Modeling and Analysis of Gene Regulatory Networks - Modeling in Computational Biology and Biomedicine - page 75

SMBioNet (Selection of Models of Biological Networks)
http://www.i3s.unice.fr/ ∼ richard/smbionet
Modeling and model-checking analysis of GRN, based on a discrete, logical
formalism (see Sect. 2.3.2.4 ).
The Biochemical Abstract Machine BIOCHAM
http://contraintes.inria.fr/BioCham
A modeling environment for systems biology, with features for inferring unknown
model parameters from temporal logic constraints.
SBML (Systems Biology Markup Language)
http://sbml.org/Main Page
A standard formalism for the construction and exchange of computer models of
biological processes.

Acknowledgements It is a pleasure for GB, JPC and AR to thank the biologist Janine Guespin-
Michel, who has actively participated to the definition of our formal logic methodology in such a
way that our techniques from computer science and the SMBioNet software become truly useful
for biologists. She has also been at the origin of the Pseudomonas aeruginosa hypothesis. The
authors would also like to thank F. Cazals for his remarks and careful reading of the chapter.

List of Acronyms

DNA Deoxyribose Nucleic Acid

mRNA messenger Ribonucleic Acid

GRN Gene Regulatory Networks

PWA Piecewise affine

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