Skip to main content

Reasoning on the response of logical signaling networks with Answer Set Programming

Project description

[![Conda package](https://anaconda.org/bioasp/caspo/badges/version.svg)](https://anaconda.org/bioasp/caspo) [![Documentation Status](https://readthedocs.org/projects/caspo/badge/?version=latest)](http://caspo.readthedocs.io/en/latest/?badge=latest) [![license](https://img.shields.io/badge/license-GPLv3+-brightgreen.svg)](https://www.gnu.org/licenses/gpl.html) [![Gitter](https://badges.gitter.im/bioasp/community.svg)](https://gitter.im/bioasp/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)

### Reasoning on the response of logical signaling networks

The manual identification of logic rules underlying a biological system is often hard, error-prone and time consuming. Further, it has been shown that, if the inherent experimental noise is considered, many different logical networks can be compatible with a set of experimental observations. Thus, automated inference of logical networks from experimental data would allow for identifying admissible large-scale logic models saving a lot of efforts and without any a priori bias. Next, once a family a logical networks has been identified, one can suggest or design new experiments in order to reduce the uncertainty provided by this family. Finally, one can look for intervention strategies that force a set of target species or compounds into a desired steady state. Altogether, this constitutes a pipeline for automated reasoning on logical signaling networks. Hence, the aim of caspo is to implement such a pipeline providing a powerful and easy-to-use software tool for systems biologists.

### Documentation

Detailed documentation about how to install and use caspo is available at http://caspo.readthedocs.io.

### Samples

Sample files are included with caspo and available for [download](http://bioasp.github.io/caspo/data.zip)

### Citation

caspo: a toolbox for automated reasoning on the response of logical signaling networks families. (2017). Bioinformatics. [DOI](https://doi.org/10.1093/bioinformatics/btw738)

### Related publications * Designing experiments to discriminate families of logic models. (2015). Frontiers in Bioengineering and Biotechnology 3:131. [DOI](http://dx.doi.org/10.3389/fbioe.2015.00131)

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for caspo, version 4.0.0
Filename, size File type Python version Upload date Hashes
Filename, size caspo-4.0.0-py3-none-any.whl (73.9 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size caspo-4.0.0.tar.gz (979.7 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page