Revision with unchanged content. The field of biochemical modeling & analysis is faced with an unprecedented flood of experimental data in molecular biology. While the experimental techniques 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. Aiming to complement hypothesis-driven & reductionistic biological research, and not replace it, a systems biologist relies on the tools of mathematical modeling to be able to contribute meaningfully to any ongoing bio-molecular systems research. The intent of this thesis is to present a framework & toolbox for biochemical systems modeling. The research presented 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.