CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways

Bioinformatics. 2010 Dec 1;26(23):2997-9. doi: 10.1093/bioinformatics/btq585. Epub 2010 Oct 14.


Summary: Systems biology relies increasingly on collaborations between several groups with different expertise. Therefore, the systems biology community is adopting standards that allow effective communication of concepts, as well as transmission and processing of pathway information. The Systems Biology Graphical Notation (SBGN) is a graphical language for biological pathways that has both a biological as well as a computational meaning. The program CellDesigner allows the codification of biological phenomena in an SBGN compliant form. CellPublisher is a web server that allows the conversion of CellDesigner files to web-based navigatable diagrams based on the user interface of Google maps. Thus, CellPublisher complements CellDesigner by facilitating the understanding of complex diagrams and by providing the possibility to share any CellDesigner diagram online with collaborators and get their feedback. Due to the intuitive interface of the online diagrams, CellPublisher serves as a basis for discovery of novel properties of the modelled networks.

Availability: The freely available web server and the documentation can be accessed at: http://cellpublisher.gobics.de/. The source code and the offline version for Microsoft Windows are freely available at http://sourceforge.net/projects/cellpublisher/.

Contact: jstuelk@gwdg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Gene Expression Regulation
  • Internet
  • Metabolic Networks and Pathways*
  • Models, Biological
  • Signal Transduction*
  • Software*
  • Systems Biology / methods*