Conversion from SBML to XPP

XPP-Aut is a numerical analysis software. It permits to solve differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.

The java SBML to XPP converter is developed inside the System Biology Format Converter (SBFC) framework that will allow us and contributors to add easily new converter. The framework is developed on sourceforge, see the System Biology Format Converter project pages.

Java Version

Quick Setup

Download and unpack the sbml2xpp-1.2.tar.gz file, move to the folder that have been created and run:

./sbml2xpp.sh [file.xml | folder]

Will try to transform SBML (any *.xml files if you put a folder) into XPP
The output file(s) will be in the same folder as the SBML file(s) with an extension .xpp

Prerequisite

• java 1.5 or higher. You can find it here

• Apache Ant 1.6.5 or higher (only needed to build from source). You can find it here

Build

If you want to modify the sources and build the jar file
just type on the sbml2xpp folder:

ant jar
to generate the jar file

ant javadoc
to generate the java documentation

Download

• sbml2xpp-1.2.tar.gz

Getting Help and Support

Please send any help requests or bug reports to :

XSL version

Quick Setup

To generate an XPP-Aut ode file from an SBML model, run:

Xalan MyModel_sbml.xml sbml_xpp16.xsl > MyModel.xpp

You can download the XSL stylesheet in the section below.

Download

1. sbml_xpp16.xsl
2. xpp_math16.xsl
3. xpp_test16.xsl
4. xpp_variable16.xsl
5. bounds16.xsl

Documentation

The conversion is performed in one XSLT pass, but using five stylesheets.

1. Test if we can convert this SBML model

We are calling several templates and running several tests to see if we can reasonably convert the SBML model.

• First we count the number of XPP parameters that would be created, and if this number is above 300, XPP will not be able to handle the file. Xpp parameter are compartment, global parameter, species with their attribute constant=true and all local parameter, as they are always constant.
  
• Second, if there is any events we cannot convert the model. Also, the program was written for SBML level 2 version 1, so will disregard any new SBML elements introduced since then.
  
• Third, we control the units of the model, if there is user-defined units that do not change an SBML built-in unit, we cannot currently convert this model.
  
• Last, we check the MathML to see if there is any user-defined functions or some MathML functions that we cannot handle in XPP, in that case we cannot convert the model either.

2. Writing the XPP file

Here is what we wrote to the ode file :

• all SBML ids are changed to comply to the XPP rules. In XPP id should be 9 character long maximum and we have to put the local parameter in the same id space as all the others.
• the name of the SBML model as a comment, in general we put a comment for each SBML element that we include in the ode file
• we declare several functions used in the MathML expression and that do not exist by default in XPP, like root, power,..
• the compartment elements as para or init
• the global parameters elements as para or init
• the species elements as para or init
• d species/dt=ODE (if this species actually be affected by reaction/kineticLaw) (ODE should be concentration/time, but kineticLaw usually be substance/time, depending on species unit) (in ODE all the reaction/kineticLaw will be represented as RXNindex)
• rules
• reaction/kineticLaw
• we set several XPP values to be able to simulate the model
• done (the word "done" as to be written at the end of an Xpp ode file)