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#*  FILE:  SBML2STOCHKIT CONVERTER README
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#*  AUTHOR: HongLi
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#*  CREATED: Mar 06, 2005
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SBML2STOCHKIT CONVERTER README

0. Recommend the java version "1.4.2_01"

1. How to use the parser
          
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)  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

4) Get the result
   
   The results are in the subdirectory of $CONVERTER_HOME with the model name 
   you specified in your SBML file.
          
2. Specifying Parameters for the Converter
   
1) After sepcifying the model, give the <listOfSpecies>,
    including the initial value for each species
    (This is the number of molecules of sepcies, 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>
          
