SBGN Software

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

Software tool assisting in supporting SBGN

The implementation of SBGN support in software tools may be facilitated by the use of an XML exchange format: SBGNML. SBGNML can be processed and generated by a standard library: libsbgn. Libsbgn is a community project and everyone is welcome to participate.

Discussions around SBGNBML and libsbgn take place on sbgn-libsbgn-discuss

One can compare the rendering of SBGN-ML by the different software using Frank Bergmann's Render Comparison site.

Software providing support for SBGN

The following is a list of software packages known to provide (or have started to develop) support for SBGN notations. As the list grows, we envision more sophisticated way of recording support, but we hope this will be useful nevertheless. The webpages and e-mail addresses (remove spaces) were correct at the time of recording.

• Arcadia - Contact: alice . villeger @ manchester . ac . uk
• Athena - Contact: fbergman @ u . washington . edu
• Biological Connection Markup Language (BCML) - Contact: duccio . cavalieri @ unifi . it
• BiNoM - Contact: laurence . calzone @ curie . fr
• BIOCHAM - Contact: prijatelkatadadicka @ yahoo . com
• BioModels Database - Contact: biomodels-net-team @ lists . sourceforge . net
• BioPAX - Contact: demir @ cbio . mskcc . org
• BioUML - Contact: fedor @ developmentontheedge . com
• ByoDyn
• CellDesigner - Version 4.x supports SBGN Process Diagram Level 1. Contact: info @ celldesigner . org
• Dunnart Contact: Sarah.Boyd @ infotech . monash . edu . au
• Edinburgh Pathway Editor - Contact: asorokin @ inf . ed . ac . uk or Stuart Moodie: smoodie @ ed . ac.uk
• iPathways - Contact: ghosh @ sbi . jp
• JWS Online - Contact: jls @ sun . ac . za
• Mayday - Contact: battke @ informatik.uni-tuebingen.de
• Netbuilder (Apostrophe) - Contact: k . wegner @ herts . ac . uk
• PANTHER - Contact: mi @ ai . sri . com
• PathwayLab - Contact: mats . jirstrand @ fcc . chalmers . se
• Reactome - Contact: eschmidt @ ebi . ac . uk
• SBGN-ED (Vanted) - Contact: czauderna @ ipk-gatersleben . de or schreibe @ ipk-gatersleben . de
• SubtiPathways - Contact: jstuelk @ gwdg . de
• Systems Biology Metabolic Modeling assistant - Contact: sbmm @ uma . es
• VISIBIOweb - Contact: ugur @ cs . bilkent.edu.tr