The Kappa platform for rule-based modeling

International audienceAbstractMotivation:We present an overview of the Kappa platform, an integrated suite of analysis andvisualization techniques for building and interactively exploring rule-based models. The main compo-nents of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa StoryExtractor. In addition to these components, we describe the Kappa User Interface, which includes arange of interactive visualization tools for rule-based models needed to make sense of the complexityof biological systems. We argue that, in this approach, modeling is akin to programming and can like-wise benefit from an integrated development environment. Our platform is a step in this direction.Results:We discuss details about the computation and rendering of static, dynamic, and causalviews of a model, which include the contact map (CM), snaphots at different resolutions, thedynamic influence network (DIN) and causal compression. We provide use cases illustrating howthese concepts generate insight. Specifically, we show how the CM and snapshots provide infor-mation about systems capable of polymerization, such as Wnt signaling. A well-understood modelof the KaiABC oscillator, translated into Kappa from the literature, is deployed to demonstrate theDIN and its use in understanding systems dynamics. Finally, we discuss how pathways might bediscovered or recovered from a rule-based model by means of causal compression, as exemplifiedfor early events in EGF signaling.Availability and implementation:The Kappa platform is available via the project website at kappa-language.org. All components of the platform are open source and freely available through theauthors’ code repositories