BioPSy Version 1.0
BioPSy is a tool that performs parameter synthesis on biological models specified using the Systems Biology Markup Language (SBML) and corresponding time series data. BioPSy utilises the Satisfiability Modulo Theories (SMT) solver, dReal, to determine the range of acceptable parameter values within a given domain. A model using parameter sets computed with BioPSy is formally guaranteed to satisfy the desired behaviour.
BioPSy is a Java application and requires Java JRE 6 or higher to run. If you download the precompiled jar file with binaries, you'll need to change the permissions of the files and add the directory you extracted them in to your PATH:
chmod a+rx dReal ParSyn
chmod a+r BioPSy.jar
export PATH=$PWD:$PATH
BioPSy can then be run by executing java -jar BioPSy.jar.
Alternatively, BioPSy can be compiled by downloading the source, browsing to the BioPSy directory, and executing ant:
cd BioPSy
ant
This will compile the application and produce a jar file in BioPSy/bin.
Before running BioPSy, add BioPSy/bin to your PATH:
export PATH=<BioPSy Directory Location>/BioPSy/bin:$PATH
To run BioPSy, execute java -jar BioPSy.jar.