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    58 repositories

    • VoltageClampModel-new

      Public
      A mathematical model of voltage clamp artefacts and compensation, with reference implementations and links to publications
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•0•Updated Mar 11, 2026Mar 11, 2026

    • pcpostprocess

      Public
      A Python package to run Lei et al. (2019) quality control on patch-clamp time-series data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•23•3•Updated Feb 11, 2026Feb 11, 2026

    • binding_model_OED

      Public
      Code for optimal experimental design paper
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Feb 3, 2026Feb 3, 2026

    • markov-builder

      Public
      Tool for building and manipulating Markov models of ion-channel kinetics
      pythonmarkov-modelherg
      pythonmarkov-modelhergherg-channel-kinetics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•1•1•Updated Dec 18, 2025Dec 18, 2025

    • hergModels

      Public
      Python
      •2•1•1•0•Updated Dec 18, 2025Dec 18, 2025

    • ContinuationForOptimisation

      Public
      Using limit cycle continuation methods to speed up evaluation of ion channel cell models
      Julia
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Nov 24, 2025Nov 24, 2025

    • L-type-Ca-rundown-experiments

      Public
      An investigation of rundown in automated patch clamp L-type calcium current
      Jupyter Notebook
      •
      Other
      •0•2•0•0•Updated Oct 28, 2025Oct 28, 2025

    • syncropatch_export

      Public
      A Python package to export SynroPatch 384 data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•21•0•Updated Oct 17, 2025Oct 17, 2025

    • summer-school-2025

      Public
      Summer school 2025 notebooks, for use in Google Colab
      Jupyter Notebook
      •0•0•0•0•Updated Oct 9, 2025Oct 9, 2025

    • space-filling-designs

      Public
      Phase-voltage space filling optimal designs in Matlab
      MATLAB
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Sep 19, 2025Sep 19, 2025

    • ina-midpoints

      Public
      Data and figures for "Variability in reported midpoints of (in)activation for cardiac INa"
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Sep 3, 2025Sep 3, 2025

    • VoltageClampModel

      Public
      Code to add a mathematical model of voltage-clamp artefacts to your ion channel simulations
      modelingelectrophysiologyhigh-throughput
      modelingelectrophysiologyhigh-throughputartefactshergpatch-clampvoltage-clampvariabilityion-channel-kinetics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•0•0•Updated Aug 31, 2025Aug 31, 2025

    • protocol-design-hERG

      Public
      Voltage clamp protocol design for hERG.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • FourWaysOfFitting

      Public
      Code to compare four different ways to fit an ion current model
      Python
      •
      Other
      •3•4•1•0•Updated Jul 9, 2025Jul 9, 2025

    • ionBench

      Public
      A benchmarking tool for comparing different parameter optimization algorithms for ion channel models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•0•0•Updated Jun 27, 2025Jun 27, 2025

    • BenNevis

      Public
      "Where is Ben Nevis" presents the landscape of Great Britain as a testbed for optimisation and sampling methods.
      numerical-optimization
      numerical-optimization
      Python
      •
      Other
      •1•4•5•0•Updated Apr 23, 2025Apr 23, 2025

    • APD90_ex_vivo_vs_in_silico

      Public
      Code to reproduce the figures and results from "Comparison of in silico predictions of action potential duration in response to inhibition of IKr and ICaL with …
      Jupyter Notebook
      •0•1•0•0•Updated Apr 13, 2025Apr 13, 2025

    • nav-artefact-model

      Public
      Code for reproducing "Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings"
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Apr 11, 2025Apr 11, 2025

    • multiprotocol_data_fitting

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 3, 2025Apr 3, 2025

    • fitting-notebooks

      Public
      Examples of parameter estimation in cardiac cell electrophysiology using Myokit and PINTS.
      Jupyter Notebook
      •7•5•6•2•Updated Feb 20, 2025Feb 20, 2025

    • R56Q-modelling

      Public
      A repository to reproduce modelling results for the R56Q-hERG project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Feb 13, 2025Feb 13, 2025

    • L-type-Ca-rundown-modelling

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 19, 2024Nov 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"
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • BenNevisBenchmark

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•0•Updated Oct 9, 2024Oct 9, 2024

    • ap-nimbus-client

      Public
      JavaScript
      •
      Other
      •2•2•9•1•Updated Sep 25, 2024Sep 25, 2024

    • ap-nimbus

      Public
      Cardiac modelling in containers
      Other
      •2•1•5•0•Updated Sep 10, 2024Sep 10, 2024

    • ap-nimbus-app-manager

      Public
      API for cloudified AP Predict
      JavaScript
      •
      Other
      •0•1•0•0•Updated Sep 10, 2024Sep 10, 2024

    • appredict-docker

      Public
      Shell
      •
      Other
      •0•1•1•0•Updated Sep 10, 2024Sep 10, 2024

    • relative-contributions

      Public
      Relative contributions of transmembrane currents in human AP models
      Python
      •0•0•3•0•Updated Sep 5, 2024Sep 5, 2024

    • empirical_quantification_of_model_discrepancy

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Jun 14, 2024Jun 14, 2024