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Kappa platform
Pierre Boutillier & Mutaamba Maasha & Xing Li & H´ctor Medina-Abarca & Jean Krivine & Jérôme Feret & Ioana Cristescu & Angus Forbes & Walter Fontana.
The Kappa platform for rule-based modeling.
In Bioinformatics, Vol 34(13), July 2018.


Motivation: We present an overview of the Kappa platform, an integrated suite of analysis and visualization techniques for building and interactively exploring rule-based models. The main components of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa Story Extractor. In addition to these components, we describe the Kappa User Interface, which includes a range of interactive visualization tools for rule-based models needed to make sense of the complexity of biological systems. We argue that, in this approach, modeling is akin to programming and can likewise 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 causal views of a model, which include the contact map (CM), snaphots at different resolutions, the dynamic influence network (DIN) and causal compression. We provide use cases illustrating how these concepts generate insight. Specifically, we show how the CM and snapshots provide information about systems capable of polymerization, such as Wnt signaling. A well-understood model of the KaiABC oscillator, translated into Kappa from the literature, is deployed to demonstrate the DIN and its use in understanding systems dynamics. Finally, we discuss how pathways might be discovered or recovered from a rule-based model by means of causal compression, as exemplified for 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 the authors' code repositories.

  author    = {Pierre Boutillier and
               Mutaamba Maasha and
               Xing Li and
               H{\'{e}}ctor F. Medina{-}Abarca and
               Jean Krivine and
               J{\'{e}}r{\^{o}}me Feret and
               Ioana Cristescu and
               Angus G. Forbes and
               Walter Fontana},
  title     = {The Kappa platform for rule-based modeling},
  journal   = {Bioinformatics},
  volume    = {34},
  number    = {13},
  pages     = {i583--i592},
  year      = {2018}