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

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

Author information

1
Leibnitz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstrasse 11a, Jena, Germany. Sebastian.Vlaic@hki-jena.de

Abstract

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 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.

PMID:
23803467
DOI:
10.1093/bioinformatics/btt370
[Indexed for MEDLINE]

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