November 12, 2009

KEGGConverter: Tool for modelling Metabolic Networks

Filed under: Bioinformatics,Systems Biology — Biointelligence: Education,Training & Consultancy Services @ 7:47 am
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The Kyoto Encyclopedia of Genes and Genomes (KEGG) PATHWAY database is a valuable comprehensive collection of manually curated pathway maps for metabolism, genetic information processing and other functions. It is an integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information as shown below. Genomic and chemical information represents the molecular building blocks of life in the genomic and chemical spaces, respectively, and systems information represents functional aspects of the biological systems, such as the cell and the organism, that are built from the building blocks. KEGG has been widely used as a reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.

The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, KEGG Pathways through KGML (KEGG Markup Language) files, can provide complete reaction sets and introduce species versioning, which offers advantages for the scope of cellular metabolism simulation modelling.

In order to construct such metabolic pathways, the KEGGConvertor has been implemented. It is a tool implemented in JAVA. KEGGconverter is capable of producing integrated analogues of metabolic pathways appropriate for simulation tasks, by inputting only KGML files. The web application acts as a user friendly shell which transparently enables the automated biochemically correct pathway merging, conversion to SBML format, proper renaming of the species, and insertion of default kinetic properties for the pertaining reactions. It permits the inclusion of additional reactions in the resulting model which represent flux cross-talk with neighbouring pathways, providing in this way improved simulative accuracy.
KEGG Convertor is available here:


1 Comment »

  1. Generally I do not post on blogs, but I would love to mention that this post extremely forced me to try and do therefore! really nice post. Excellent blog with lots of helpful information !!


    Comment by eldeddebuibus — December 15, 2009 @ 3:27 pm | Reply

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