MCB Course Supplementary Material

This page contains the supplementary material for the MCB course in integrative bioinformatics day 2. All materials are provided solely for educational purposes within the course. You may download some course presentations as PDFs readable with eg. Acrobat Reader. The links to most sites are embedded in the PDFs. You may also copy-paste the commandline parameters for kegg2sbml.

Download our derived version of the kegg2sbml tool here . See the original web-site for more information. kegg2sbml 1.6.0 is provided under the LGPL license as the original software. The source code of the software can also be browsed and checked out via our SVN repository http://www.ii.uib.no/svn/eSysBio/kegg2sbml-1.6.0/ which provides public read-only access.

Updates

The latest update is kegg2sbml-1.6.0-1.tar.gz. This update should also work through transparent proxies (as in the UIB wireless network). The contained .txt files and the ChangeLog have also been updated. Also, the file kegg2sbml-1.6.0-1.tar.gz is now really gzipped.

Unpacking the archive

The archive can be extracted using archiving utilities like Winzip. Sample data is contained in the SBML and data folders in the archive. The program can fetch pathway data automatically from KEGG via FTP. Use of KEGG data is free for academic research. Commercial users require a license from KEGG to use their pathway data, you must check yourself if you comply with the kegg licensing policy.

The generated SBML can be used with CellDesigner and with ProMeTra in this course.

Last updated: 26-11-2009, Michael Dondrup, michael (dot) dondrup (at) uni (dot) no