Master 2 course C2-19 Biochemical Programming

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

Over the past two decades, 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.

Tentative schedule 2025:

20 Jan 2025 12.455-15.45 room 1004

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

27 Jan. room 1004

3 Feb.

10 Feb.

17, 24 Feb.

  • Break

3 March: final written examination

  • Written examination of both parts of the course (50%-50% grade)
  • Every electronic device disallowed
  • Any printed document allowed

Previous written examinations with solutions: