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Cited by 107Gene Regulatory Network AnalysisBioinformatics and Genomic NetworksPhilosophy and History of Science

The Kappa platform for rule-based modeling

Open access
Boutillier, Pierre, Maasha, Mutaamba, Li, Xing, Medina-Abarca, Héctor F, Krivine, Jean, Feret, Jérôme, Cristescu, Ioana, Forbes, Angus G +1 more·2018·Bioinformatics
DOI 10.1093/bioinformatics/bty272PMC PMC6022607
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Abstract

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 kappalanguage.org. All components of the platform are open source and freely available through the authors’ code repositories.

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  • Although the Wnt signaling pathway has also been used to illustrate features of rule-based modeling [95, 96], only few simulation models have been developed based on a rule-based approach.

    “Although the Wnt signaling pathway has also been used to illustrate features of rule-based modeling [95, 96], only few simulation models have been developed based on a rule-based approach.”

    From Relating simulation studies by provenance—Developing a family of Wnt signaling models (2021) · cites this paper as [95]

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References 30 · Cited by 107

Research works printed but not linked: 26

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Authors
Boutillier, P., Maasha, M., Li, X., Medina-Abarca, H. F., Krivine, J., Feret, J., Cristescu, I., Forbes, A. G., & Fontana, W.
Affiliations
  • Harvard University (US)
  • University of Vermont (US)
  • Institut de Recherche en Informatique Fondamentale (FR)
  • Département d’informatique de l’ENS (INRIA/ENS/CNRS), PSL Research University, Paris, France
  • University of California, Santa Cruz (US)
Corresponding author
  • Boutillier, Pierre
  • Forbes, Angus G
  • Fontana, Walter
ORCID
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2018-06-27
Volume
34
Issue
13
Pages
i583-i592
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/bty272
PMC
PMC6022607
OpenAlex
W2807744179
Cited by
107
References
30
Citations by year
2026: 7 · 2025: 5 · 2024: 9 · 2023: 8 · 2022: 21 · 2021: 18 · 2020: 24 · 2019: 12 · 2018: 2
FWCI
4.98
Type
journal article
Language
en
Open access
Licence
Locations
  • Bioinformatics (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, other-oa)
  • HAL (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
Funders
  • Defense Advanced Research Projects Agency
  • DARPA
  • Big Mechanism Program
  • US Army Research Office (W911NF-14-1-0367, W911NF-14-1-0395)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Social Sciences › Arts and Humanities › History and Philosophy of Science › Philosophy and History of Science
Keywords
rule-based models, interactive visualization, mathematical biology, contact maps, Wnt signaling, KaiABC oscillator, EGF signaling, pathway discovery, integrated development environment
MeSH terms
Data Visualization, Epidermal Growth Factor, Models, Biological, Software, Signal Transduction, Computational Biology, Wnt Signaling Pathway

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