Lectures on Computational Systems Biology

François Fages
EPI Contraintes, Inria Paris-Rocquencourt

Formal Cell Biology in BIOCHAM (tutorial) by François Fages and Sylvain Soliman.

8th International School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology.
In memory of Nadia Busi.
Bertinoro, Italy. Springer-Verlag, LNCS 5016. Mar. 2008.(pdf)

Master Course M2, C2-19, Master Parisien de Recherche en Informatique MPRI, Paris

Web page of the course C2-19 at MPRI.
Wiki of the course.

Slides of François Fages's lectures (12h) :

14/10/13:
Introduction (pdf, video at Collège de France)
Formal objects and reactions (pdf)
Cell signaling (pdf)
Exercise to do for the next course: use biocham-web or install Biocham on your machine, and play with the examples cell\_cycle\_Tyson\_6Var/tyson91.bc and kinetics/mapk.bc
21/10/13:
Kinetic models (pdf)
Reaction and influence graphs (pdf)
Model reductions (pdf)
Exercise to do for the next course: Solve in Biocham the 2011 examination (subject)
28/10/13:
Hierarchy of formalisms by abstract interpretation (pdf)
Type inference by abstract interpretation
Model checking of biochemical networks (pdf)
4/11/13:
Quantitative properties in temporal logic LTL(R) (pdf)
Parameter search with temporal logic constraints QFLTL(R) (pdf)
Protein structure prediction by constraint logic programming (pdf)
Perspectives (pdf)
25/11/13, 2/12/13:

Wiki

3/3/14: final examination

Examinations: Mar. 2013, Mar. 2012, Feb. 2011, Nov. 2009, Nov. 2008, Nov. 2007, Nov. 2006.

Slides of Denis Thieffry lectures (12h) :

17/1, 24/1:
Logical modelling of developmental regulatory networks (pdf)
31/1:
Discrete dynamics of biological networks: focus on the regulatory circuits (pdf)
7/2:
Logical modelling of T-helper cell differentiation (pdf)

2007 news: For its first participation, the French team was finalist and won the first prize of foundational research at the MIT iGEM 2007 competition on synthetic biology using Biocham

ICSB'10 Tutorial "New Computational Methods for Systems Biology"

Edinburgh, UK, October 10, 2010.

Slides of François Fages's tutorial (4h):

Rule-based modeling of biochemical systems
Reaction graphs and influence graphs
Demonstration of Biocham by Sylvain Soliman
Temporal Logic formalization of biological properties
Continuous satisfaction degree of temporal properties
Conclusion

Ecole Jeunes Chercheurs "Modélisation formelle de réseaux de régulation biologique"

île de Porquerolles, 6-11 juin 2010, 24-28 juin 2013.

Slides of François Fages's lectures (8h):

Lectures on Computational Methods for Systemic and Synthetic Biology