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Section: New Software and Platforms


The Biochemical Abstract Machine

Keywords: Systems Biology - Bioinformatics

Functional Description: The Biochemical Abstract Machine (BIOCHAM) is a software environment for modeling, analyzing and synthesizing biochemical reaction networks (CRNs) with respect to a formal specification of the observed or desired behavior of a biochemical system. BIOCHAM is compatible with the Systems Biology Markup Language (SBML) and contains some unique features about formal specifications in quantitative temporal logic, sensitivity and robustness analyses and parameter search in high dimension w.r.t. behavioral specifications, static analyses, and synthesis of CRNs.

Release Functional Description: influence networks with forces – PAC learning of influence networks from time series data – synthesis of continuous reaction networks for mathematical functions defined by polynomial differential equations – complete modular rewriting of Biocham in SWI-Prolog