BioASP

Answer Set Programming for Systems Biology

Overview | Applications | Answer Set Programming | Who we are

Overview

BioASP is a meta-package to create an powerful environment of Answer Set Programming for Systems Biology. The BioASP applications implement methods for analyzing metabolic, signaling and gene regulatory networks, consistency checking, diagnosis, and repair of biological data and models. They allow for computing predictions and generating hypotheses about required extensions of biological models, as well as designing new experiments and finding intervention strategies to control the biological system at hand. Google+

Applications

Installation

You can install all BioASP application at once from pypi by running: $ pip install bioasp For details on how to use each application follow the corresponding links above. If you do not have pip installed on your system, you only need to download get-pip.py. Then run the following: $ python get-pip.py Alternatively, if you prefer not to install pip, you can download the sources of BioASP and after unpacking run: $ python setup.py install Note that you may need either administrator access or a virtual environment.

Answer Set Programming

BioASP applications strongly rely on Answer Set Programming (ASP) for knowledge representation and reasoning. ASP is a declarative problem solving paradigm from the field of Logic Programming combining several computer science areas such as Knowledge Representation and Reasoning, Artificial Intelligence, Constraint Satisfaction and Combinatorial Optimization.

For more details on ASP and state-of-the-art available tools, you may want to check the website of Potassco, the Potsdam Answer Set Solving Collection.

Who we are

BioASP is developed by several people at several institutions from several countries:

If you would like to contribute in any way, your are welcome to join us at http://github.com/bioasp.