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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

  1. RapidCharacterisationProtocols RapidCharacterisationProtocols Public

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

    Python 4

  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 52 repositories
  • pcpostprocess Public
    CardiacModelling/pcpostprocess’s past year of commit activity
    Python 1 0 17 (1 issue needs help) 4 Updated Aug 30, 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 Aug 30, 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 2 Updated Aug 29, 2024
  • BenNevisBenchmark Public
    CardiacModelling/BenNevisBenchmark’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Aug 28, 2024
  • ap-nimbus-app-manager Public

    API for cloudified AP Predict

    CardiacModelling/ap-nimbus-app-manager’s past year of commit activity
    JavaScript 1 0 0 0 Updated Aug 27, 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 0 BSD-3-Clause 0 0 0 Updated Aug 23, 2024
  • syncropatch_export Public
    CardiacModelling/syncropatch_export’s past year of commit activity
    Python 1 BSD-3-Clause 0 5 0 Updated Aug 22, 2024
  • protocol-design-hERG Public

    Voltage clamp protocol design for hERG.

    CardiacModelling/protocol-design-hERG’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Aug 19, 2024
  • multiprotocol_data_fitting Public
    CardiacModelling/multiprotocol_data_fitting’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Aug 18, 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 Aug 14, 2024
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