Section: New Software and Platforms


A rule-based language for modeling interaction networks

Keywords: Systems Biology - Modeling - Static analysis - Simulation - Model reduction

Scientific Description: OpenKappa is a collection of tools to build, debug and run models of biological pathways. It contains a compiler for the Kappa Language, a static analyzer (for debugging models), a simulator, a compression tool for causal traces, and a model reduction tool.

Functional Description: Kappa is provided with the following tools: - a compiler - a stochastic simulator - a static analyzer - a trace compression algorithm - an ODE generator.

Release Functional Description: On line UI, Simulation is based on a new data-structure (see ESOP 2017 ), New abstract domains are available in the static analyzer (see SASB 2016), Local traces (see TCBB 2018), Reasoning on polymers (see SASB 2018).

  • Participants: Jean Krivine, Jérôme Feret, Kim Quyen Ly, Pierre Boutillier, Russ Harmer, Vincent Danos and Walter Fontana

  • Partners: ENS Lyon - Université Paris-Diderot - HARVARD Medical School

  • Contact: Jérôme Feret

  • URL: http://www.kappalanguage.org/