Wordprocessing

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

help Authors

[Sebastian Vlaic] [Andreas Dräger]

help Attributions

None

help Scales


Cell
Views: 2166
  • Created: 1st Jul 2013 at 23:57
  • Last updated: 24th Oct 2013 at 16:14

Related items

Ajax-loader-large

Log in / Register

Need an account?
Sign up

Forgotten password?

Front Page

Virtual Liver Network

(v.0.22.0)

Related Projects and friends


Imprint Taverna workflow workbench myExperiment JWS Online ISATAB myGrid Sabio-RK BioPortal Semantic SBML

Powered by:

Ror-logo-32

Icons:
Silk icons 1.3
Crystal Clear icons

Virtual Liver Seek uses one essential cookie to keep you session open and one cookie to keep your consent.

By continuing to use this site you agree to the use of cookies