myokit
Source code, issues, and discussions for Myokit: A tool for cardiac electrophysiology modelling and simulation
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
4 of 10 committers (40.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Source code, issues, and discussions for Myokit: A tool for cardiac electrophysiology modelling and simulation
Basic Info
- Host: GitHub
- Owner: myokit
- License: other
- Language: Python
- Default Branch: main
- Homepage: http://myokit.org
- Size: 12.5 MB
Statistics
- Stars: 42
- Watchers: 8
- Forks: 6
- Open Issues: 167
- Releases: 54
Topics
Metadata Files
README.md
Myokit is a tool for modeling and simulation of cardiac cellular electrophysiology. It's open-source, written in Python, hosted on GitHub and available on PyPi. For the latest documentation, see myokit.readthedocs.io.
More information, including examples and an installation guide, is available on myokit.org. A list of changes introduced in each Myokit release is provided in the Changelog.
Install
For full installation details (on linux, mac, or windows), please see https://myokit.org/install. A shorter installation guide for experienced users is given below.
To install Myokit, using PyQt5 for Myokit's GUI components, run:
pip install myokit[pyqt]
to use PySide2 instead, run:
pip install myokit[pyside]
If you're not planning to use the GUI components (for example to run simulations on a server), you can simply install with
pip install myokit
On Linux and Windows, start menu icons can be added by running
python -m myokit icons
To run single-cell simulations, CVODES must be installed (but Windows users can skip this step, as binaries are included in the pip install). In addition, Myokit needs a working C/C++ compiler to be present on the system.
Existing Myokit installations can be upgraded using
pip install --upgrade myokit
Quick-start guide
After installation, to quickly test if Myokit works, type
python -m myokit run example
or simply
myokit run example
To open an IDE window, type
myokit ide
To see what else Myokit can do, type
myokit -h
Contributing to Myokit
Contributing to Myokit is as easy as asking questions or posting issues and feature requests, and we have pledged to make this an inclusive experience.
We are always looking for people to contribute code too! Guidelines to help you do this are provided in CONTRIBUTING.md, but before diving in please open an issue so that we can first discuss what needs to be done.
A high-level plan for Myokit's future is provided in the roadmap.
Meet the team!
Myokit's development is driven by a team at the Universities of Nottingham, Oxford, and Macao, led by Michael Clerx (Nottingham). It is guided by an external advisory group composed of Jordi Heijman (Maastricht University), Trine Krogh-Madsen (Weill Cornell Medicine), and David Gavaghan (Oxford).
Citing Myokit
If you use Myokit in your research, please cite it using the information in our CITATION file.
We like to keep track of who's using Myokit for research (based on publications) and teaching (based on peronsal correspondence). If you've used Myokit in teaching, we're always happy to hear about it so please get in touch via the discussion board!
Owner
- Name: Myokit
- Login: myokit
- Kind: organization
- Website: http://myokit.org
- Repositories: 3
- Profile: https://github.com/myokit
Repositories for Myokit
Citation (CITATION)
To cite Myokit in publications, please use:
Clerx M, Collins P, de Lange E & Volders PGA (2016).
Myokit: A simple interface to cardiac cellular electrophysiology.
Progress in Biophysics and Molecular Biology 120, 100-114.
https://doi.org/10.1016/j.pbiomolbio.2015.12.008
A BibTeX entry for LaTeX users is
@article{Clerx2016Myokit,
title = {Myokit: A simple interface to cardiac cellular electrophysiology},
author = {Clerx, Michael and Collins, Pieter and de Lange, Enno and Volders, Paul G. A.},
journal = {Progress in Biophysics and Molecular Biology},
year = {2016},
volume = {120},
number = {1--3},
pages = {100--114},
issn = {0079-6107},
doi = {10.1016/j.pbiomolbio.2015.12.008}
}
GitHub Events
Total
- Create event: 29
- Release event: 5
- Issues event: 29
- Watch event: 7
- Delete event: 26
- Issue comment event: 82
- Push event: 122
- Pull request review event: 61
- Pull request review comment event: 55
- Pull request event: 48
- Fork event: 1
Last Year
- Create event: 29
- Release event: 5
- Issues event: 29
- Watch event: 7
- Delete event: 26
- Issue comment event: 82
- Push event: 122
- Pull request review event: 61
- Pull request review comment event: 55
- Pull request event: 48
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Michael Clerx | m****x@c****k | 1,591 |
| Michael Clerx | m****x@n****k | 578 |
| DavAug | d****n@g****t | 278 |
| martinjrobins | m****s@g****m | 98 |
| Michael Clerx | M****x | 74 |
| Rebecca Rumney | r****y@w****k | 28 |
| teosbpl | b****r@i****l | 6 |
| Your Name | y****u@e****m | 4 |
| Chon Lok Lei | c****i@g****m | 4 |
| Rebecca-Rumney | 5****y | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 47
- Total pull requests: 44
- Average time to close issues: 9 months
- Average time to close pull requests: 7 days
- Total issue authors: 9
- Total pull request authors: 4
- Average comments per issue: 1.13
- Average comments per pull request: 1.34
- Merged pull requests: 33
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 22
- Pull requests: 24
- Average time to close issues: 1 day
- Average time to close pull requests: 2 days
- Issue authors: 6
- Pull request authors: 3
- Average comments per issue: 0.91
- Average comments per pull request: 1.04
- Merged pull requests: 20
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- MichaelClerx (35)
- martinjrobins (4)
- mjowen (2)
- finsberg (1)
- pezzus (1)
- joeyshuttleworth (1)
- chonlei (1)
- mirams (1)
- ThomasMBury (1)
Pull Request Authors
- MichaelClerx (37)
- martinjrobins (3)
- kwabenantim (2)
- mjowen (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 2,202 last-month
- Total dependent packages: 4
- Total dependent repositories: 7
- Total versions: 53
- Total maintainers: 1
pypi.org: myokit
A modeling and simulation tool for cardiac cellular electrophysiology
- Homepage: http://myokit.org
- Documentation: http://docs.myokit.org
- License: BSD 3-clause license
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Latest release: 1.38.0
published 7 months ago
Rankings
Maintainers (1)
Dependencies
- PyQT *
- PySide *
- configparser *
- lxml *
- matplotlib >=1.5
- numpy *
- scipy *
- setuptools *
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