Abstract: Computational Systems Biology, Reaction Systems, and Constraint Programming Tools
Systems biology aims at understanding complex biological processes in terms of their basic mechanisms at the molecular level in cells. The bet of applying formal methods to the analysis of biochemical reaction systems, designed by natural evolution, has led to interesting challenges in computer science, and new model-based insights in cell biology. In this talk, I shall review the development over the last decade of the biochemical abstract machine (Biocham) software environment for modelling molecular reaction systems, performing various static analyses using constraint logic programming tools, and formalising biological behaviors in quantitative temporal logic for inferring non-measurable reaction rates,evaluate robustness, and start deciphering natural biochemical programs in the cell.