Parisian Master of Research in Computer Science
Master Parisien de Recherche en Informatique (MPRI)

Biochemical Programming (24h, 3 ECTS)

Coordinator: François Fages.

Teachers in 2019-2020

Aims

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.

Evaluation

The evaluation is composed of one written examination and one project. Previous exams are available on teachers' pages (see the course handouts section below). For the written examination, all non-electronic documents are allowed.

Course outline

1. Protein interaction calculus (Jean Krivine, 12h)

  • Introduction to biological models and rule-based modeling in the Kappa-calculus
  • Scalable stochastic simulation algorithm, introduction to the KaSim tool.
  • Theoretical computer science techniques applied to bio modeling: causality analysis, static analysis.
  • Advanced modeling: the compartmentalization issue.

2. Chemical reaction network (CRN) programming (François Fages, 12h)

  • Introduction to the Biochemical Abstract Machine tool Biocham-4
  • Hierarchy of semantics: differential (ODE), stochastic (CTMC), discrete (Petri net), Boolean
  • Turing completeness of continuous CRNs and compilation of mixed analog/digital programs
  • Behavioral specifications in (quantitative) temporal logic, model-checking and model synthesis

Course handouts

Course handouts can be found here:

French and English

The lectures will be given in English upon request. All slides, documents and the examination subjects will be in English.

Related courses

2.11.1 Approximation Algorithms & molecular programming 2.06.1 Abstract interpretation 2.29.1 Graph algorithms 2.35.1 Constraint programming 2.03.1 Concurrency

Prerequisites

Knowledge in formal methods in computer science and in differential calculus are useful but not a prerequisite.

There is no prerequisite in Biology, the basics of cell biology will be introduced as needed through examples all along the course.

Pedagogic team

F. Fages DR Inria Saclay-Ile de France
J. Krivine CR CNRS Paris 7

Tentative calendar

On Fridays 12.45-15.45

Dec 6 JK 1
Dec 13 JK 2
Dec 20 JK 3
Dec 21 - Jan 5 Christmas vacations
Jan 10 JK 4
Jan 17 FF 1
Jan 24 FF 2
Jan 31 FF 3
Feb 7 FF 4
Feb 14 Break
Feb 20 Break
Feb 28 Written exam: all printed documents allowed, any electronic device disallowed
Mar 7 Oral presentation of projects

Bibliography

  • Computational systems biology. H. Kitano, Nature, 420(6916), pp. 206-210, 2002.
  • Rule Based Modelling of Cellular Signalling. V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine. Proceedings of CONCUR’07 : 18th International Conference on concurrency theory. Springer-Verlag, LNCS 4703, 2007.
  • Artificial Intelligence in Biological Modeling. F. Fages. In A Guided Tour of Artificial Intelligence Research. Springer-Verlag, to appear. ( pdf)
  • Cells as Machines: towards Deciphering Biochemical Programs in the Cell. F. Fages and S. Soliman. In Proc. 10th International Conference on Distributed Computing and Internet Technology ICDCIT'14, pages 50–67, volume 8337 of Lecture Notes in Computer Science. Springer-Verlag, 2014. ( pdf)
  • Formal cell biology in BIOCHAM. F. Fages and S. Soliman, 8th International School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology, Springer-Verlag, LNCS 5016, 2008. ( pdf)
  • Synthetic biology: New engineering rules for an emerging discipline. E. Andrianantoandro, S. Basu, D. Karig, and R. Weiss, Molecular Systems Biology, 2006.
  • La révolution transhumaniste, comment la technomédecine et l'uberisation du monde vont bouleverser nos vies. L. Ferry. Plon, 2016.

Previous years

Some former students of this course who continued working in Computational Systems Biology:

  • 2004-2005: Jean Krivine, CNRS Paris-Diderot; Colas Le Guernic, New York University;
  • 2005-2006: Sylvain Pradalier, Dassault-Systèmes; Fabien Tharissan, MdC UPMC;
  • 2006-2007: Aurélien Rizk, Paul Sherrer Institute Zurich;
  • 2008-2009: Steven Gay, Univ. Louvain la Neuve; Laurent Bulteau, Univ. Nantes;
  • 2011-2012: Guillaume Madelaine, Univ. Lille;
  • 2013-2014: Andrea Beica, ENS Paris;
  • 2014-2015: Virgile Andreani, Inria Saclay;
  • 2016-2017: Arthur Carcano, CRI Paris;
 
Universités partenaires Université Paris-Diderot
Université Paris-Saclay
ENS Cachan École polytechnique Télécom ParisTech
ENS
Établissements associés Université Pierre-et-Marie-Curie CNRS INRIA CEA