ArticleMethodsX2016
A computationally efficient algorithm for fitting ion channel parameters.
Article in MethodsX, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- Parameter inference for stochastic reaction models of ion channel gating from whole-cell voltage-clamp data.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2025Article
- Creating Computational Models of Ion Channel Dynamics.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Emerging methods to model cardiac ion channel and myocyte electrophysiology.Biophysics reviews · 2023Review
- Ion channel model reduction using manifold boundaries.Journal of the Royal Society, Interface · 2022Article
- Creating Ion Channel Kinetic Models Using Cloud Computing.Current protocols · 2022Article
- Article
- Identification of structures for ion channel kinetic models.PLoS computational biology · 2021Article
- A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms.PLoS computational biology · 2020Article
- Calibration of ionic and cellular cardiac electrophysiology models.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- Four Ways to Fit an Ion Channel Model.Biophysical journal · 2019Article
- Phenomenological models of NaScientific reports · 2019Article
- A Molecularly Detailed NaJACC. Basic to translational science · 2019Article
- How to Connect Cardiac Excitation to the Atomic Interactions of Ion Channels.Biophysical journal · 2018Review
- Mechanisms and models of cardiac sodium channel inactivation.Channels (Austin, Tex.) · 2017Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Continuous time Markov models have been widely used to describe ion channel kinetics, providing explicit representation of channel states and transitions. Fitting models to experimental data remains a computationally demanding task largely due to the high cost of model evaluation. Here, we propose a method to efficiently optimize model parameters and structure. Voltage clamp channel protocols can be decomposed into a series of fixed steps of constant voltage resulting in a set of linear systems of differential equations. Given the linear systems, ODE integration can be swapped for the faster matrix exponential routine. With our parallelized implementation, optimized models are able to reproduce a wide range of experimentally collected data within one minute, a 50 times speedup over ODE integration. •The cost of the objective function is reduced by employing the matrix exponential•The likelihood of convergence is improved by applying synchronous start simulated annealing•The approach was tested by optimizing parameters for a model of the cardiac voltage-gated Na
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.