Lectures on Computational Systems Biology

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

François Fages, Vincent Schächter
Grégory Batt, Jean Krivine

2009-2010

Web page of the course C2-19 at MPRI.

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)

Slides of François Fages's lectures (2009-2010):

Introduction (video at Collège de France)
Formal molecules and reaction rules in BIOCHAM
Continuous dynamics. Kinetic models (corrected version)
Qualitative properties formalized in temporal logic CTL (corrected version)
Quantitative properties in LTL(R) and pLTL(R)
Reaction hypergraphs and influence graphs
Hierarchy of semantics and typing by abstract interpretation
Parameter optimization w.r.t. QFLTL(R) properties
Robustness analysis w.r.t. QFLTL(R) properties
TP Biocham. Biocham v2.9 for Mac OS. Biocham's reference manual (html, pdf)
Protein structure prediction

Examinations: Nov. 2009, Nov. 2008, Nov. 2007, Nov. 2006.

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

Slides of 2007-2008.

Computational Methods for Systemic and Synthetic Biology