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On the encoding and decoding of calcium signals in hepatocytes
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Exposures
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
An updated computational model of rabbit sinoatrial action potential to investigate the mechanisms of heart rate modulation.
An updated computational model of rabbit sinoatrial action potential to investigate the mechanisms of heart rate modulation.
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
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
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)
Computational Mechanics of the Heart
Computational Mechanics of the Heart
Laminar structure of the Heart: A mathematical model.
Laminar structure of the Heart: A mathematical model.
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
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
Laminar structure of the Heart: A mathematical model.
Laminar structure of the Heart: A mathematical model.
Cortassa et al. (2006) ECME model
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
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
Vasalou, Henson, 2010
A multiscale model to investigate circadian rhythmicity of pacemaker neurons in the suprachiasmatic nucleus
Smith, Abdala, Koizumi, Rybak, Paton, 2007
Synaptic coupling
Preinspiratory neuron
Early inspiratory neuron
Augmenting expiratory neuron
Postinspiratory neuron
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
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
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
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
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
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)
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)
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
Tabak, Mascagni, Bertram, 2010
Mechanism for the Universal Pattern of Activity in Developing Neuronal Networks
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
Elowitz, Leibler, 2000
A Synthetic Oscillatory Network of Transciptional Regulators
Farhy, Bowers, Veldhuis, 2007
Female-specific model and GHRH alone is being injected
Male-specific model and GHRH alone is being injected
Friel, 1995
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model
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)
Goldbeter, 1995
A model for circadian oscillations in the Drosophila period protein (PER)
Goldbeter,
A model for the dynamics of human weight cycling
Goldbeter, Dupont, Berridge, 1990
Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation
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
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
[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
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
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
Model of a rabbit Purkinje cell
Virtual Bacterial Photography
Virtual Bacterial Photography
Computational Mechanics of the Heart
Computational Mechanics of the Heart
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 1A
Switching from Simple to Complex Oscillations in Calcium Signaling 1B
Switching from Simple to Complex Oscillations in Calcium Signaling 1C
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 (model A)
Covering a broad dynamic range: information processing at the erythropoietin receptor (model B)
Covering a broad dynamic range: information processing at the erythropoietin receptor (model C)
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 (Model A)
On the encoding and decoding of calcium signals in hepatocytes (Model B)
On the encoding and decoding of calcium signals in hepatocytes (Model C)
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 (model a)
Mitochondria regulate the amplitude of simple and complex calcium oscillations (model b)
Mitochondria regulate the amplitude of simple and complex calcium oscillations (model 2a)
Mitochondria regulate the amplitude of simple and complex calcium oscillations (model 2b)
Mitochondria regulate the amplitude of simple and complex calcium oscillations (model 3a)
Mitochondria regulate the amplitude of simple and complex calcium oscillations (model 3b)
Mitochondria regulate the amplitude of simple and complex calcium oscillations (model 4a)
Mitochondria regulate the amplitude of simple and complex calcium oscillations (model 4b)
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
Myocardial contractility and regional work throughout the cardiac cycle using FEM and MRI
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
Library of metabolic components in CellML
A human ventricular cell model for investigation of cardiac arrhythmias under hyperkalaemic conditions
Carro_Rodriguez_Laguna_Pueyo_2011_EPI.cellml
Workflows for analysis of valvular and aortic disease
Workflows for analysis of valvular and aortic disease
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
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.
Documentation
barodiagram.bmp