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.
Detailed documentation about how to install and use caspo is available here.
Sample files are included with caspo and available for download
caspo: a toolbox for automated reasoning on the response of logical signaling networks families. (2017). Bioinformatics. DOI
Designing experiments to discriminate families of logic models. (2015). Frontiers in Bioengineering and Biotechnology 3:131. DOI
Learning Boolean logic models of signaling networks with ASP. (2015). Theoretical Computer Science. DOI
Reasoning on the Response of Logical Signaling Networks with ASP. (2014). John Wiley & Sons, Inc. DOI
Minimal intervention strategies in logical signaling networks with ASP. (2013). Theory and Practice of Logic Programming. DOI
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. (2013). Bioinformatics. DOI
Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming. (2012) The 10th Conference on Computational Methods in Systems Biology. DOI