https://github.com/sysbiochalmers/ecm_yeast
Automated pipeline for full kinetic parameterization of a reduced model for Saccharomyces cerevisiae's central carbon metabolism.
https://github.com/sysbiochalmers/ecm_yeast
Last synced: about 1 year ago
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Automated pipeline for full kinetic parameterization of a reduced model for Saccharomyces cerevisiae's central carbon metabolism.
- Host: GitHub
- URL: https://github.com/sysbiochalmers/ecm_yeast
- Owner: SysBioChalmers
- License: mit
- Created: 2018-11-09T08:02:13.000Z (over 7 years ago)
- Default Branch: devel
- Last Pushed: 2020-08-27T10:52:17.000Z (almost 6 years ago)
- Last Synced: 2025-06-25T05:54:25.359Z (about 1 year ago)
- Language: MATLAB
- Homepage:
- Size: 9.58 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ECM_yeast [](https://gitter.im/SysBioChalmers/ECM_yeast?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
Automated pipeline for full kinetic parameterization of a reduced model for Saccharomyces cerevisiae's central carbon metabolism. As an output an SBtab model file incorporating Kcats, KMs and equilibrium constants into modular rate laws for all reactions in the original network is obtained.
## KeyWords
**Repo Category:** Metabolic modelling; **Utilisation:** Constraint-based modelling of metabolism; **Field:** Protein allocation studies;**Omic Source:** Proteomics, Metabolomics; **Taxonomy:** *S. cervisiae*
Last update: 2019-09-11
This repository is administered by [@IVANDOMENZAIN](https://github.com/IVANDOMENZAIN), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology
## Installation
### Required Software
- [MATLAB](http://www.mathworks.com/) (7.5 or higher)
- The [COBRA toolbox for MATLAB](https://github.com/opencobra/cobratoolbox)
- The [RAVEN toolbox for MATLAB](https://github.com/SysBioChalmers/RAVEN)
- The [libSBML MATLAB API](https://sourceforge.net/projects/sbml/files/libsbml/MATLAB%20Interface)(version 5.17.0 is recommended).
- [SBtab toolbox for MATLAB](https://github.com/liebermeister/sbtab-matlab)
- Python 3.6
- [Pandas Python library](https://pandas.pydata.org/)
- [NumPy Python library](https://numpy.org/)
- [eQuilibrator](http://equilibrator.weizmann.ac.il/)
### Installation Instructions
* Clone master branch from [SysBioChalmers GitHub](https://github.com/SysBioChalmers/CHASSY_multiOmics_Analysis).
* In a terminal/command shell run the following commands:
- `pip install pandas`
- `git clone https://gitlab.com/elad.noor/equilibrator-api.git`
- `cd equilibrator-api`
- `python setup.py install`
## Development Guidelines
Anybody is welcome to contribute to the development of **OrthOmics**, but please abide by the following guidelines.
Each function should start with a commented section describing the function and explaining the parameters. Existing functions can clarify what style should be used. When making *any* changes to an existing function (`*.R`-file), change the date and name of developer near the bottom of this commented section.
### Bugfixes, new features and functions
* For any development, whether bugfixes, introducing new functions or new/updated features for existing functions: make a separate branch from `devel` and name the branch for instance after the function/feature you are fixing/developing. If you work on a fix, start the branch name with `fix/`, if you work on a feature, start the branch name with `feat/`. Examples: `fix/format_reactions` or `feat/new_algorithms`.
* Make commits to this branch while developing. Aim for backwards compatibility.
* When you are happy with your new function/feature, make a pull request to the `devel` branch. Also, see [Pull request](#pull-request) below.
### Semantic commits
Use semantic commit messages to make it easier to show what you are aiming to do:
* `chore`: updating binaries (`R` workspaces), UniProt databases, omics data files, etc.
* `doc`: updating documentation (`README` files) or explanatory comments in functions.
* `feat`: new feature added, e.g. new function introduced / new parameters / new algorithm / etc.
* `fix`: bugfix.
* `refactor`: see [code refactoring](https://en.wikipedia.org/wiki/Code_refactoring).
* `style`: minor format changes of functions (spaces, semi-colons, etc., no code change).
Examples:
```
feat: add new proteins normalization method
chore: update UniProt database for CENPK113-7D
fix: variable name corrected in `load_ProtData` function
```
More detailed explanation or comments can be left in the commit description.
### Pull request
* No changes should be directly commited to the `master` or `devel` branches. Commits are made to side-branches, after which pull requests are made for merging with `master` or `devel`.
* The person making the pull request and the one accepting the merge _cannot_ be the same person.
* A merge with the master branch invokes a new release.
## Contributors
- Iván Domenzain ([@IVANDOMENZAIN](https://github.com/IVANDOMENZAIN)), Chalmers University of Technology, Gothenburg Sweden
- Avlant Nilsson ([@avlant](https://github.com/avlant)), Department of Biological Engineering, Massachusetts Institute of Technology