi_difrancesco_2012.cellml
Fink, Slepchenko, Moraru, Watras, Schaff, Loew, 2000
An image-based model of calcium waves in differentiated neuroblastoma cells
Fink, Slepchenko, Moraru, Watras, Schaff, Loew, 2000
An image-based model of calcium waves in differentiated neuroblastoma cells
Butera, Rinzel, Smith, 1999
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: Single Cell Model
Computational models of ventricular- and atrial-like human induced pluripotent stem cell derived cardiomyocytes
Computational models of ventricular- and atrial-like human induced pluripotent stem cell derived cardiomyocytes
The Noble (1962) cell model
The Noble (1962) cell model
The Noble (1962) cell model
The Noble (1962) cell model
Viewing the PCA visualiser for the Medrano-Gracia model
Edwards, 2010
Edwards 2010
Butera, Rinzel, Smith, 1999
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: Single Cell Model
Spronck, 2012
Spronck 2012
Decker, Heijman, Silva, Hund, Rudy, 2009
Properties and ionic mechanisms of action potential adaptation, restitution, and accommodation in canine epicardium
Butera, Rinzel, Smith, 1999
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: Single Cell Model
Butera, Rinzel, Smith, 1999
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: Single Cell Model
Carro, Rodriguez, Laguna, Pueyo (2011)
Carro_Rodriguez_Laguna_Pueyo_2011_EPI.cellml
Carro_Rodriguez_Laguna_Pueyo_2011_ENDO.cellml
Simple 2nd order linear ODE, a classical mathematical model
Simple 2nd order linear ODE, a classical mathematical model
Laminar structure of the Heart: A mathematical model.
Laminar structure of the Heart: A mathematical model.
Cell viability models for tissue exposed to ablative temperatures.
Arrenhius
Moussa, Tell & Cravalho 1979
Jung 1986
O'Neill et al. 2011
Cell Viability Models for Tissue Exposed to Ablative Temperatures
Arrenhius
Moussa, Tell & Cravalho 1979
Jung 1986
O'Neill et al. 2011
Cortassa et al. (2006) ECME model
cellml
cellml-1.0
Fujita, Toyoshima, Uda, Ozaki, Kubota, Kuroda, 2010
Decoupling of receptor and downstream signals in the Akt pathway by its low-pass filter characteristics: EGF-dependent Akt pathway model
Decoupling of receptor and downstream signals in the Akt pathway by its low-pass filter characteristics: NGF-dependent Akt pathway model
Decoupling of receptor and downstream signals in the Akt pathway by its low-pass filter characteristics: EGFR-inhibited Akt pathway model
Computational Mechanics of the Heart
Computational Mechanics of the Heart
Renal SGLT1 model
Renal SGLT1 model
Eskandari, Wright, Loo 2005
Renal SGLT1 model
Chang, Fujita, 1999
Thiazide-sensitive Na-Cl cotransporter
Eskandari, Wright, Loo 2005
Renal SGLT1 model
Mackenzie, Loo, Panayotova-Heiermann and Wright, 1996
Renal SGLT2 model
Renal Na+/H+ antiporter (NHE3) model
Renal Na+/H+ antiporter (NHE3) model
Renal Na+/H+ antiporter (NHE3) model - figure 2
Renal Na+/H+ antiporter (NHE3) model - figure 3
Weinstein_1995_NHE3_Fig3b.cellml
Renal Na+/H+ antiporter (NHE3) model - figure 4
Renal Na+/H+ antiporter (NHE3) model - figure 4b
Renal Na+/H+ antiporter (NHE3) model - figure 5
Reconstruction of the action potential of ventricular myocardial fibres
Reconstruction of the action potential of ventricular myocardial fibres
Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes
acikgoz_2009a.cellml
acikgoz_2009b.cellml
Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes
Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes
Sine approximations in CellML
Sine approximations in CellML
Sine approximations in CellML
Vasalou, Henson, 2010
A multiscale model to investigate circadian rhythmicity of pacemaker neurons in the suprachiasmatic nucleus
Chang, Fujita, 1999
Thiazide-sensitive Na-Cl cotransporter
Smith, Abdala, Koizumi, Rybak, Paton, 2007
Synaptic coupling
Preinspiratory neuron
Early inspiratory neuron
Augmenting expiratory neuron
Postinspiratory neuron
Faber, Rudy, 2000 and Tong, Ghouri, Taggart, 2014
Updated Faber and Rudy 2000 model with a corrected description of T-type calcium current
Updated previously modified (with Ito and Irel) Faber and Rudy 2000 model with a corrected description of T-type calcium current
Tong, Choi, Kharche, Holden, Zhang, Taggart, 2011
A computational model of the ionic currents, Ca2+ dynamics and action potentials underlying contraction of isolated uterine smooth muscle
Tong, Tribe, Smith, Taggart, 2014
Computational modeling reveals key contributions of KCNQ and hERG currents to the malleability of uterine action potentials underpinning labor
Guccione, Mcculloch, Waldman, 1991
guccione.cellml
Oyehaug, Ostby, Lloyd, Ottersen, Omholt, Einevoll, 2009
Dependence of spontaneous neuronal firing and depolarization block on astroglial membrane processes
Dependence of spontaneous neuronal firing and depolarization block on astroglial membrane processes
An analysis of deformation-dependent electromechanical coupling in the mouse heart
An analysis of deformation-dependent electromechanical coupling in the mouse heart
Gattoni 2016
NormalModel
Sham_AB_models
Oyehaug, Ostby, Lloyd, Ottersen, Omholt, Einevoll, 2009
Dependence of spontaneous neuronal firing and depolarization block on astroglial membrane processes: Fig 2A
Dependence of spontaneous neuronal firing and depolarization block on astroglial membrane processes: Fig 2B
Models for the OpenCOR and PMR tutorial by Peter Hunter
vanderpol.cellml
Firstorder.cellml
lorenz.cellml
SimpleFirstOrderEqn.cellml
potassium_ion_channel.cellml
sodium_ion_channel.cellml
Models for the OpenCOR and PMR tutorial by Peter Hunter
vanderpol.cellml
Firstorder.cellml
lorenz.cellml
SimpleFirstOrderEqn.cellml
potassium_ion_channel.cellml
sodium_ion_channel.cellml
Models for the OpenCOR and PMR tutorial by Peter Hunter
vanderpol.cellml
Firstorder.cellml
lorenz.cellml
SimpleFirstOrderEqn.cellml
potassium_ion_channel.cellml
sodium_ion_channel.cellml
Chang, Fujita, 1999
Thiazide-sensitive Na-Cl cotransporter
Eskandari, Wright, Loo 2005
Renal SGLT1 model
Mackenzie, Loo, Panayotova-Heiermann and Wright, 1996
Renal SGLT2 model
Noble, 1962
A Modification of the Hodgkin-Huxley Equations Applicable to Purkinje Fibre Action and Pace-Maker Potentials
Basket Catheter Emulator
Synchronized Scene Viewer
libnz_ac_auckland_abi_medtech_synchronizedviewer.dll
libnz_ac_auckland_abi_medtech_synchronizedviewer.so
H+-ATPase (V-type) Model
H+-ATPase (V-type) Model
H+-ATPase (V-type) Model - Example
Na+/K+-ATPase (sodium-potassium pump)
Na+/K+-ATPase Model
Na+/K+-ATPase Model - Example
Na+/HCO3- Cotransporter
Na+/HCO3- Cotransporter (NBC) Model
Na+/HCO3- Cotransporter (NBC) Model - Example
Oyehaug, Ostby, Lloyd, Omholt, Einevoll, 2011
Dependence of spontaneous neuronal firing and depolarization block on astroglial membrane processes: Fig 2A
Dependence of spontaneous neuronal firing and depolarization block on astroglial membrane processes: Fig 2B
Na+/H+ Exchanger (NHE3) Model
NHE3 Model
NHE3 Model - Figure 2
NHE3 Model - Figure 3A
NHE3 Model - Figure 3B
NHE3 Model - Figure 4A
NHE3 Model - Figure 4B
Fujita, Toyoshima, Uda, Ozaki, Kubota, Kuroda, 2010
Decoupling of receptor and downstream signals in the Akt pathway by its low-pass filter characteristics: EGF-dependent Akt pathway model
Decoupling of receptor and downstream signals in the Akt pathway by its low-pass filter characteristics: NGF-dependent Akt pathway model
Decoupling of receptor and downstream signals in the Akt pathway by its low-pass filter characteristics: EGFR-inhibited Akt pathway model
Cl-/HCO3- Exchanger (AE1) Model
AE1 Model
AE1 Model - Figure 2A
AE1 Model - Figure 2B
AE1 Model - Figure 2C
AE1 Model - Figure 2D
AE1 Model - Figure 2E
AE1 Model - Figure 2F
AE1 Model - Figure 3A
AE1 Model - Figure 3B
AE1 Model - Figure 3C
AE1 Model - Figure 3D
Maurya, Bornheimer, Venkatasubramanian, Subramaniam, 2005
Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module
Wang, Cirit, Haugh, 2009
PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk
De Vries, Sherman, 2000
Channel Sharing in Pancreatic Beta-Cells Revisited: Enhancement of Emergent Bursting by Noise
Shiferaw, Watanabe, Garfinkel, Weiss, Karma, 2003
Model of Intracellular Calcium Cycling in Ventricular Myocytes
Conradie, Bruggeman, Ciliberto, Csikasz-Nagy, Novak, Westerhoff, Snoep,
Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex
Rice, Winslow, Hunter, 1999
Comparison of putative cooperative mechanisms in cardiac muscle: length dependence and dynamic responses (model 1)
Comparison of putative cooperative mechanisms in cardiac muscle: length dependence and dynamic responses (model 2)
Comparison of putative cooperative mechanisms in cardiac muscle: length dependence and dynamic responses (model 3)
Comparison of putative cooperative mechanisms in cardiac muscle: length dependence and dynamic responses (model 4)
Comparison of putative cooperative mechanisms in cardiac muscle: length dependence and dynamic responses (model 5)
Li, Smith, 2009
Li_Smith_2009_C57BL7_WT.cellml
Oyehaug, Ostby, Lloyd, Omholt, Einevoll, 2011
Dependence of spontaneous neuronal firing and depolarization block on astroglial membrane processes: Fig 2A
Dependence of spontaneous neuronal firing and depolarization block on astroglial membrane processes: Fig 2B
Volume mesh of liver
Volume mesh of liver
Morris, Lecar, 1981
Voltage oscillations in the barnacle giant muscle fiber: reduced model
Voltage oscillations in the barnacle giant muscle fiber: complete model
Alexander, Wahl, 2010
Self-tolerance and Autoimmunity in a Regulatory T Cell Model: System 1
Self-tolerance and Autoimmunity in a Regulatory T Cell Model: System 2
Self-tolerance and Autoimmunity in a Regulatory T Cell Model: System 3
Self-tolerance and Autoimmunity in a Regulatory T Cell Model: System 4
Moore, Li, 2004
A Mathematical Model for Chronic Myelogenous Leukemia (CML) and T Cell Interaction (Decreasing CML Variant)
A Mathematical Model for Chronic Myelogenous Leukemia (CML) and T Cell Interaction (Increasing CML Variant)
A Mathematical Model for Chronic Myelogenous Leukemia (CML) and T Cell Interaction (CML Recovery Variant)
A model for pacemaking in substantia nigra neurons (A simple model based on a spherical geometry)
francis_garcia_middleton_2012_spherical_Fig5.3.sedml
francis_garcia_middleton_2012_spherical.cellml
A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry
A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry
A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry
A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry
A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry
Aguda, B, 1999
A quantitative analysis of the kinetics of the G2 DNA damage checkpoint system
3fd
gupta_2009.cellml
Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation
Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation
Aslanidi 2009
Optimal velocity and safety of discontinuous conduction through the heterogeneous Purkinje-ventricular junction
Volume mesh of liver
Volume mesh of liver
Fenton, Karma, 1998
Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation (BR Model)
Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation (GP Model)
Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation (MBR Model)
Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation (MLR-1 Model)
Bagci 2008
Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis (Model II)
Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis (Model III)
Alexander, Wahl, 2010
Self-tolerance and Autoimmunity in a Regulatory T Cell Model: System 1
Self-tolerance and Autoimmunity in a Regulatory T Cell Model: System 2
Self-tolerance and Autoimmunity in a Regulatory T Cell Model: System 3
Self-tolerance and Autoimmunity in a Regulatory T Cell Model: System 4
Bondarenko, Szigeti, Bett, Kim, Rasmusson, 2004
Computer model of action potential of mouse ventricular myocytes (Apical Cell Description)
Computer model of action potential of mouse ventricular myocytes (Septal Cell Description)
Benson, Aslanidi, Zhang, Holden, 2008
The canine virtual ventricular wall: a platform for dissecting pharmacological effects on propagation and arrhythmogenesis (Epicardial Cell Model)
The canine virtual ventricular wall: a platform for dissecting pharmacological effects on propagation and arrhythmogenesis (Endocardial Cell Model)
The canine virtual ventricular wall: a platform for dissecting pharmacological effects on propagation and arrhythmogenesis (Midmyocardial Cell Model)
Barberis, Klipp, Vanoni, Alberghina, 2007
Cell Size at S Phase Initiation: An Emergent Property of the G1/S Network
Ben-Tal, 2006
Simplified models for gas exchange in the human lungs
Chen, Calzone, Csikasznagy, Cross, Novak, Tyson, 2004
chen_calzone_csikasznagy_cross_novak_tyson_2004.cellml
Novak, Tyson, 1993
Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos: parameter values have been taken from the original published paper to reproduce figure 4A.
Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos: parameter values have been taken from the SBML model in the BioModels Database and the model simulates the synthesis and degradation of cyclin.
Cardiovascular Circulation Windkessel
Lumped-parameter cardiovascular model with Windkessel after-load
EAtrium.cellml
EVentricle.cellml
ModelLeftHeart.cellml
ModelWindKessel.cellml
ParaLeftHeart.cellml
ParaSys.cellml
ParaWindKessel.cellml
TempCDa.cellml
TempCDv.cellml
TempRC.cellml
Units.cellml
Models for the OpenCOR and PMR tutorial by Peter Hunter
vanderpol.cellml
Firstorder.cellml
lorenz.cellml
SimpleFirstOrderEqn.cellml
potassium_ion_channel.cellml
sodium_ion_channel.cellml
Goldbeter, Dupont, Berridge, 1990
Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation
Testing linkage between SVG images and CellML/SED-ML documents
periodic-stimulus.sedml
HH-model
Tabak, Mascagni, Bertram, 2010
Mechanism for the Universal Pattern of Activity in Developing Neuronal Networks
Testing linkage between SVG images and CellML/SED-ML documents
periodic-stimulus.sedml
HH-model
Cui, Kaandorp, 2006
Mathematical modeling of calcium homeostasis in yeast cells
Vasalou, Henson, 2010
A multiscale model to investigate circadian rhythmicity of pacemaker neurons in the suprachiasmatic nucleus
Collier et al (1996) Delta-Notch model
collier-2cell.xml
single-cell.xml
Bornheimer, Maurya, Farquhar, Subramaniam, 2004
Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction
A 0D model of the Heart
Kholodenko, Demin, Moehren, Hoek, 1999
Quantification of short term signalling by the epidermal growth
Elowitz, Leibler, 2000
A Synthetic Oscillatory Network of Transciptional Regulators
Computational analysis of the human sinus node action potential: model development and effects of mutations
HumanSAN_FFWS_2017.cellml
Farhy, Bowers, Veldhuis, 2007
Female-specific model and GHRH alone is being injected
Male-specific model and GHRH alone is being injected
BG Mica models
BG tutorial model solid mechanics 4 Lorenz s-domain.cellml
Noble 1962 model for Physiome article
experiments
potassium_channel_model.xml
potassium_channel_n_gate_model.xml
Friel, 1995
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model
A model of intracellular pH control
A model of intracellular pH control
A model of intracellular pH control
A model of intracellular pH control
A model of intracellular pH control
A model of intracellular pH control
Tran 2017 - Cross-bridge model of shortening heat
Tran 2010
A metabolite-sensitive, thermodynamically-constrained model of cardiac cross-bridge cycling: Implications for force development during ischemia
Varela - Canine Atrial Cell Models
Varela_LA_2016.cellml
Varela_RA_2016.cellml
Varela_PV_2016.cellml
Varela - Canine Atrial Cell Models
Varela_LA_2016.cellml
Varela_RA_2016.cellml
Varela_PV_2016.cellml
Varela - Canine Atrial Cell Models
Varela_LA_2016.cellml
Varela_RA_2016.cellml
Varela_PV_2016.cellml
Morgan, Colman, Chubb, Seemann, Aslanidi, 2016
Morgan atrial fbroblast 2016.cellml
Goldbeter, 1991
A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase (Model without MIRIAM annotations)
A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase (Model with MIRIAM annotations)
Atrial fibroblast model
Morgan atrial fibroblast 2016.cellml
SED-ML example
lorenz.cellml
SED-ML example
vanderpol.cellml
Goldbeter, 1995
A model for circadian oscillations in the Drosophila period protein (PER)
Goldbeter,
A model for the dynamics of human weight cycling
Hill, 1972 - a model of feto-maternal oxygen exchange
Feto_maternal_Oxygen_transfer.cellml
O'Hara-Rudy-CiPA-v1.0 (2017)
ohara_rudy_cipa_v1_2017.cellml
HH Sodium Current model for estimation task
sodium_ion_channel.cellml
The ORd human ventricular action potential model
The ORd human ventricular action potential model
action-potential.xml
Goldbeter, Dupont, Berridge, 1990
Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation
Steady state HMT
1998_nash.cellml
Bernus, Wilders, Zemlin, Verschelde, Panfilov, 2002
A computationally efficient electrophysiological model of human ventricular cells
Goldbeter, Gonze, Pourquie, 2007
Sharp Developmental Thresholds Defined Through Bistability By Antagonistic Gradients of Retinoic Acid and FGF Signaling
Guyton, Volume Receptors, 2008
Description of Guyton volume receptors module
Description of Guyton volume receptors module
Clancy, Rudy, 2002
Na Channel Mutation That Causes Both Brugada Syndrome and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism (Wild Type Epicardial Cell)
Na Channel Mutation That Causes Both Brugada Syndrome and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism (INa1795insD Mutant Endocardial Cell)
Na Channel Mutation That Causes Both Brugada Syndrome and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism (INa1795insD Mutant Epicardial Cell)
Na Channel Mutation That Causes Both Brugada Syndrome and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism (INa1795insD Mutant Midmyocardial Cell)
Na Channel Mutation That Causes Both Brugada Syndrome and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism (Wild Type Endocardial Cell)
Na Channel Mutation That Causes Both Brugada Syndrome and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism (Wild Type Midmyocardial Cell)
Clancy, Rudy, 2001
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death (Wild Type Epicardial Cell)
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death (IKrN629D Mutant Epicardial Cell)
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death (IKr629D Mutant Midmyocardial Cell)
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death (IKrR56Q Mutant Epicardial Cell)
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death (IKrR56Q Mutant Midmyocardial Cell)
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death (IKrT474I Mutant Epicardial Cell)
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death (IKrT474I Mutant Midmyocardial Cell)
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death (INaKPQ Mutant Epicardial Cell)
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death (Wild Type Midmyocardial Cell)
Nelson, Perelson, 1995
Modeling defective interfering virus therapy for AIDS: conditions for DIV survival (No DIV Interference)
Modeling defective interfering virus therapy for AIDS: conditions for DIV survival (DIV Interference)
Schoeberl, Eichler-Jonsson, Gilles, Muller, 2002
Computational Modeling of the Dynamics of the MAP Kinase Cascade Activated by Surface and Internalized EGF Receptors.
Friel, 1995
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model
The Epithelial Transport
Computational analysis of the human sinus node action potential: model development and effects of mutations
HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.cellml
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model
Paci, Hyttinen, Aalto-Setala, Severi 2013 HiPSC models
Computational models of ventricular- and atrial-like human induced pluripotent stem cell derived cardiomyocytes
Computational models of ventricular- and atrial-like human induced pluripotent stem cell derived cardiomyocytes
Grandi et al. 2011 Human Atrial Action Potential and Ca2+ Model
grandi_2011_atrial_with_meta.cellml
O'Hara-Rudy-CiPA-v1.0 (2017)
O'Hara-Rudy CiPA v1.0 (2017)
Fenton, Karma, 1998
Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation (BR Model)
Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation (GP Model)
Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation (MBR Model)
Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation (MLR_1 Model)
Fenton, Karma, 1998
Renal Na+/H+ antiporter (NHE3) model
Renal Na+/H+ antiporter (NHE3) model
Renal Na+/H+ antiporter (NHE3) model - figure 2
Renal Na+/H+ antiporter (NHE3) model - figure 3
Weinstein_1995_NHE3_Fig3b.cellml
Renal Na+/H+ antiporter (NHE3) model - figure 4
Renal Na+/H+ antiporter (NHE3) model - figure 4b
Renal Na+/H+ antiporter (NHE3) model - figure 5
Model of a rabbit Purkinje cell
purkinje_model.cellml
Grandi, Pasqualini, Bers, 2009
A novel computational model of the human ventricular action potential and Ca transient
Envelope Stimulus Protocol
IV Stimulus Protocol
No Stimulus Protocol
Pace1 Stimulus Protocol
Pace2 Stimulus Protocol
Pace4 Stimulus Protocol
PaceNew Stimulus Protocol
Recovery Stimulus Protocol
Voltage Clamp Stimulus Protocol
A novel computational model of the human ventricular action potential and Ca transient
Winslow, Rice, Jafri, Marban, O'Rorke, 1999
Mechanisms of Altered Excitation-Contraction Coupling in Canine Tachycardia-Induced Heart Failure, II Model Studies
C. Trovato, E. Passini, N. Nagy, et al. (2019),A computational human cardiac Purkinje electrophysiological model
C. Trovato, E. Passini, N. Nagy, et al. (2019),A computational human cardiac Purkinje electrophysiological model (sedml)
Tomek, Jakub, et al. (2019)- A computational human ventricular electrophysiological model
Tomek, Jakub, et al. (2019)- A computational human ventricular electrophysiological model (endocardial)
Tomek, Jakub, et al. (2019)- A computational human ventricular electrophysiological model (epicardial)
Tomek, Jakub, et al. (2019)- A computational human ventricular electrophysiological model (midmyocardial)
Trovato, Passini, Nagy, et al. (2019),A computational human cardiac Purkinje electrophysiological model
Trovato, Passini, Nagy, et al. (2019),A computational human cardiac Purkinje electrophysiological model (sedml)
SED-ML simulation for Di Francesco and Noble (1985).
SED-ML simulation for Di Francesco and Noble (1985).
SED-ML simulation for Di Francesco and Noble (1985).
McIntyre, Richardson, Grill, 2001
Modeling the excitability of mammalian nerve fibers: influence of afterpotentials on the recovery cycle
Butera, Rinzel, Smith, 1999
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: 5 Cell Model
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: 10 Cell Model
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: Single Cell Model
Model of a rabbit Purkinje cell
Model of a rabbit Purkinje cell
Ni et al. 2017 Human atrial model
Computational analysis of the human sinus node action potential: model development and effects of mutations
HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.cellml
Computational analysis of the human sinus node action potential: model development and effects of mutations
HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.cellml
Computational analysis of the human sinus node action potential: model development and effects of mutations
HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.cellml
Generic rat bladder scaffold
Generic cat bladder scaffold
Generic human heart scaffold
Generic pig heart scaffold
Model of a rabbit Purkinje cell
corrias_rabbit_purkinje_model_2011.cellml
Generic rat heart scaffold
Generic mouse colon scaffold
Generic rat stomach scaffold
Generic mouse lung scaffold
Generic human colon scaffold
Generic pig colon scaffold
Generic human lung scaffold
Generic human lung scaffold
Koivumäki, Korhonen, Tavi 2011 Atrial AP model
Koivumäki, Korhonen, Tavi 2011 Atrial AP model
Koivumäki, Korhonen, Tavi 2011 Human Atrial AP model
koivumaki-2011-pmr.cellml
Voigt, Heijman et al. 2013 Human Atrial AP model
Voigt, Heijman et al. 2013 Human Atrial AP model
Voigt, Heijman et al. 2013 human atrial AP model
Voigt, Heijman et al. 2013 Human Atrial AP model
An encoding of the human ORd model by Steve Neiderer
The ORd human ventricular action potential model
Rat whole body scaffold
Generic human lung scaffold
Generic mouse lung scaffold
Generic mouse lung scaffold
mouseLungsMesh.exf
Generic human lung scaffold
humanLungsMesh.exf
rat flatmap
manifest.json
Virtual Bacterial Photography
Virtual Bacterial Photography
Ni et al. 2017 Human Atrial model
ni_2017.cellml
Generic rat stomach scaffold
Generic human stomach scaffold
Carro, Rodríguez, Laguna, Pueyo (2011)
Carro_Rodriguez_Laguna_Pueyo_2011_EPI.cellml
Carro_Rodriguez_Laguna_Pueyo_2011_ENDO.cellml
Carro, Rodríguez, Laguna, Pueyo (2011)
Carro_Rodriguez_Laguna_Pueyo_2011_ENDO.cellml
Carro_Rodriguez_Laguna_Pueyo_2011_EPI.cellml
Hodgkin & Huxley (1952) model
experiments
components
Generic human bladder scaffold
Generic cat bladder scaffold
Generic rat bladder scaffold
Generic human lung scaffold
Generic human lung scaffold
Generic mouse lung scaffold
Generic rat lung scaffold
Generic human heart scaffold
Generic pig heart scaffold
Generic rat heart scaffold
Rat whole-body scaffold with embedded organs
Computational Mechanics of the Heart
Computational Mechanics of the Heart
Loewe-Lutz-Fabbri-Severi human sinus node cellular electrophysiology model
LoeweLutzFabbriSeveri.cellml
Model of Human Jejunal Smooth Muscle Cell Electrophysiology
Components
Experiments
Generic rat brainstem scaffold
Generic human brainstem scaffold
Human whole-body scaffold with embedded organs
Model of Human Jejunal Smooth Muscle Cell Electrophysiology
Components
Experiments
Laminar structure of the Heart: A mathematical model.
Laminar structure of the Heart: A mathematical model.
Switching from Simple to Complex Oscillations in Calcium Signaling
Switching from Simple to Complex Oscillations in Calcium Signaling
Switching from Simple to Complex Oscillations in Calcium Signaling
Switching from Simple to Complex Oscillations in Calcium Signaling
The Glucose-induced Switch Between Glycogen Phosphorylase and Glycogen Synthase in the Liver: Outlines of a Theoretical Approach
The Glucose-induced Switch Between Glycogen Phosphorylase and Glycogen Synthase in the Liver: Outlines of a Theoretical Approach
The Glucose-induced Switch Between Glycogen Phosphorylase and Glycogen Synthase in the Liver: Outlines of a Theoretical Approach
The Glucose-induced Switch Between Glycogen Phosphorylase and Glycogen Synthase in the Liver: Outlines of a Theoretical Approach
The ORd human ventricular action potential model
Ohara_Rudy_2011.cellml
action-potential.xml
Teusink, Westerhoff, Snoep, Passarge, Reijenga, Esgalhado, van der Weijden, Schepper, Walsh, Bakker, van Dam, 2000
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.
The Lorenz Attractor, a classical mathematical model
The Lorenz Attractor, a classical mathematical model
The Lorenz Attractor, a classical mathematical model
The Lorenz Attractor, a classical mathematical model
The Lorenz Attractor, a classical mathematical model
The Lorenz Attractor, a classical mathematical model
The Lorenz Attractor, a classical mathematical model
The Lorenz Attractor, a classical mathematical model
The Lorenz Attractor, a classical mathematical model
The Lorenz Attractor, a classical mathematical model
Luo, Rudy, 1994
A Dynamic Model of the Cardiac Ventricular Action Potential I. Simulations of Ionic Currents and Concentration Changes
Dependence of the period on the rate of protein degradation in minimal models for circadian oscillations
A Model For Circadian PER Oscillations In Drosophila
Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation
Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation
Latency correlates with period in a model for signal-induced Ca2l oscillations based on Ca"2-induced Ca2+ release
Latency correlates with period in a model for signal-induced Ca2l oscillations based on Ca"2-induced Ca2+ release
Leloup, Goldbeter, 2004
Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms
Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation
Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation
Activation of the Liver Glycogen Phosphorylase by Ca2+ Oscillations: a Theoretical Study
gall_2000.cellml
gall_2000b.cellml
Covering a broad dynamic range: information processing at the erythropoietin receptor
Covering a broad dynamic range: information processing at the erythropoietin receptor
Covering a broad dynamic range: information processing at the erythropoietin receptor
Covering a broad dynamic range: information processing at the erythropoietin receptor
Wang, Sobie, 2008
Mathematical model of the neonatal mouse ventricular action potential
Grandi, Pasqualini, Bers, 2009
A novel computational model of the human ventricular action potential and Ca transient
Envelope Stimulus Protocol
IV Stimulus Protocol
No Stimulus Protocol
Pace1 Stimulus Protocol
Pace2 Stimulus Protocol
Pace4 Stimulus Protocol
PaceNew Stimulus Protocol
Recovery Stimulus Protocol
Voltage Clamp Stimulus Protocol
A novel computational model of the human ventricular action potential and Ca transient
Beeler-Reuter Mammalian Ventricular Model 1977
Beeler-Reuter Mammalian Ventricular Model 1977
On the encoding and decoding of calcium signals in hepatocytes
On the encoding and decoding of calcium signals in hepatocytes
On the encoding and decoding of calcium signals in hepatocytes
On the encoding and decoding of calcium signals in hepatocytes
Dynamic Model of Amino Acid and Carbohydrate Metabolism in Primary Human Liver Cells
Dynamic Model of Amino Acid and Carbohydrate Metabolism in Primary Human Liver Cells
Simulations of the effects of inositol 1,4,5-trisphosphate 3-kinase and 5-phosphatase activities on Ca2+ oscillations
Simulations of the effects of inositol 1,4,5-trisphosphate 3-kinase and 5-phosphatase activities on Ca2+ oscillations
Mitochondria regulate the amplitude of simple and complex calcium oscillations
Mitochondria regulate the amplitude of simple and complex calcium oscillations
Mitochondria regulate the amplitude of simple and complex calcium oscillations
Mitochondria regulate the amplitude of simple and complex calcium oscillations
Mitochondria regulate the amplitude of simple and complex calcium oscillations
Mitochondria regulate the amplitude of simple and complex calcium oscillations
Mitochondria regulate the amplitude of simple and complex calcium oscillations
Mitochondria regulate the amplitude of simple and complex calcium oscillations
Mitochondria regulate the amplitude of simple and complex calcium oscillations
Improvement of metabolic performance of primary hepatocytes in hyperoxic cultures by vitamin C in a novel small-scale bioreactor
Improvement of metabolic performance of primary hepatocytes in hyperoxic cultures by vitamin C in a novel small-scale bioreactor
Bifurcation analysis of the regulatory modules of the mammalian G1/S transition
Bifurcation analysis of the regulatory modules of the mammalian G1/S transition
Bugenhagen 2010
baroreflex.cellml
barodiagram.bmp
Canine Biventricular RC Heart
Canine Biventricular RC Heart
Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes
acikgoz_2009a.cellml
acikgoz_2009b.cellml
Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes
Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes
Canine Biventricular RC Heart
Canine Biventricular RC Heart
Myocardial contractility and regional work throughout the cardiac cycle using FEM and MRI
Canine Biventricular RC Heart
Mathematical modeling of mechanically modulated rhythm disturbances in homogeneous and heterogeneous myocardium with attenuated activity of na+ -k+ pump
Mathematical modeling of mechanically modulated rhythm disturbances in homogeneous and heterogeneous myocardium with attenuated activity of na+ -k+ pump
Mathematical modeling of mechanically modulated rhythm disturbances in homogeneous and heterogeneous myocardium with attenuated activity of na+ -k+ pump
Mathematical modeling of mechanically modulated rhythm disturbances in homogeneous and heterogeneous myocardium with attenuated activity of na+ -k+ pump
Mathematical modeling of mechanically modulated rhythm disturbances in homogeneous and heterogeneous myocardium with attenuated activity of na+ -k+ pump
Mathematical modeling of mechanically modulated rhythm disturbances in homogeneous and heterogeneous myocardium with attenuated activity of na+ -k+ pump
Laminar structure of the Heart: A mathematical model.
Laminar structure of the Heart: A mathematical model.
Myocardial contractility and regional work throughout the cardiac cycle using FEM and MRI
Myocardial contractility and regional work throughout the cardiac cycle using FEM and MRI
Volume mesh of liver
Volume mesh of liver
Computational Mechanics of the Heart
Computational Mechanics of the Heart
Butera, Rinzel, Smith, 1999
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: 5 Cell Model
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: 10 Cell Model
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. II. Populations of Coupled Pacemaker Neurons: Single Cell Model
Reconstruction of the action potential of ventricular myocardial fibres
Reconstruction of the action potential of ventricular myocardial fibres
Andre playing with nested tasks in SED-ML
A model for pacemaking in substantia nigra neurons (A simple model based on a spherical geometry)
A model for pacemaking in substantia nigra neurons (A simple model based on a spherical geometry)
Ionic mechanisms for electrical heterogeneity between rabbit Purkinje fiber and ventricular cells
Edwards, 2010
Hunter, Smaill, Hunter, 1995
A pole-zero constitutive law for myocardium
Guccione, Mcculloch, Waldman, 1991
guccione.cellml
Sine approximations in CellML
Sine approximations in CellML
Sine approximations in CellML
An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis
An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis
Spronck, 2012
Davies isAP 2012
Davies ISAP 2012
Davies ISAP 2012
Davies ISAP 2012
Hunter, Smaill, Hunter, 1995
A pole-zero constitutive law for myocardium
Andre's Hodgkin & Huxley with CellML
Learning CellML by example: The Hodgkin & Huxley model
An analysis of deformation-dependent electromechanical coupling in the mouse heart
An analysis of deformation-dependent electromechanical coupling in the mouse heart
Andre's Hodgkin & Huxley with CellML
VPH-MIP standardisation & ontologies module, CellML case study
Hunter, Smaill, Hunter, 1995
A pole-zero constitutive law for myocardium
Reconstruction of the action potential of ventricular myocardial fibres, with modifications to demonstrate uncertainty.
Reconstruction of the action potential of ventricular myocardial fibres, with modifications to demonstrate uncertainty.
Severi, Fantini, Charawi, Difrancesco, 2012
severi_fantini_charawi_difrancesco_2012.cellml
Generic human heart scaffold
ViewCreation-previous-docs
Generic mouse heart scaffold
ViewCreation-previous-docs
Generic rat heart scaffold
ViewCreation-previous-docs
Generic human lung scaffold
ViewCreation-previous-docs
Generic mouse lung scaffold
ViewCreation-previous-docs
Generic rat lung scaffold
ViewCreation-previous-docs
Generic pig lung
ViewCreation-previous-docs
Generic pig lung
Generic rat lung scaffold
Generic Mouse Bladder Scaffold
Generic rat bladder scaffold
Grandi et al. 2011 Atrial Action Potential and Ca2+ Model
grandi_2011_atrial_with_meta.cellml
FAIR DOs example 4.2
FAIRDO BG example 4.2.cellml
Generic pig stomach scaffold
Generic mouse stomach scaffold
Generic mouse stomach scaffold
Tong, Choi, Kharche, Holden, Zhang, Taggart, 2011 - Reduced Model
Simple RTM Model Doc Page
A 3D human whole-body model with integrated organs, vasculature, musculoskeletal and nervous systems for mapping nerves
mapclient workflow
Generic pig brainstem scaffold
Reproducibility of the computational model of induced pluripotent stem-cell derived cardiomyocytes
Channels.cellml
Current_Ica.cellml
Current_If.cellml
Current_Ik1.cellml
Current_Ikr.cellml
Current_Iks.cellml
Current_Ina.cellml
Current_Ito.cellml
gating_Ica.cellml
gating_Icat.cellml
gating_If.cellml
gating_Ik1.cellml
gating_Ikr.cellml
gating_Iks.cellml
gating_Ina.cellml
gating_Ito.cellml
parameter_Ica.cellml
parameter_If.cellml
parameter_Ik1.cellml
parameter_Ikr.cellml
parameter_Iks.cellml
parameter_Ina.cellml
parameter_Ito.cellml
parameter.cellml
unit.cellml
fig2.py
fig3.py
fig4.py
fig5.py
fig6.py
fig7.py
fig8.py
fig9.py
fig10.py
BG_HaiMurphy
BG_HaiMurphy.cellml
exposure
SERCA protein knowledge page
BG_SERCA.cellml
exposure
Funny current channel knowledge page
BG_funny.cellml
exposure
Ryanodine receptor knowledge page
exposure
BG_RyR.cellml
argon cube demo
CubeSquareLine.neon
Generic cat bladder scaffold
Generic human stomach scaffold
Generic pig stomach scaffold
Generic mouse lung scaffold
Generic pig lung
Generic human esophagus scaffold
Cardiovascular model with the feedback loops
Model of Excitation-Contraction in a uterine SMC
Components
Experiments
A computational human atrial myofibroblast electrophysiological model
Kp protein knowledge page
BG_Kp.cellml
Mechanistic PK-PD model of alendronate treatment of postmenopausal osteoporosis predicts bone site-specific response
Mechanistic PK-PD model of alendronate treatment of postmenopausal osteoporosis predicts bone site-specific response: hip
Mechanistic PK-PD model of alendronate treatment of postmenopausal osteoporosis predicts bone site-specific response: lumbar spine
TO knowledge page
BG_to.cellml
Argon SDS Demo
multiview.argon
The Physics of Physiology - Example 2: A mechanical system
FAIRDO BG example 3.2.cellml
FAIR DOs example 4.2
FAIRDO BG example 4.2.cellml
BG_cAMP
exposure
BG_cAMP.cellml
Generic mouse lung scaffold
Generic mouse brainstem scaffold
Cardiac Cellular Electrophysiological Modelling
CaL protein knowledge page
exposure
BG_LCC.cellml
The Heijman et al. 2011 model of the canince ventricular AP, with signalling
heijman-2011.cellml
BG_RTK
BG_RTK.cellml
BG_RTK.sedml
exposure
Generic sheep brainstem
Biceps femoris long
generated.neon
Biceps femoris short
generated.neon
Gastrocnemius
generated.neon
Gracilis
generated.neon
Popliteus
generated.neon
Rectus femoris
generated.neon
Sartorius
generated.neon
Semimembranosus
generated.neon
Semitendinosus
generated.neon
Vastus Intermedius
generated.neon
Vastus lateralis
generated.neon
Vastus medialis
generated.neon
Abductor digiti minimi
generated.neon
Abductor pollicis brevis
generated.neon
Abductor pollicis longus
generated.neon
Anconeus
generated.neon
Biceps brachii
generated.neon
Brachialis
brachialis2.neon
Brachioradialis
generated.neon
Coracobrachialis
generated.neon
Deltoid
generated.neon
Dorsal interossei I
generated.neon
Dorsal interossei II
generated.neon
Dorsal interossei III
generated.neon
Dorsal interossei IV
generated.neon
Extensor carpi radialis brevis
generated.neon
Extensor carpi radialis longus
generated.neon
Extensor carpi ulnaris
generated.neon
Extensor digiti minimi
generated.neon
Extensor digitorum
generated.neon
Extensor indicis
generated.neon
Extensor pollicis brevis
generated.neon
Extensor pollicis longus
generated.neon
Flexor carpi radialis
generated.neon
Flexor carpi ulnaris
generated.neon
Flexor digiti minimi
generated.neon
Flexor digitorum profundus
generated.neon
Flexor digitorum superficialis
generated.neon
Flexor pollicis brevis
generated.neon
Flexor pollicis longus
generated.neon
Infraspinatus
generated.neon
Lumbrical I
generated.neon
Lumbrical II
generated.neon
Lumbrical III
generated.neon
Lumbrical IV
generated.neon
Opponens digiti minimi
generated.neon
Opponens pollicis
generated.neon
Palmar interossei I
generated.neon
Palmar interossei II
generated.neon
Palmaris brevis
generated.neon
Gastrocnemius
generated.neon
Digastricus Anterior
generated.neon
DIGASTRICUS POSTERIOR
generated.neon
Geniohyoideus
generated.neon
Longus Capitis
generated.neon
Longus Colli Inferior
generated.neon
Longus Colli Superior
generated.neon
Longus Colli Vertical
generated.neon
Mylohyoideus
generated.neon
Omohyoideus
generated.neon
Pharyngeal Constrictor
generated.neon
Platysma
generated.neon
Rectus Capitis Anterior
generated.neon
Rectus Capitis Lateralis
generated.neon
Scalenus Anterior
generated.neon
Scalenus Medius
generated.neon
Scalenus Posterior
generated.neon
Splenius Capitis
generated.neon
Sternocleidomastoid
generated.neon
Sternohyoideus
generated.neon
Sternothyroideus
generated.neon
Stylohyoideus
generated.neon
Thyrohyoideus
generated.neon
Trapezius
generated.neon
Digastric
generated.neon
Geniohyoid
generated.neon
Lateral Pterygoid Left
generated.neon
Lateral Pterygoid Right
generated.neon
Masseter Left
generated.neon
Masseter Right
generated.neon
Medial Pterygoid Left
generated.neon
Medial Pterygoid Right
generated.neon
Mylohyoid
generated.neon
Temporalis Left
generated.neon
Temporalis Right
generated.neon
CAPITATE
generated.neon
DISTAL_PHALANX_I
generated.neon
DISTAL_PHALANX_II
generated.neon
DISTAL_PHALANX_III
generated.neon
DISTAL_PHALANX_IV
generated.neon
DISTAL_PHALANX_V
generated.neon
HAMATE
generated.neon
HUMERUS
generated.neon
METACARPAL_I
generated.neon
METACARPAL_II
generated.neon
MIDDLE_PHALANX_II
generated.neon
MIDDLE_PHALANX_III
generated.neon
MIDDLE_PHALANX_IV
generated.neon
MIDDLE_PHALANX_V
generated.neon
PISIFORM
generated.neon
FIBULA
generated.neon
HIP
generated.neon
PATELLA
generated.neon
TIBIA
generated.neon
PROXIMAL_PHALANX_I
generated.neon
PROXIMAL_PHALANX_II
generated.neon
PROXIMAL_PHALANX_III
generated.neon
PROXIMAL_PHALANX_V
generated.neon
RADIUS
generated.neon
SCAPHOID
generated.neon
TRAPEZIUM
generated.neon
TRAPEZOID
generated.neon
ULNA
generated.neon
SLC transporters
Facilitated transporter
Electrogenic cotransporter
Cardiac Cellular Electrophysiological Modelling
CaT protein knowledge page
exposure
BG_TCC.cellml
Generic pig stomach scaffold
The Physics of Physiology - Example 1: An electrical circuit
FAIRDO BG example 3.1.cellml
FAIRDO BG example 3.1.1.cellml
BG_crossbridge_TRPN
exposure
BG_crossbridge_TRPN.cellml
Generic human lung scaffold
Generic mouse lung scaffold
Generic human heart scaffold
Generic mouse heart scaffold
FCU_cardiacAP_composite
exposure
Generic pig lung
Generic rat lung scaffold
Generic rat heart scaffold
Generic pig heart scaffold
BG_B1AR
exposure
BG_B1AR.cellml
Generic human stomach scaffold
K ATP protein knowledge page
BG_K_ATP.cellml
exposure
Generic pig colon scaffold
KIR protein knowledge page
BG_KACh.cellml
exposure
Model of Human Jejunal Smooth Muscle Cell Electrophysiology
Components
Experiments
Generic human small intestine scaffold
ViewCreation-previous-docs
Cardiovascular model with the feedback loops
models
simulation.json
SinglePASMC
Experiments
BG_PLC
BG_PLC.cellml
exposure
SLC transporters
Facilitated transporter
Electrogenic cotransporter
Human whole-body scaffold with embedded organs
mapclient_workflow
Reproducibility of the computational model of induced pluripotent stem-cell derived cardiomyocytes
CellML
RST
figures
Generic human brainstem scaffold
ViewCreation-previous-docs
Generic mouse brainstem scaffold
ViewCreation-previous-docs
Generic rat brainstem scaffold
ViewCreation-previous-docs
Generic sheep brainstem
ViewCreation-previous-docs
Generic rat stomach scaffold
ViewCreation-previous-docs
Generic human esophagus scaffold
ViewCreation-previous-docs
Generic mouse colon scaffold
ViewCreation-previous-docs
Generic pig colon scaffold
ViewCreation-previous-docs
Pig whole-body with embedded organs using automatic workflow for inserting the organs
Saucerman, Brunton, Michailova, McCulloch, 2003
Modeling beta-adrenergic control of cardiac myocyte contractility in silico
Loewe-Lutz-Fabbri-Severi human sinus node cellular electrophysiology model
LoeweLutzFabbriSeveri.cellml
Generic rat stomach scaffold
Potassium delayed rectifier channel knowledge page
BG_Kr.cellml
exposure
Rat whole-body with embedded organs using automatic workflow for inserting the organs
Cardiovascular model with the feedback loops
models
Cardiovascular model with the feedback loops
models
FCU_adenylylCyclase
FCU_adenylylCyclase.cellml
exposure
FCU_adenylylCyclase
FCU_adenylylCyclase.cellml
exposure
ECC_MSK (Rios et al. 1993)
Experiments
PMCA knowledge page
BG_pCa.cellml
exposure
Iancu, Jones, Harvey, 2007
Compartmentation of cAMP signaling in cardiac myocytes: a computational study
Generic human colon scaffold
Generic mouse colon scaffold
Generic pig colon scaffold
Generic human stomach scaffold
Reproducibility of the computational model of induced pluripotent stem-cell derived cardiomyocytes
Components
Experiments
The Physics of Physiology - Example 6: An enzyme-catalyzed reaction and Michaelis-Menten kinetics
FAIRDO BG example 3.6.cellml
FAIR DOs example 3.7
FAIRDO BG example 3.7.cellml
Generic human gastrointestinal tract scaffold
ViewCreation-previous-docs
ECC_MSK (Rios et al. 1993)
Experiments
FCU_adenylylCyclase
FCU_adenylylCyclase.cellml
exposure
Generic human colon scaffold
Generic mouse small intestine scaffold
ViewCreation-previous-docs
Single PASMC model (Gosak et al 2014)
Experiments
Generic pig lung
Thoracic Verterae 1
generated.neon
Thoracic Vertebrae 3
generated.neon
Cervical Vertebra 2
generated.neon
Cervical Vertebra 6
generated.neon
Cervical Vertebra 7
generated.neon
Intervertebral Disc of C2
generated.neon
Intervertebral Disc of C3
generated.neon
Documentation