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SBML2GraphML

Visualizes an SBML model as a GraphML file. The graph can be compiled to PDF using GraphVisualizer.

The libSBML library with Java support is needed. When compiling libSBML on Unix, use "configure --with-java" to enable Java support. You may need to compile with -O0 instead of -O2; replace all instances of -O2 with -O0 in ./configure of libSBML (only) if the default -O2 does not work. You need to put both libsbmlj.so and libsbml.so on your library path.

Version 1.0
Bundle tools
Categories Pathway
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker View/Report issues
Requires colt.jar (jar) ; csbl-javatools.jar (jar) ; jung-algorithms-2.0.jar (jar) ; jung-api-2.0.jar (jar) ; jung-graph-impl-2.0.jar (jar) ; jung-io-2.0.jar (jar) ; libsbmlj.jar (jar)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
model SBML Mandatory The SBML model.

Outputs

Name Type Description
graph GraphML The GraphML file.

Parameters

Name Type Default Description
includeNodes string "*" Names of nodes to be included in the graph. This enables to plot a subset of the model. The special value * includes all nodes (i.e., all species and all reactions).

Test cases

Test case Parameters IN
model
OUT
graph
case1 (missing) model (missing)
case2 properties model (missing)

includeNodes=MKKK,MKKK_PP,MKK,MAPK,MAPK_PP


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