Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
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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: – notebooks of Master classes – graphical user interface on top of Jupyter – synthesis of at most binary reactions with minimisation of the variables for negative values – detection of model reduction by subgraph epimorphism – option for partial tropical equilibrations