GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML

Bioinformatics. 2013 Sep 1;29(17):2216-7. doi: 10.1093/bioinformatics/btt370. Epub 2013 Jun 26.


GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in systems biology markup language. Providing a graphical user interface, the networks can be annotated via the simple object access protocol (SOAP)-based application programming interface of BioMart Central Portal and minimum information required in the annotation of models registry. Additionally, we provide an R-package, which processes the output of supported inference algorithms and automatically passes all required parameters to GRN2SBML. Therefore, GRN2SBML closes a gap in the processing pipeline between the inference of gene regulatory networks and their subsequent analysis, visualization and storage.

Availability: GRN2SBML is freely available under the GNU Public License version 3 and can be downloaded from

Supplementary information: General information on GRN2SBML, examples and tutorials are available at the tool's web page.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Gene Regulatory Networks*
  • Software*
  • Systems Biology / methods