Systems biology aims at understanding complex biological processes in terms of their basic mechanisms at the molecular level in cells. The bet of applying theoretical computer science concepts and software engineering methods to the analysis of distributed biochemical reaction systems in the cell, designed by natural evolution, has led to interesting challenges in computer science, and new model-based insights in biology. In this paper, we review the development over the last decade of the biochemical abstract machine (Biocham) software environment for modeling cell biology molecular reaction systems, reasoning about them at different levels of abstraction, formalizing biological behaviors in temporal logic with numerical constraints, and using them to infer non-measurable kinetic parameter values, evaluate robustness, decipher natural biochemical processes and implement new programs in synthetic biology.