Genome Informatics 14: 621--622 (2003) 621 OBIYagns: A Biochemical Simulator in Grid (original) (raw)

Abstract

Introduction A computer simulation of mathematical models on cellular biochemical networks has been recognized as a useful tool for biological researchers to understand the dynamics and regulation mechanism of biochemical behavior and to set up subsequent working hypotheses for their future experiments. Until now, several programs such as Gepasi [5], E-Cell [7], Virtual Cell [4] and GENESIS [6] have been available for such purposes. Mathematical modeling requires a set of parameters (kinetic constants and physiological concentration of the cellular components), however, there are no experimental methods to measure all of such parameters with accuracy. Therefore, estimation of biological parameters based on any observable wet-lab data is essential for construction of the model. And, this estimation process often requires huge computer resources which one organization cannot a#ord. 2 Method We developed OBIYagns (Yet Another Gene Network Simulator) with parameter estimators distribute

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