kinetics
Python package for modelling enzyme reactions using Monte carlo sampling from parameter distributions
Science Score: 39.0%
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✓DOI references
Found 2 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (11.0%) to scientific vocabulary
Keywords
Repository
Python package for modelling enzyme reactions using Monte carlo sampling from parameter distributions
Basic Info
Statistics
- Stars: 31
- Watchers: 1
- Forks: 6
- Open Issues: 4
- Releases: 18
Topics
Metadata Files
README.md
kinetics
kinetics is a package for modelling reactions using ordinary differential equations. It's primarily aimed at modelling enzyme reactions, although can be used for other purposes.
See the Documentation for more information.
kinetics uses scipy.integrate.odeint to solve ordinary differential equations, but extends upon this to allow the use of parameter distributions rather than single parameter values. This allows error to be incorporated into the modelling.
kinetics uses scipy's probability distributions, with a large number of distributions to choose from. Typically uniform, normal, log-uniform or log-normal distributions are used.
Documentation: ReadTheDocs
Github: kinetics
Requirements: NumPy, SciPy, matplotlib, tqdm, pandas, SALib, seaborn, and deap.
Installation: pip install kinetics
Features
- Construct systems of ODEs simply by selecting suitable rate equations and naming parameters and species
- Use either simple parameter values or probability distributions
- Run sensitivity analysis using SALib
- Easily plot model runs using predefined plotting functions
- Optimisation using genetic algorithm using DEAP (coming soon)
Owner
- Name: William Finnigan
- Login: willfinnigan
- Kind: user
- Location: Manchester
- Repositories: 5
- Profile: https://github.com/willfinnigan
GitHub Events
Total
- Create event: 5
- Release event: 1
- Issues event: 1
- Watch event: 4
- Delete event: 3
- Push event: 16
- Pull request event: 2
Last Year
- Create event: 5
- Release event: 1
- Issues event: 1
- Watch event: 4
- Delete event: 3
- Push event: 16
- Pull request event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| William Finnigan | w****n@g****m | 235 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 8
- Total pull requests: 13
- Average time to close issues: 2 months
- Average time to close pull requests: 1 minute
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 12
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: about 14 hours
- Average time to close pull requests: less than a minute
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 3.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- willfinnigan (6)
- wlawler45 (1)
- blacall (1)
Pull Request Authors
- willfinnigan (14)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 88 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 18
- Total maintainers: 1
pypi.org: kinetics
Python code to run kinetic models of enzyme reactions
- Homepage: https://github.com/willfinnigan/kinetics
- Documentation: https://kinetics.readthedocs.io/
- License: MIT
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Latest release: 1.4.5
published 9 months ago
Rankings
Maintainers (1)
Dependencies
- SALib *
- deap *
- matplotlib *
- numpy *
- pandas *
- scipy *
- seaborn *
- tqdm *
- SALib *
- deap *
- matplotlib *
- numpy *
- pandas *
- scipy *
- seaborn *
- tqdm *