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Revision with unchanged content. The field of biochemical modeling & analysis is faced with an unpre cedented flood of experimental data in molecular biology. While the experimental tech ni ques continue to leapfrog ahead in the speed & volume, the methods of analysis & interpretation, however, are still playing ´catch-up´. The notions of systems analysis have found a new foothold, under the banner of ´Systems Biology´, with a promise to uncover the rationale for the designs of biological systems from their parts lists. Ai ming to complement hypothesis-driven & reductionistic biological re search, and not replace it, a systems biologist relies on the tools of mathe matical modeling to be able to contribute meaningfully to any ongoing bio-molecular systems research. The intent of this thesis is to present a frame work & toolbox for biochemical systems modeling. The re search presen ted here builds upon the tenets of a well-established approach to biological systems modeling & analysis, called Biochemical Systems Theory (BST), which is almost 40 years old. The thesis presents the features of a MATLAB-based software application that has been built upon the framework of BST and is aptly named as Biochemical Systems Toolbox.

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I work on computational analysis of metabolic pathways such as glycolysis in lactic acid bacteria. The objective is to uncover regulatory mechanisms of the organism to enable efficient control of metabolite production. Analysis involves mixed-mode modeling (bottom-up/ top-down/ partial modeling & stoichiometric/ kinetic models) & parameter estimation.

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