CONVERTER

SBML (Systems Biology Makeup Language) is a computer-readable format for representing models of biochemical reaction networks. SBML can enable the convenient description of metabolic networks, cell-signaling pathways, regulatory networks, and many others. Dozens of software packages support this format. Many biochemical problems are written as SBML files. For the convenience of SBML users, we provide an easy SBML to STOCHKIT Converter using Java.

Software needed: Java. (Java "1.4.2_01" is recommend)

How to use the Converter:

1. Set the environment variable
   
   a)setenv CONVERTER_HOME  (The home dir for the package)
   Example:  setenv CONVERTER_HOME $HOME/converter
   
   b)setenv LD_LIBRARY_PATH (The dir for the libs)
   Please specify the $CONVERTER_HOME/lib to be one of them
   Example:  Setenv LD_LIBRARY_PATH "$CONVERTER_HOME/lib: $LD_LIBRARY_PATH"
   
2. Write the SBML file for your model
   Our SBML2STOCHKIT CONVERTER can accept standard Version1(level 1 and 2) and Version 2 SBML files with  requests.(For details, see the following section). 
   
3. Check the sub directory
   make sure that you have the sub dir  with the model name you specified in your SBML file in the $CONVERTER_HOME
   
4. Run the Converter with the following command in the converter home dir
   java -classpath .:./jar:./jar/parser.jar:./jar/xerces.jar Converter test.xml 100
   Note: test.xml is the file name of your SBML file and 10 is how long you want to simulate
   
5. Get the result
   The results are in the subdirectory of $CONVERTER_HOME with the model name you specified in your SBML file.
   
   Specifying Parameters for the Converter

1. After specifying the model, give the <listOfSpecies>, including the initial value for each species
   (This is the number of molecules of species, NOT the concentration)
   Example:
   <specie name="S1" compartment="DimerDecay" initialAmount="1000" boundaryCondition="false" />
   
2. In the <listOfReactions> specify the kinetic lawfor each reaction
   Example:
   <kineticLaw formula="c1*S1">
   
3. In the <kineticLaw formula="c1*S1"> specify theParameter
   Example:
   <listOfParameters>
   <parameter name="c1" value="1"/>
   </listOfParameters>
   
   For details, please read the UserGuide.