Copenhagen Programming Language Seminar

A platform for the Simulation and analysis of bio molecular systems in the kappa-calculus

Jean Krivine
LIX, École Polytechnique

Thursday, March 29th, Time: 15:15 - 16:00
IT University of Copenhagen, Rued Langgaards Vej 7, auditorium 4


Joint work with Vincent Danos (Laboratoire Preuves Programmes et Systèmes,CNRS, France), Jerome Feret (Ecole Normale Supérieure, Paris), Walter Fontana (Systems Biology Department, Harvard Medical School, US).

In this talk we present Simplx, a tool currently in development at Plectix Biosystems (Boston, US) allowing to analyse and simulate large bio molecular systems. The tool relies on an agent based formalism called the kappa-calculus [1]. We first present the kappa-calculus in which states, called solutions or systems, are graphs where connections are made on sites and transitions are generated by a restricted class of graph- rewriting rules. We will then proceed with the technical description of Simplx features.

[1] Formal Molecular Biology (TCS 325, 2004) Vincent Danos, Cosimo Laneve.

Scientific host: Arne John Glenstrup. Administrative host: Camilla Torp-Smith. All are welcome.
The Copenhagen Programming Language Seminar (COPLAS) is a collaboration between DIKU, ITU, KVL and RUC. COPLAS is sponsored by the FIRST Graduate School.
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