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Héctor F. Medina-Abarca

dblp:222/4683 · DBLP profile ↗
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1ranked-venue papers
0as first author
0since 2021 · last 2018
—ORCID · unresolved

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 2 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › systems biology
rule-based modeling
0.312018
The Kappa platform for rule-based modeling · Bioinform. 2018
Bioinformatics and computational biology › systems bioinformatics › pathway analysis
signaling pathway analysis
0.112018
The Kappa platform for rule-based modeling · Bioinform. 2018

Methods — techniques the papers use, named apart from their topics

static analysis · 0.3kappa simulator · 0.3dynamic influence network · 0.3
YearPublicationVenuePosition
2018 The Kappa platform for rule-based modeling
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.
Pierre Boutillier, Mutaamba Maasha, Héctor F. Medina-Abarca, Jean Krivine, Jérôme Feret, Ioana Cristescu, Angus G. Forbes, Walter Fontana
Bioinform.4