Section: Software and Platforms

Integration of our tools in larger software environments

Most of our software were designed as "bricks" that can combined through workflow application such as Mobyle. It worths considering them into larger dedicated environments to benefit from the expertise of other research groups.

Web servers In collaboration with the GenOuest ressource center, most our tools are made available through several web portals.

• The mobyle@GenOuest portal is the generic web server of our ressource center. It hosts the ingranalysis, meneco, caspo, lombarde and shogun tools [website] .

• The Mobyle@Biotempo server is a mobyle portal for system biology with formal approaches. It hosts the memap, memerge, meneco, ingranalysis, cadbiom and pogg tools [website] .

Dr Motif This resource aims at the integration of different software commonly used in pattern discovery and matching. This resource also integrates Dyliss pattern search and discovery software [website] .

ASP4biology and BioASP It is a meta-package to create a powerful environment of biological data integration and analysis in system biology, based on knowledge representation and combinatorial optimization technologies (ASP). It provides a collection of python applications which encapsulates ASP tools and several encodings making them easy to use by non-expert users out-of-the-box. [Python package] [website] .

ASP encodings repository This suite comprises projects related to applications of Answer Set Programming using Potassco systems (the Potsdam Answer Set Solving Collection, bundles tools for Answer Set Programming developed at the University of Potsdam). These are usually a set of encodings possibly including auxiliary software and scripts [respository] .