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    56 repositories

    • fitting-notebooks

      Public
      Examples of parameter estimation in cardiac cell electrophysiology using Myokit and PINTS.
      Jupyter Notebook
      •6•4•6•2•Updated Feb 12, 2025Feb 12, 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•0•0•0•Updated Feb 8, 2025Feb 8, 2025

    • 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
      •0•3•22•3•Updated Feb 7, 2025Feb 7, 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 new human ex-vivo recordings"
      Jupyter Notebook
      •0•1•0•0•Updated Feb 2, 2025Feb 2, 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•2•0•0•Updated Jan 29, 2025Jan 29, 2025

    • binding_model_OED

      Public
      Code for optimal experimental design paper
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 27, 2025Jan 27, 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•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • L-type-Ca-rundown-experiments

      Public
      An investigation of rundown in automated patch clamp L-type calcium current
      Jupyter Notebook
      •
      Other
      •0•1•0•1•Updated Dec 24, 2024Dec 24, 2024

    • multiprotocol_data_fitting

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • FourWaysOfFitting

      Public
      Code to compare four different ways to fit an ion current model
      Python
      •
      Other
      •3•4•1•0•Updated Dec 11, 2024Dec 11, 2024

    • markov-builder

      Public
      Tool for building and manipulating Markov models of ion-channel kinetics
      markov-modelhergherg-channel-kineticspython
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•0•2•Updated Dec 11, 2024Dec 11, 2024

    • BenNevis

      Public
      "Where is Ben Nevis" presents the landscape of Great Britain as a testbed for optimisation and sampling methods.
      numerical-optimization
      Python
      •
      Other
      •1•3•5•0•Updated Dec 11, 2024Dec 11, 2024

    • 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 Nov 21, 2024Nov 21, 2024

    • 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

    • VoltageClampModel

      Public
      Code to add a mathematical model of voltage-clamp artefacts to your ion channel simulations
      modelingelectrophysiologyhigh-throughputartefactshergpatch-clampvoltage-clampvariabilityion-channel-kinetics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Sep 19, 2024Sep 19, 2024

    • ap-nimbus

      Public
      Cardiac modelling in containers
      Other
      •2•1•4•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

    • syncropatch_export

      Public
      A Python package to export SynroPatch 384 data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•3•0•Updated Aug 22, 2024Aug 22, 2024

    • protocol-design-hERG

      Public
      Voltage clamp protocol design for hERG.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 19, 2024Aug 19, 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

    • 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 May 2, 2024May 2, 2024

    • model-reduction-manifold-boundaries

      Public
      Code for model reduction using manifold boundaries
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•4•0•Updated Feb 23, 2024Feb 23, 2024

    • MarkovModels

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Nov 8, 2023Nov 8, 2023

    • hERG-binding-mechanisms

      Public
      Source code and data for reproducing "The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk".
      uncertaintyhergin-silicodrug-induced-arrhythmiasdrug-binding
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•0•0•Updated Oct 25, 2023Oct 25, 2023

    • qc_viewer

      Public
      Visualiser for quality control checks on automated patch-clamp machines
      CSS
      •1•0•0•0•Updated Sep 28, 2023Sep 28, 2023