Section: New Software and Platforms

New tools for dynamics

Participants : Jérémie Bourdon [contact] , Jeanne Cambefort [contact] , Damien Eveillard, Anne Siegel, Nathalie Théret, Santiago Videla [contact] .

In 2014, the tool caspo was extended to new functionnalities.

caspo: Cell ASP Optimizer In the new version of caspo, automated inference of logical networks from experimental data allows 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 (i.e. inclusion minimal sets of knock-ins and knock-outs) 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. [doc and download as a python package] [web server] .