BioRuler is a library developed on top of the ReGraph library, which serves as a bridge between biological data formats describing protein-protein interactions and graph-based representation of knowledge.
Our main motivation while developing this library was to enable the user to automatically convert protein-protein interaction data in any standard format to its graph representation following a domain-specific meta-model of choice. We would also like to give the user the possibility to manipulate this graph representation, and finally, to automatically export it to the respective Kappa code, ready for simulations, static analysis, etc.
Currently the importer from BioPAX format and the exporter to Kappa are implemeted.
To use BioPAX importer you need to have Java installed.
To use Kappa exporter you need to have OCaml installed.
The following Python 3 packages are required:
cycler==0.10.0
decorator==4.0.10
JPype1==0.6.1
matplotlib==1.5.1
networkx==1.11
numpy==1.11.1
pyparsing==2.1.5
python-dateutil==2.5.3
pytz==2016.4
ReGraph==0.1
six==1.10.0
wheel==0.24.0
To avoid manual installation and to easily set up development environment you may consider following the instructions below:
virtualenv venv -p path/to/your/python3
To activate the virtual environment
source venv/bin/activate
To install required dependencies
pip install -r requirement.txt
In order to install the ReGraph library you have to clone this repository using SSH
git clone git@github.com:eugeniashurko/ReGraph.git
or using HTTPS
https://github.com/eugeniashurko/ReGraph.git
Install the library with
python setup.py install
The tests are run on the PID: the Pathway Interaction Database
python test.py
Please find examples of use in kappa_graph_kappa.py and test_kappa.py, you can test them by running
python test_kappa.py compilation of a nugget defined in the python file
or
python kappa_graph_kappa.py you will need a test.ka file in the current directory containing some kappa code to import and to export back
You'll need to clone Kappa-Dev/KaSim repository, and to install Yojson package. Then put kappa_to_graph.ml on the root folder of KaSim and run
ocamlbuild -pkg yojson kappa_to_graph.byte
You can now use the outputed file as parser in KappaExporter's uncompile method.