A theoretical model of slow wave regulation using voltage-dependent synthesis of inositol 1, 4, 5-trisphosphate
The system of equations and figures presented in Imtiaz et al. (2002) are verified and reproduced in the current curation paper.
Leyla Noroozbabaee, Mohammad Imtiaz, Dirk Van Heldenn, Peng Du, David P. Nickerson
Jan 20, 2023
The system of equations and figures presented in Imtiaz et al. (2002) are verified and reproduced in the current curation paper.
Reproducibility Study of Computational Modelling of Glucose Uptake by SGLT1 and GLUT2 in the Enterocyte
Afshar et al. (2021) generated a computational model of non-isotonic glucose uptake by small intestinal epithelial cells. The model incorporates apical uptake via SGLT1 and GLUT2, basolateral efflux into the blood via GLUT2 and cellular volume changes in response to non-isotonic conditions.
Nima Afshar, Soroush Safaei, David P. Nickerson, Peter J. Hunter, Vinod Suresh
Jan 19, 2023
Afshar et al. (2021) generated a computational model of non-isotonic glucose uptake by small intestinal epithelial cells. The model incorporates apical uptake via SGLT1 and GLUT2, basolateral efflux into the blood via GLUT2 and cellular volume changes in response to non-isotonic conditions.
Reproducibility Study for a Computational Model of the Neurovascular Coupling Unit
The mechanistic model of neurovascular coupling was developed and studied by Sten et al. (2020). This model describes and predicts the arteriolar dilation data of mice under various stimulations while anaesthetised and awake. We reconstructed the model in CellML, using a modular approach for each neuronal pathway, and successfully reproduced the original experiments.
Sergio Dempsey, Gunnar Cedersund, Maria Engström, Gonzalo Maso Talou, Soroush Safaei
Jan 11, 2023
The mechanistic model of neurovascular coupling was developed and studied by Sten et al. (2020). This model describes and predicts the arteriolar dilation data of mice under various stimulations while anaesthetised and awake. We reconstructed the model in CellML, using a modular approach for each neuronal pathway, and successfully reproduced the original experiments.
Computational modeling of anoctamin 1 calcium-activated chloride channels as pacemaker channels in interstitial cells of Cajal
Lees-Green et al. (2014) describes a biophysical computational model of anoctamin 1 calcium-activated chloride channels. The system of equations and simulation results are verified and reproduced.
Leyla Noroozbabaee, David P. Nickerson, Peng Du
Jan 11, 2023
Lees-Green et al. (2014) describes a biophysical computational model of anoctamin 1 calcium-activated chloride channels. The system of equations and simulation results are verified and reproduced.
Retrospective
Jan 27, 2022
Retrospective
Jan 27, 2022
Spindle Model Responsive to Mixed Fusimotor Inputs: an updated version of the Maltenfort and Burke (2003) model
The muscle spindle model presented in Maltenfort & Burke (2003) calculates muscle spindle primary afferent feedback depending on the muscle fibre stretch and fusimotor drive.
Laura Schmid, Thomas Klotz, Utku Ş. Yavuz, Mitchell Maltenfort, Oliver Röhrle
Jan 27, 2022
The muscle spindle model presented in Maltenfort & Burke (2003) calculates muscle spindle primary afferent feedback depending on the muscle fibre stretch and fusimotor drive.
Mathematical model of excitation-contraction in a uterine smooth muscle cell
The model incorporates processes of intracellular Ca²⁺ concentration control, myosin light chain (MLC) phosphorylation and stress production.
Weiwei Ai, Limor Freifeld, David P Nickerson
Oct 27, 2021
The model incorporates processes of intracellular Ca²⁺ concentration control, myosin light chain (MLC) phosphorylation and stress production.
A kinetic model of β-adrenergic control in cardiac myocytes
The system of equations and figures presented in Saucerman et al., 2003 are verified and reproduced in this paper’s curation effort.
Shelley Fong, Jeffrey J. Saucerman
Sep 23, 2021
The system of equations and figures presented in Saucerman et al., 2003 are verified and reproduced in this paper’s curation effort.
A Quantitative Model of Human Jejunal Smooth Muscle Cell Electrophysiology
The Poh et al. (2012) paper describes the first biophysically based computational model of human jejunal smooth muscle cell (hJSMC) electrophysiology. The ionic currents are described by either a traditional Hodgkin-Huxley (HH) formalism or a deterministic multi-state Markov (MM) formalism.
Weiwei Ai, David P. Nickerson
Sep 9, 2021
The Poh et al. (2012) paper describes the first biophysically based computational model of human jejunal smooth muscle cell (hJSMC) electrophysiology. The ionic currents are described by either a traditional Hodgkin-Huxley (HH) formalism or a deterministic multi-state Markov (MM) formalism.
Reproducibility study of the Fabbri et al. 2017 model of the human sinus node action potential
The sinoatrial node (SAN) is the natural pacemaker of the mammalian heart. It has been the subject of several mathematical studies, aimed at reproducing its electrical response under normal sinus rhythms, as well as under various conditions.
Nima Afshar, Alan Fabbri, Stefano Severi, Alan Garny, David Nickerson
Sep 1, 2021
The sinoatrial node (SAN) is the natural pacemaker of the mammalian heart. It has been the subject of several mathematical studies, aimed at reproducing its electrical response under normal sinus rhythms, as well as under various conditions.
Computational Modelling of Glucose Uptake in the Enterocyte
An implemented model of glucose absorption in the enterocyte, as previously published by Afshar et al. (2019).
Nima Afshar, Soroush Safaei, David P. Nickerson, Peter J. Hunter, Vinod Suresh
Oct 1, 2020
An implemented model of glucose absorption in the enterocyte, as previously published by Afshar et al. (2019).
Computational Modeling of Coupled Energetics and Mechanics in the Rat Ventricular Myocardium
A multi-scale model computational model of myocardial energetics—oxidative ATP synthesis, ATP hydrolysis, and phosphate metabolite kinetics—and myocardial mechanics used to analyze data from a rat model of cardiac decompensation and failure.
Bahador Marzban, Rachel Lopez, Daniel A. Beard
Sep 15, 2020
A multi-scale model computational model of myocardial energetics—oxidative ATP synthesis, ATP hydrolysis, and phosphate metabolite kinetics—and myocardial mechanics used to analyze data from a rat model of cardiac decompensation and failure.
Model of skeletal muscle cramp and its reversal
We reproduce muscle cramp, as well as its prevention and reversal, by investigating muscle contraction and cramp, in which calcium regulatory networks are involved, using the extended model in comparison with the original model.
Kazuyo Tasaki, Penelope J. Noble, Alan Garny, Paul R. Shorten, Nima Afshar, Denis Noble
Aug 28, 2020
We reproduce muscle cramp, as well as its prevention and reversal, by investigating muscle contraction and cramp, in which calcium regulatory networks are involved, using the extended model in comparison with the original model.
Retrospective
Aug 28, 2020
Retrospective
Aug 28, 2020
Incorporation of sarcolemmal calcium transporters into the Shorten et al. (2007) model of skeletal muscle: equations, coding and stability
We describe a major development of the Shorten et al. (2007) model of skeletal muscle electrophysiology, biochemistry and mechanics.
Penelope J. Noble, Alan Garny, Paul R. Shorten, Kazuyo Tasaki, Nima Afshar, Denis Noble
Aug 28, 2020
We describe a major development of the Shorten et al. (2007) model of skeletal muscle electrophysiology, biochemistry and mechanics.
Retrospective
Aug 27, 2020
Retrospective
Aug 27, 2020
The cardiac Na+/K+ ATPase: An updated, thermodynamically consistent model
The Na⁺/K⁺ ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na⁺ and K⁺ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte Na⁺/K⁺ ATPase to study extracellular potassium accumulation during ischaemia, demonstrating the ability to recapitulate a wide range of experimental data, but unfortunately there was no archived code associated with the original manuscript.
Michael Pan, Peter J. Gawthrop, Joseph Cursons, Kenneth Tran, Edmund J. Crampin
Aug 27, 2020
The Na⁺/K⁺ ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na⁺ and K⁺ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte Na⁺/K⁺ ATPase to study extracellular potassium accumulation during ischaemia, demonstrating the ability to recapitulate a wide range of experimental data, but unfortunately there was no archived code associated with the original manuscript.
The Boron & De Weer Model of Intracellular pH Regulation
The classic Boron & De Weer (1976) paper provided the first evidence of active regulation of pH in cells by an energy-dependent acid-base transporter. This Physiome paper seeks to make that model, and the experimental conditions under which it was developed, available in a reproducible and well-documented form, along with a software implementation that makes the model easy to use and understand.
Rossana Occhipinti, Soroush Safaei, Peter J. Hunter, Walter F. Boron
Aug 27, 2020
The classic Boron & De Weer (1976) paper provided the first evidence of active regulation of pH in cells by an energy-dependent acid-base transporter. This Physiome paper seeks to make that model, and the experimental conditions under which it was developed, available in a reproducible and well-documented form, along with a software implementation that makes the model easy to use and understand.
Bond Graph Model of Cerebral Circulation: Toward Clinically Feasible Systemic Blood Flow Simulations
The primary paper Safaei et al. (2018) proposed an anatomically detailed model of the human cerebral circulation that runs faster than real-time on a desktop computer and is designed for use in clinical settings when the speed of response is important.
Shan Su, Pablo J. Blanco, Lucas O. Müller, Peter J. Hunter, Soroush Safaei
Aug 26, 2020
The primary paper Safaei et al. (2018) proposed an anatomically detailed model of the human cerebral circulation that runs faster than real-time on a desktop computer and is designed for use in clinical settings when the speed of response is important.
