论文信息 - OBIYagns: A Biochemical Simulator in Grid Environment

OBIYagns: A Biochemical Simulator in Grid Environment

A computer simulation of mathematical models on cellular biochemical networks has been recognizedas a useful tool for biological researchers to understand the dynamics and regulation mechanismof 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 beenavailable forsuchpurposes. Mathematical modeling requiresa set ofparameters (kinetic constants andphysiological concentration of the cellular components), however, there are no experimental methodsto measure all of such parameters with accuracy. Therefore, estimation of biological parameters basedon any observable wet-lab data is essential for construction of the model. And, this estimation processoften requires huge computer resources which one organization cannot a ord.

[1] Shuhei Kimura,et al. A Genetic Algorithm with Distance Independent Diversity Control for High Dimensional Function Optimization. , 2003 .

[2] Shuhei Kimura,et al. Development of Biochemical System Simulator with Parameter Estimator , 2002 .

[3] Pedro Mendes,et al. GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems , 1993, Comput. Appl. Biosci..

[4] Masaru Tomita,et al. E-CELL: software environment for whole-cell simulation , 1999, Bioinform..

[5] S. Kimura,et al. A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling. , 2003, The Biochemical journal.

[6] L. Loew,et al. The Virtual Cell: a software environment for computational cell biology. , 2001, Trends in biotechnology.

[7] Upinder S. Bhalla,et al. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks , 2003, Bioinform..