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Section: Partnerships and Cooperations
International Initiatives
Participation In other International Programs
EXEK
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Partner: Inria Paris-Rocquencourt, École normale supérieure de Lyon Université Paris-Diderot,
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Abstract: Our overarching objective is Executable Knowledge: to make modeling and knowledge representation twin sides of biological reasoning. This requires the definition of a formal language with a clear operational semantics for representing proteins and their interaction capabilities in terms of agents and rules informed by, but not exposing, biochemical and biophysical detail. Yet, to achieve Executable Knowledge we need to go further:
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Bridge the gap between rich data and their formal representation as executable model elements. Specifically, we seek an intermediate, but already formal, knowledge representation (meta-language) to express granular data germane to interaction mechanisms; a protocol defining which and how data are to be expressed in that language; and a translation procedure from it into the executable format.
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Implement mathematically sound, fast, and scalable tools for analyzing and executing arbitrary collections of rules.
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Develop a theory of causality and attendant tools to extract and analyze the unfolding of causal lineages to observations in model simulations.
We drive these technical goals with the biological objective of assembling rule-based models germane to Wnt signaling in order to understand the role of combinatorial complexity in robustness and control.
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Inria International Labs
Xavier Rival attended the LIAMA Open Day in July 2014, gave a talk on “Modular Construction of Shape-Numeric Analyzers” and participated to the associated Summer School, giving a one day introduction to Verification by Abstract Interpretation.
Inria International Partners
Informal International Partners
Research on abstract domains for memory states involves the group of Bor-Yuh Evan Chang (University of Colorado at Boulder, Colorado, USA).
Research on sensitivity is done in partnership with the group of Sukyoung Ryu (Assistant Professor at KAIST, Daejeon, Korea).
Research on numeric abstract domain is done in partnership with the groups of Ji Wang and Liqian Chen (National University of Defense Technology, Changsha, China) and of Deepak Kapur (University of New Mexico, USA).