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BioNet Reasoning

Command line application for modeling biological systems. It allows to reason, i.e. predict, explain, and plan, about biological systems that are described in the action language C_TAID.

general

Command line application for modeling biological systems. It allows to reason, i.e. predict, explain, and plan, about biological systems that are described in the action language C_TAID.

examples

Examples for knowledge bases, observations and queries describing the sulfur starvation response-pathway of Arabidopsis thaliana using the action language C_TAID are provided in examples.tar.gz.

dependencies

The Java application requires two additional software packages, lparse (lparse-1.0.17.tar.gz) and smodels (smodels-2.28.tar.gz). They are provided by the Helsinki University of Technology.

documentation

A comprehensive documentation of the action language C_TAID and the two supported translations can be found here (BioNetReasoningLong.pdf).
A short introduction to the syntax of the BioNetReasoning Tool and how it can be used to model biological systems can be found here (BioNetReasoningShort.pdf).

downloads
program file: BioNetReasoning.jar
examples: examples.tar.gz
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