bidomainbem
Science Score: 67.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: iop.org -
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○Scientific vocabulary similarity
Low similarity (7.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: David-M-Czerwonky
- Language: Fortran
- Default Branch: main
- Size: 42.5 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Simulation code for Czerwonky, D. M., Aberra, A. S., & Gomez, L. J. (2023). A boundary element method of bidomain modeling for predicting cellular responses to electromagnetic fields. Journal of Neural Engineering. Read it here: https://iopscience.iop.org/article/10.1088/1741-2552/ad5704/meta
Code Overview
We provide two folders of codes: (1) the bidomain BEM codes (2) the hybrid cable codes
The BidomainCodes folder contains our implementations of bidomain integral equation derived in the above Journal of Neural Engineering Publication. This implementation leverages MATLAB with the support of C, and Fortran libaries to solve the bidomain integral equation. We provide testing scripts for simplistic transcanial electric stimulation (TES), transcranial magnetic stimulation (TMS), and deep brain stimulation (DBS) scenarios.
The HybridCableCodes folder contains a MATLAB implementation of the Hybrid Cable approach as detailed in figure 1 of Joucla, S., Glière, A., & Yvert, B. (2014). Current approaches to model extracellular electrical neural microstimulation. Frontiers in computational neuroscience, 8, 13. The only difference is that instead of using an FEM solver, we use a modified set of 0th order BEM codes orginally from the following repository: https://github.com/luisgo/TMSEfieldSolvers.
System requirements
All codes require a 64-bit system and Windows operating systems. All codes require an instillation of MATLAB 2021b or later. The bidomain solver codes are unacclerated so running the codes is computationally expensive. We recommend using simple test scenarios with less than 5,000 triangle elements for a system with 32 GB of RAM memory or less.
Owner
- Login: David-M-Czerwonky
- Kind: user
- Repositories: 1
- Profile: https://github.com/David-M-Czerwonky
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Czerwonky" given-names: "David" orcid: "https://orcid.org/0009-0001-5560-4835" - family-names: "Gomez" given-names: "Luis" orcid: "https://orcid.org/0000-0002-7699-2160" title: "Bidomain BEM" version: 1 doi: date-released: 2024-05-10 url: "https://github.com/David-M-Czerwonky/BidomainBEM"