Website for GINsim (Gene Interaction Network Simulator)

This repository generates the website for GINsim at https://ginsim.github.io/ using MkDocs.

You if you want to test/run it locally, you need to install some dependencies using pip.

Preparation

Create a virtual environment

However, some distributions prevent the installation of pip packages system-wide. If you're in this situation, please install/use a virtual environment.

Most likely you have the latest Python version. In this case, it suffices to run:

$ python -m venv myenv
$ source myenv/bin/activate

Alternatively, if you need a bit more flexibility you will need to install the package virtualenv and then run:

$ virtualenv myenv
$ source myenv/bin/activate

Install mkdocs

Please install the necessary Python dependencies:

pip install mkdocs               # the website static generator
pip install mkdocs-material      # the site theme
pip install mkdocs-bibtex        # for bibliography support 
pip install mkdocs-macros-plugin # automatic generation of model repository

Running mkdocs

If all the necessary dependencies are installed, you can now run mkdocs using the live preview mode, where every file change that you do is immediately reflected on the webpage.

mkdocs serve

and see the following link where the GINsim website is being locally served:

INFO    -  [10:28:04] Serving on http://127.0.0.1:8000/

Updating the website

Website structure

The website has the following structure:

docs/
├── contact
├── css
├── documentation
│   ├── analyses
│   ├── dyn
│   ├── formats
│   ├── gui
│   ├── introduction
│   ├── layouts
│   └── lrg
├── install
└── models

Adding a model

In docs/models/ create a new directory, and put your model files and images inside the directory. Create an index.md file inside respecting the format exemplified in the following example:

---
title: Blabla model of blabla
taxon: 
- SomeTaxon
- YetAnotherTaxon
process: 
- SomeProcess
- YetAnotherProcess
submitter: T. MyName
supporting_paper: KeyInBibTex
files: 
- GINsim_model_file.zginml
- SBML_model_file.smbl
file_descriptions: 
- GINsim logical model of blabla
- SBML-qual model of blabla
---

This is a description of the model ...

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Updating the https://ginsim.github.io/ website

Just commit your files, and the github pages workflow will run mkdocs and update the site in a few minutes. You can check the status of the page build and deployment in the Actions tab of github repository.