- Article -
| In Silico Biology 7 S1, 08 (2007); ©2007, Bioinformation Systems e.V. |
Usage of reaction kinetics data stored in databases - a modeler's point of view
Ursula Kummer
Faculty of Biosciences, BIOQUANT, INF 267, 69120 Heidelberg and
Bioinformatics and Computational Biochemistry Group, EML Research, Schloss-
Wolfsbrunnenweg 33, 69118 Heidelberg, Germany
* Corresponding author
Email: ursula.kummer@eml-r.villa-bosch.de
Edited by I. Rojas and U. Wittig (guest editors); received and accepted March 21, 2007; published March 29, 2007
Abstract
Computational approaches to biochemistry like modeling and simulation are dependent on the availability of kinetic information. This information can either be directly derived from experimental data generated by collaborators or has to be digged up from literature, often both. More recently, data stored in databases has started to be a valuable addition as a source of enzyme kinetic data. In order to faciliate modeling and simulation, various tools have been developed in recent years. However, automatizing steps in setting up, analyzing or simulating models requires the data to be in defined formats. Crucial points are addressed below.
Keywords: modeling, simulation, enzyme kinetics, database use