The Virtual Cell SBML Converter

• SBMLConverter is a command line program used to convert SBML files to VCML and vice versa (import SBML files to VCML and export VCML files to SBML)

• This code is based on VCell_4.6_ALPHA_37 (Eclipse svn://code/vcell/trunk/VCell; Revision : 3293)

• This version uses libSBML 3.0.2 with Expat, Java bindings.

• Note : This version of the converter presently runs under Java 1.5, but has problems under Java 1.6

• To run the converter, the following files are required (see attachments below):
  • SbmlConverter.jar - the main converter class and other referenced Virtual Cell code need to import/export
  • thirdParty.jar - related third party classes used in Virtual Cell (e.g., ucar.units, jscl, org.jdom, etc. packages)
  • sbmlj.jar - libSBML related jar file
  • Note : If the XXX.jar files are saved as XXX.zip while downloading the attachment, please make sure to change them to XXX.jar
  • For Windows, the following files are required:
    • sbml.dll, sbmlj.dll, expat.dll - libSBML related libraries
    • IDAStandalone.exe - IdaStandaloneSolver^? executable for Windows
  • For Linux, the following files are required:
    • libsbml.so, libsbmlj.so, libexpat.so - libSBML related libraries
    • IDAStandalone - IdaStandaloneSolver^? executable for Linux
  • For Mac, the following files are required:
    • libsbml.jnilib, libsbmlj.jnilib, libexpat.jnilib - libSBML related libraries
    • IDAStandaloneMacG5 or IDAStandaloneMacIntel - IdaStandaloneSolver^? executable for Mac
• Miscellaneous files (under attachments):
  • some example SBML and VCML files
  • In case you need to view the source for the jar file, you can access it with vc_src.zip

• To run this standalone executable from a command prompt :
  • It is easier if the related JAR and DLL files are in the same directory!
  • Navigate to the directory where SbmlConverter.jar is located
  • At the prompt type :

java.exe -cp thirdParty.jar;sbmlj.jar;SbmlConverter.jar org.vcell.sbml.test.SbmlConverter -export | import Relative_Path_of_File_To_Export_or_Import.xml [-simulate]

Note :

• use either -export or -import
• The -simulate option is available only for import
• specify the relative path of the input file name if not in local directory.

For example:

Export : java.exe -cp thirdParty.jar;sbmlj.jar;SbmlConverter.jar org.vcell.sbml.test.SbmlConverter -export VCML\dlb_vcml.xml (where the input file is in directory VCML within current directory)

Import :

For just importing : java.exe -cp thirdParty.jar;sbmlj.jar;SbmlConverter.jar org.vcell.sbml.test.SbmlConverter -import SBML\BM2_sbml.xml

For importing and simulating a default simulation: java.exe -cp thirdParty.jar;sbmlj.jar;SbmlConverter.jar org.vcell.sbml.test.SbmlConverter -import BM2_sbml.xml -simulate

(where the input file is in directory SBML within current directory)

Notes about the Export and Import options:

• Export from VCell -> SBML:
  • Each non-spatial (non-stochastic) application (with default parameter values) is exported into a separate file, and any simulation with parameter overrides (including parameter scans) is exported into separate files (different files for different parameter scan values).
  • The output (SBML) file names are named with the following convention : Biomodel_Name_i_j_k.xml, where Biomodel_Name is name of biomodel; i is the i-th application; j is the j-th simulation (only if simulation has overriden parameters); k is the k-th parameter-scan (if simulation has parameter scans).

• Import from SBML -> VCell:
  • Output files are named as : sbmlFileName.vcml
  • If the -simulate option is used for import, the math is generated for the default simulationContext (application) in the imported biomodel, and a default simulation is created which has the following settings : End time = 10 secs ; No. of Time Steps = 1000 ; Solver = IDAStandaloneSolver^? (variable time step) ; Forced uniform output time step = 0.01
  • This updated biomodel application (with generated math and default simulation) is stored in another VCML file : sbmlFileName_IDA_simulation.vcml
  • When the simulation is run, the IDA solver input (settings) are stored in sbmlFileName.idaInput file
    • Note: If user wants to change default settings of end time or no. time steps (output time step), it can be changed in the .idaInput file and the simulation can be run separately using the IDAStandalone.exe
  • The output from the IDAStandaloneSolver^? is saved to a sbmlFileName.ida file
  • The generated results are stored in a CSV file : sbmlFileName.csv
    • Note: The values for time and species concentration in the CSV file are in the units specified in the SBML model that was imported. For example, if the SBML model had its time units in minutes (instead of default secs) and species units were in milli-molar, even though VCell deals with time in secs and species concetration in uM, the output in the CSV file is converted to the units that were specified in the SBML model (i.e., time is in minutes and species are in milli-molar).