Course handouts C2-19 Biochemical Programming 2018-2019

Master Parisien de Recherche en Informatique University Paris Diderot, UPMC, Paris-Saclay, X, ENS.

Over the past decade, formal methods from Theoretical Computer Science have been successfully applied in Life Sciences to decipher biological processes, mostly at the molecular and cellular levels. This course aims at presenting these methods and research issues in computational systems biology and synthetic biology. It is based on the vision of cells as machines - biochemical reaction systems as programs and on the use of concepts and tools from Computer Science to master the complexity of cell processes. Unlike most programs, biochemical computation involves state transitions that are stochastic rather than deterministic, continuous-time rather than discrete-time, poorly localized in compartments instead of well-structured in modules, and created by evolution instead of by rational design. The course will address fundamental research issues in Computer Science about the interplay between structure and dynamics in large interaction networks, and on the mixed continuous (analog) and discrete (digital) computation model of biochemical networks.

Slides of Fran├žois Fages (12h) and practical work (TDs) with BIOCHAM-4 notebooks online at

18 Jan 2019:

25 Jan 2019:

1 Fev 2019:

8 Feb 2019:

1 March 2019: written examination (March 19, correction)

(8 March 2019: oral presentation of Kappa projects)

Previous course C2-19 Computational Methods for Systems Biology and Synthetic Biology