https://github.com/sybila/ebcsgen

eBCSgen - BioChemical Space Language support tool.
https://github.com/sybila/ebcsgen

mechanistic-models modeling rule-based-modelling simulation systems-biology

Last synced: about 1 year ago
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eBCSgen - BioChemical Space Language support tool.

• Host: GitHub
• URL: https://github.com/sybila/ebcsgen
• Owner: sybila
• License: mit
• Created: 2020-01-31T12:51:02.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2024-11-25T11:05:49.000Z (over 1 year ago)
• Last Synced: 2025-04-12T05:39:50.058Z (about 1 year ago)
• Topics: mechanistic-models, modeling, rule-based-modelling, simulation, systems-biology
• Language: JavaScript
• Homepage: https://ebcsgen.readthedocs.io/
• Size: 4.12 MB
• Stars: 2
• Watchers: 4
• Forks: 4
• Open Issues: 25
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

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# eBCSgen

eBSCgen is a tool for development and analysis of models written in Biochemical Space Language (BCSL). 

The tool is deployed online as a part of [BioDivine](https://biodivine-vm.fi.muni.cz/galaxy/) Galaxy toolset.

For more information about the tool, see [Wiki](https://github.com/sybila/eBCSgen/wiki).

**To get started with the usage of Galaxy Platform and eBCSgen, we recommend this [tutorial](https://github.com/sybila/eBCSgen/blob/master/docs/eBCSgen_tutorial.pdf).**

## Installation

### Conda

Install `eBCSgen` from Bioconda with:

```

# install eBCSgen in a new virtual environment to avoid dependency clashes

conda create --name eBCSgen python=3.9

conda activate eBCSgen

conda install --channel bioconda --channel conda-forge eBCSgen

```

### Docker

You can also use prebuild [docker image](https://hub.docker.com/r/sybila/ebcsgen).

### Galaxy

`eBCSgen` is also available as a series of Galaxy tools available in the main [toolshed](https://toolshed.g2.bx.psu.edu/).

## Developer Documentation

### Setup

Create your development environment using the provided [script](conda/environment.yml) via conda to install all required dependencies.

### Contributing

We appreciate contributions - feel free to open an issue on our repository, create your own fork, work on the problem and post a PR. 

Please adhere to the [versioning](https://semver.org/spec/v2.0.0.html).

### Testing

All functionality is tested with the [pytest](https://docs.pytest.org/en/6.2.x/contents.html) framework.