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 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. or andraeger@eng.ucsd.edu © 2013 The Author.