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Component
SBML2GraphMLVisualizes 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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