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@CardiacModelling

Cardiac Modelling

Codes and Resources from the University of Nottingham's cardiac modelling team and collaborators
readme.md

Cardiac Modelling Team

Team led by Gary Mirams, and based at the Centre for Mathematical Medicine & Biology, University of Nottingham.

If you are looking for live web-based tools like ApPortal or the Web Lab please see links here.

To find the repos associated with our papers, please see our list of publications which contains a link for each publication.

In addition there are other pinned repos that we expect to be most useful, which may not be associated with papers, for instance:

  • RapidCharacterisationProtocols for our latest protocols that characterise ion currents quickly and efficiently by providing rich information for training mathematical models.
  • fitting-notebooks which give tutorials about how we would fit data from these protocols including lots of important detail on optimisation algorithms, parameter transforms, priors and more.
  • VoltageClampModel which provides code to simulate voltage clamp artefacts, which can be added to any ion channel or action potential model to simulate realistic voltage clamp artefacts for use in forward and inverse problems involving comparison with real experimental data.

Pinned Loading

  1. RapidCharacterisationProtocols RapidCharacterisationProtocols Public

    Collection of experimental protocols in common patch clamp formats for rapid characterisation of ion channels

    Python 5

  2. VoltageClampModel VoltageClampModel Public

    Code to add a mathematical model of voltage-clamp artefacts to your ion channel simulations

    Python 3

  3. fitting-notebooks fitting-notebooks Public

    Examples of parameter estimation in cardiac cell electrophysiology using Myokit and PINTS.

    Jupyter Notebook 4 5

Repositories

Showing 10 of 53 repositories
  • fitting-notebooks Public

    Examples of parameter estimation in cardiac cell electrophysiology using Myokit and PINTS.

    CardiacModelling/fitting-notebooks’s past year of commit activity
    Jupyter Notebook 4 5 6 2 Updated Nov 22, 2024
  • pcpostprocess Public

    A Python package to run Lei et al. (2019) quality control on patch-clamp time-series data.

    CardiacModelling/pcpostprocess’s past year of commit activity
    Python 2 BSD-3-Clause 0 32 (1 issue needs help) 4 Updated Nov 21, 2024
  • nav-artefact-model Public

    Code for reproducing "Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings"

    CardiacModelling/nav-artefact-model’s past year of commit activity
    Jupyter Notebook 1 BSD-3-Clause 0 0 0 Updated Nov 21, 2024
  • multiprotocol_data_fitting Public
    CardiacModelling/multiprotocol_data_fitting’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Nov 20, 2024
  • L-type-Ca-rundown-modelling Public
    CardiacModelling/L-type-Ca-rundown-modelling’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Nov 19, 2024
  • stochastic-gating Public

    Code to replicate the analyses from the article "Parameter inference for stochastic reaction models of ion channel gating from whole-cell voltage-clamp data"

    CardiacModelling/stochastic-gating’s past year of commit activity
    R 0 BSD-3-Clause 0 0 0 Updated Nov 18, 2024
  • ionBench Public

    A benchmarking tool for comparing different parameter optimization algorithms for ion channel models

    CardiacModelling/ionBench’s past year of commit activity
    Python 2 BSD-3-Clause 1 0 0 Updated Nov 14, 2024
  • L-type-Ca-rundown-experiments Public

    An investigation of rundown in automated patch clamp L-type calcium current

    CardiacModelling/L-type-Ca-rundown-experiments’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Nov 13, 2024
  • binding_model_OED Public

    Code for optimal experimental design paper

    CardiacModelling/binding_model_OED’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Nov 1, 2024
  • FourWaysOfFitting Public

    Code to compare four different ways to fit an ion current model

    CardiacModelling/FourWaysOfFitting’s past year of commit activity
    Python 4 3 1 0 Updated Oct 28, 2024
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