Software support

This page summarizes what we know about software support for SBGN languages. This knowledge comes from a variety of sources, and is not necessarily complete. If your software and/or database is not listed below, or if you know of another effort, please post a message to sbgn-discuss@googlegroups.com.

Software

The following is a list of software packages known to provide support for SBGN. The links to the software packages were correct at the time of recording.

Software Package V / E PD ER AF SBGN-ML
Arcadia V + - - -
Athena E + - - -
Beacon Pathway Editor E - - + -
BIOCHAM E + - - -
Biographer E + + + +
BioUML V + - - -
CellDesigner E + - - +
ChiBE E + - - -
COPASI V + - - -
CySBGN V + + + +
Dunnart E + - - -
Edinburgh Pathway Editor E + + + -
EscherConverter V + - - +
geneXplain platform E + - - -
iPathways V + - - -
JWS Online V + - - -
KEGGtranslator V + - - +
Krayon for SBGN E + - - +
Mayday MGV V + - - -
Mimoza V + - - -
Netbuilder’ E + - - -
Newt Editor E + - + +
Omix E - - - +
PathVisio E + + + +
PathwayLab E + - - -
SBGN-ED E + + + +
SBGNTikZ E + + + -
SBGNViz V + - - +
SBML Layout Viewer V + + + +
SBMM assistant V + - - -
VISIBIOweb V + - - +
yEd Graph Editor E + - + -

V / E - Viewer or Editor
PD – Process Description, ER – Entity Relationship, AF – Activity Flow
SBGN-ML - Load SBGN maps from SBGN-ML format and/or save SBGN maps to SBGN-ML format (see also File Formats)
“+” supported, “-“ not supported

Databases

The following is a list of databases known to provide SBGN maps. The links to the databases were correct at the time of recording.

Database PD ER AF SBGN-ML
Atlas of Cancer Signalling Networks + - - -
AlzPathway + - - -
BioModels Database + - - -
iPAVS + - - -
MetaCrop + - - +
NaviCell + - - -
PANTHER Pathway + - - +
Parkinson’s disease map + - - -
Path2Models* + - + +
Reactome + - - +
RIMAS + - - -
SubtiPathways + - - -

*Path2Models is part of the BioModels Database
PD – Process Description, ER – Entity Relationship, AF – Activity Flow
SBGN-ML - Download of SBGN maps in SBGN-ML format (see also File Formats)
“+” supported, “-“ not supported

File Formats

SBGN-ML

The implementation of SBGN support in software packages may be facilitated by the use of the XML-based file format SBGN-ML. SBGN-ML can be processed and generated by the standard library LibSBGN. LibSBGN is a community project and everyone is welcome to participate.

Discussions around SBGN-ML and LibSBGN take place on sbgn-libsbgn-discuss.

One can compare the rendering of SBGN-ML by different software packages on the LibSBGN Render Comparison site.

BioPAX-SBGN Mapping

Biological Pathways Exchange (BioPAX) is a standard that aims to provide integration, exchange, visualization and analysis of biological pathway data. A substantial amount of BioPAX Level 3 concepts can be represented in SBGN PD via BioPAX-SBGN Mapping. More information regarding BioPAX-SBGN Mapping software can be found here.

Biological Connection Markup Language (BCML)

The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML can be automatically converted into a SBGN-compliant graphical representation. More information regarding BCML software can be found here.