BioPSy v1.2.1

• Improved error handling
• dReal3 static binary included (much faster!)

BioPSy v1.2

BioPSy is a tool that performs parameter set 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 and numerically 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 can run BioPSy 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.

BioPSy v1.1

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

chmod a+rx dReal ParSyn
chmod a+r BioPSy.jar

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. To run BioPSy, execute java -jar BioPSy.jar.

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.