Section: Software

Dynamics: actor/parameter combination controlling the response of a system

We wish to develop tools predicting some characteristics of a biological system behavior from incomplete sets of parameters or observations.

• caspo: Cell ASP Optimizer. We have implemented a Python package which combines BioASP (http://www.cellnopt.org/ ) and CellNOpt(http://www.cs.uni-potsdam.de/ ̃sthiele/bioasp/ ) to provide an easy to use software for learning Boolean logic models using ASP [19] . The software is available for download(http://pypi.python.org/pypi/caspo ) and also as a web service through the Mobyle framework.

• Event network and quantitative time-series data: POGG (http://pogg.genouest.org/wiki.php/Home ). POGG is a tool developed in collaboration with the LINA lab (Nantes) that uses mean dynamics to score the respective relevance of regulatory pathways in a higher-scale phenotype. It was applied to the quantitative prediction of protein quantities under exponential growth [2] . It predicts the main features of a Markov chain model derived from a reaction-based model when confronted to a single time-series quantitative observation.