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Software support

This page summarises 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.

The following are lists of software packages known to provide support for editing and visualising in SBGN Process Description (PD), Entity Relationship (ER) and Activity Flow (AF) with and without SBGN-ML file format support.

Editors

Software PD ER AF SBGN-ML support Availability
CellDesigner* Installers for Win/Mac/Lin
Krayon for SBGN IDE or Win installer
Newt Editor In-browser
Omix Commercial/free trial
PathVisio Web start/binary
SBGN-ED VANTED plugin
yEd** Installers for Win/Mac/Lin

* The cd2sbgnml converter enables bidirectional convertsion to/from SBGN-ML.

** In combination with the ySBGN converter, yEd can be seen as an editor with SBGN-ML import and export enabled.

Visualisers and Formats Converters

Software PD ER AF Formats Availability
CySBGN SBML → SBGN Cytoscape plugin
EscherConverter Esher JSON → SBGN JAR file
KEGGtranslator KEGG-ML → SBGN JAR file
SBML Layout Viewer SBML → SBGN NET library
ChiBE BioPAX → SBGN Istallers for Win/Mac/Linux
SBGNTikZ LaTex → SBGN TeX package
STON SBGN-ML → Neo4j Library for Neo4j
SBGNViz SBGN-ML → image In-browser
ySBGN GraphML ↔ SBGN-ML Maven install


Tools using SBGN

Software PD ER AF Type of a tool
BIOCHAM Modeling
BioUML Modeling & Bioinformatics
COPASI Modeling
JWS Online Modeling
geneXplain platform Modeling & Bioinformatics
MINERVA Server supporting SBGN maps


Databases and collections of SBGN maps

Database PD ER AF SBGN-ML export Type of maps
AlzPathway CellDesigner generated
Asthma Maps yED generated
Atlas of Cancer Signalling Networks CellDesigner generated
BioModels Database JWS generated
Metabolism Regulation maps yED generated
MetaCrop SBGN-ED generated
NaviCell CellDesigner generated
PANTHER Pathway CellDesigner generated
Parkinson's disease map CellDesigner generated
Path2Models* PathVisio and SBGN-ED generated
Pathway Commons
PathWhiz SBGN-ML export
Reactome Diagram JS or GWT
RIMAS SBGN-ED generated
SubtiPathways CellDesigner generated
Virtual Metabolic Human ReconMaps CellDesigner generated

* Path2Models is part of the BioModels Database.

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.

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.

Archive of old tools

Software PD ER AF Active
Arcadia
Athena
Beacon Pathway Editor
Biographer
Dunnart
Edinburgh Pathway Editor 2007 - 2011
Netbuilder'
iPathways 2011 - 2017
Mayday MGV
Mimoza
PathwayLab
SBMM assistant
iPAVS
VISIBIOweb 2002