Course handouts C2-19 Biochemical Programming 2020-2021

Master Parisien de Recherche en Informatique University Paris Diderot, UPMC, Paris-Saclay, X, ENS (pedagogical server)

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.

The lectures of François Fages will be given by visioconference on Zoom with instructions sent by email (the session will open at 4pm and will close at 7.15)

18 Jan 2022 Break

25 Jan 2022 16h15-19h15

1er Feb 2022 16h15-19h15

8 Feb 2022 16h15-19h15

15 Feb 2022 16h15-19h15

22 Feb 2022 Break

1 Mar 2022: Written examination

Previous year 2020-2021

The lectures will contain practical work (TDs) online using BIOCHAM-4 notebooks at

  • at the end of each TD, please send your notebook with your answers by email to
  • you can send a second version of your notebook with your answers to the questions not treated during the TDs by the next week-end.
  • you are welcomed (and even encouraged to break loneliness) to work with a binomial with the only constraint of changing of binomial every week
  • your grade will be the mean of your scores for the TDs.

19 Jan 2021:

2 Feb 2021:

9 Feb 2021:

16 Feb 2021:

Previous written examinations with solutions: March 2020, March 2019, Feb 2017, Nov 2015, Feb 2015, Mar. 2014, Mar. 2013, Mar. 2012, Feb. 2011, Nov. 2009, Nov. 2008, Nov. 2007, Nov. 2006.

Previous year 2019-2020

24 Jan 2020:

31 Jan 2020:

7 Feb 2020:

14 Feb 2020: Jean Krivine

21 Feb 2020:

28 Feb 2020: written examination 13h00-15h00

6 March 2020: oral presentation of Kappa projects

Previous course up to 2017

 C2-19 Computational Methods for Systems Biology and Synthetic Biology