https://github.com/alexoarga/findcritical
A desktop app, web app and CLI to operate and find vulnerabilities in SBML metabolic networks.
https://github.com/alexoarga/findcritical
cobra metabolic-models sbml
Last synced: 7 months ago
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A desktop app, web app and CLI to operate and find vulnerabilities in SBML metabolic networks.
- Host: GitHub
- URL: https://github.com/alexoarga/findcritical
- Owner: alexOarga
- Created: 2019-12-15T22:01:38.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2022-12-27T15:34:27.000Z (almost 3 years ago)
- Last Synced: 2025-01-23T18:49:31.433Z (9 months ago)
- Topics: cobra, metabolic-models, sbml
- Language: Python
- Homepage: https://findcritical.readthedocs.io/en/latest/
- Size: 6.25 MB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# findCritical
[](https://findcritical.readthedocs.io/en/latest/?badge=latest) [](https://github.com/RichardLitt/standard-readme)
The documentation can be found at [readthedocs](https://findcritical.readthedocs.io/en/latest/) and can also be [downloaded](https://readthedocs.org/projects/findcritical/downloads/).
# Download
### Windows
[windows-v1.1.0.zip](https://github.com/alexOarga/findCritical/releases/download/v1.1.0/windows-v1.1.0.zip)
### Linux
[linux-v1.1.0.zip](https://github.com/alexOarga/findCritical/releases/download/v1.1.0/linux-v1.1.0.zip)
# Source
## Table of Contents
- [Install source requirements](#install-source-requirements)
- [CLI/GUI](#cligui)
- [WEB](#WEB)
- [Run](#Run)
- [CLI](#CLI)
- [GUI](#GUI)
- [WEB](#web-1)
- [Maintainers](#maintainers)
- [Contributing](#contributing)
- [License](#license)
## Install source requirements
### CLI/GUI
```sh
$ pip3 install -r build/requirements.txt
```
### WEB
```sh
$ pip3 install -r main/WEB/requirements.txt
```
## Run
### CLI
```sh
$ python3 /main/CLI/FindCritical.py [-h] [-v] -i
[-o ]
[-swD ] [-sF ]
[-swDF ]
optional arguments:
-h, --help show this help message and exit
-v, --verbose Print feedback while running.
-i Input metabolic model. Allowed file formats: .xml .json
.yml
-o Output spreadsheet file with results. Allowed file
formats: .xls .ods
-swD Save output model without Dead End Metabolites. Allowed
file formats: .xml .json .yml
-sF Save output model with reactions bounds updated with
Flux Variability Analysis. Allowed file formats: .xml
.json .yml
-swDF Save output model with reactions bounds updated with
Flux Variability Analysis and without Dead End
Metabolites. Allowed file formats: .xml .json .yml
```
### GUI
```
$ python3 main/GUI/run_GUI.py
```
### WEB
```
$ sudo service redis-server start
# Change secret-key in 'main/WEB/DjangoProject/settings.py'
$ python3 manage.py runserver
```
Go to http://127.0.0.1:8000/app/
## Maintainers
[@alexOarga](https://github.com/alexOarga)
## Contributing
Feel free to dive in! [Open an issue](https://github.com/alexOarga/findCritical/issues/new) or submit PRs.
Standard Readme follows the [Contributor Covenant](http://contributor-covenant.org/version/1/3/0/) Code of Conduct.
## License
[MIT](LICENSE) © Alex Oarga