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

Abstract:

Summary: GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in SBML. Providing a graphical user interface, the networks can be annotated via the SOAP-based application programming interface of BioMart Central Portal and MIRIAM 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 http://www.hki-jena.de/index.php/0/2/490.

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

Contact: sebastian.vlaic@hki-jena.de

10.1093/bioinformatics/btt370

Projects: A3.4: Linking signalling to metabolic functions, A3.6: Transcription factor network and links to metabolism in NAFLD

Bioinformatics
Bioinformatics 29(17) : 2216
26th Jun 2013

S. Vlaic, B. Hoffmann, P. Kupfer, M. Weber, A. Drager

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[Sebastian Vlaic] [Andreas Dräger]

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Cell
Views: 2037
  • Created: 1st Jul 2013 at 23:57
  • Last updated: 24th Oct 2013 at 16:14

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