Software support

Software
Databases
File Formats

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 or database is not listed below, or if you know of another effort, please post a message to sbgn-discuss.

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	+	+	+	+
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	+	+	+	+
SBGN-ED/VANTED	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.