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    54 repositories

    • ContinuationForOptimisation

      Public
      Using limit cycle continuation methods to speed up evaluation of ion channel cell models
      Julia
      •0•0•0•0•Updated Jan 9, 2025Jan 9, 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•23•4•Updated Jan 8, 2025Jan 8, 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

    • fitting-notebooks

      Public
      Examples of parameter estimation in cardiac cell electrophysiology using Myokit and PINTS.
      Jupyter Notebook
      •6•4•6•2•Updated Dec 11, 2024Dec 11, 2024

    • 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 Nov 29, 2024Nov 29, 2024

    • binding_model_OED

      Public
      Code for optimal experimental design paper
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 29, 2024Nov 29, 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•4•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

    • hERGRapidCharacterisation

      Public
      Rapid characterisation of hERG channel kinetics
      modelingelectrophysiologyhigh-throughputhergpatch-clampvoltage-clampion-channelstemperature-dependenceherg-channel-kinetics
      Python
      •
      Other
      •4•3•0•0•Updated Sep 8, 2023Sep 8, 2023

    • ap-nimbus-deploy

      Public archive
      Shell
      •
      Other
      •0•0•0•0•Updated Aug 2, 2023Aug 2, 2023