The Kappa platform for rule-based modeling
Abstract
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jun 27, 2018
- Source ID
- 10.1093/bioinformatics/bty272
Entities
People
- Angus G. Forbes
- Héctor F Medina-abarca
- Ioana Cristescu
- Jean Krivine
- Jérôme Feret
- Mutaamba Maasha
- Pierre Boutillier
- Walter Fontana
- Xing Li
Organizations
- Army Research Office
- Defense Advanced Research Projects Agency
- Harvard Medical School
- Institut National de Recherche en Informatique et en Automatique
- Paris Diderot University
- University of California, Santa Cruz