SBML Parts Decomposition Tool

Biochemical Pathway Component Finder

Ever wanted to extract a particular enzyme or reaction from a computational model? Perhaps not, but those of you who have, there is now a tool available to do that very task. Maxwell Neal from University of Washington wrote a tool that reads the entire biomodels database and allows a user to search on any part, organism etc. The tool then searches all the models (~300) and presents a selection of enzyme/reaction parts that matches the search. For example, if you were building a model of glycolysis and wanted a kinetic model for phosphofructokinase (pfk), you can use Max’s tool to search for pfk. The screenshot below shows the result of such a search:

Because biomodels contains multiple glycolytic models, there will be multiple choices for a suitable pfk kinetic model. Once the search is done, simply select the enzyme model that is most appropriate for your model. Since biomodels holds about 300 models, there are thousands of potential parts to be extracted for these models.The software has a couple of nice features, it has a form of intelli-sense when typing in the name of an enzyme etc, which makes finding somthing much much easier. The search itself is very fast because the software will cache models locally if desired, even the entire database. Finally you can use simple Boolean operators (AND, OR, NOT) to narrow down your search.

The tool only works because of the meticulous effort expended by groups headed by Mike Hucka at Caltech and Nicolas Le Novere at EBI. This application is a great example of the utility of proper annotation and curation of data.

If you’re interested in the tool you can find more at Max’s web site.

Download from sourceforge, runs under Windows, Mac and Linux (Windows version comes with an easy setup app).

Disclaimer: Max did 95% of the work but I contributed to testing and some of the feature suggestions.

This entry was posted in Enzyme Kinetics, General Science Interest, Modeling, Pathways, SBML. Bookmark the permalink.

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