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Section: Software

OpenKappa

Participants : Monte Brown [Harvard Medical School] , Vincent Danos [University of Edinburgh] , Jérôme Feret [Correspondent] , Walter Fontana [Harvard Medical School] , Russ Harmer [Harvard Medical School] , Jean Krivine [Paris VII] .

OpenKappa is a collection of tools to build, debug and run models of biological pathways. It contains a compiler for the Kappa Language [61] , a static analyzer [60] (for debugging models), a simulator [59] , a compression tool for causal traces [58] , and a model reduction tool [7] ,[15] ,[13] .

OpenKappa is developped since 2007 and, the OCaml version currently consists of 46 000 lines of OCaml. Software are available in OCaml and in Java. Moreover, an Eclipse pluggin is available.

OpenKappa is freely available on the web at http://kappalanguage.org under the LGPL license. Discussion groups are also available on line.

Current external users include the Ecole Polytechnique Federale de Lausanne, the UNAM-Genomics Mexico team. It is used as pedagocical material in graduate lessons at Harvard Medical School, and at the Interdisciplinary Approaches to Life science (AIV) Master Program (Université de Médecine Paris-Descartes).


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