Master 2 course 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 addresses 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

  • Introduction to Chemical Reaction Networks (CRNs) pdf - mp4
  • Abstract interpretation of CRNs: hierarchy of semantics, typings pdf - mp4

1er Feb 2022 16h15-19h15

8 Feb 2022 16h15-19h15

15 Feb 2022 16h15-19h15

22 Feb 2022 Break

1 Mar 2022 Break (changed!)

8 Mar 2022 16h15-19h15 room 1002

  • Written examination for both parts of the course (50%-50% grade)

Previous written examinations with solutions: March 2022, (March 2021 programming/modeling project), March 2020, March 2019, (March 2018 programming/modeling project), Feb 2017, Nov 2015 (plus March 2016 programming/modeling project), Feb 2015, Mar. 2014, Mar. 2013, Mar. 2012, Feb. 2011, Nov. 2009, Nov. 2008, Nov. 2007, Nov. 2006.

Previous course up to 2017 and summer schools

C2-19 Computational Methods for Systems Biology and Synthetic Biology