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DSGRN

Dynamic Signatures Generated by Regulatory Networks

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Documentation

Overview

This project uses computational dynamics to produce dynamical surveys of switching models of regulatory networks. The resulting data is stored into a database which can then be queried for further research.

Installation

To get the latest tagged version from the PyPI repository:

pip install DSGRN

To uninstall:

pip uninstall DSGRN

Installing from source

Assuming you have a C++ compiler and the Python 3 dependencies installed on your system, you can install from source with the command:

pip install --upgrade --force-reinstall --no-deps --no-cache-dir git+https://github.com/marciogameiro/DSGRN.git

Alternatively, you can clone the GitHub repository and install with:

git clone https://github.com/marciogameiro/DSGRN.git
cd DSGRN
./install.sh

If you don't have all the dependencies installed or if the above fails, see Install.md for some options on how to proceed. Installing DSGRN as above on a Mac usually fails with the C++ compiler and the Python provided by Apple. In that case you need to install new versions as described in the link above.

Usage

To check if DSGRN is installed do

import DSGRN

network = DSGRN.Network("X1 : (~X1)(X2)\n X2 : (X1)(~X2)")
DSGRN.DrawGraph(network)

This should plot the network

See the GettingStarted.ipynb jupyter notebook in the Tutorials folder for the basic usage of DSGRN.

Examples and Documentation

See Tutorials folder for examples.

Also see the documentation.