CONTRAINTES - 2012 - Annual activity report

CONTRAINTES

CONTRAINTES - 2012

Project-Team Contraintes

Members

Overall Objectives

Introduction
Highlight on modeling GPCR signaling, publication in Molecular Systems Biology with Robert Lefkowitz, recipient of the Nobel prize in Chemistry
Highlight: Cells driven by a computer, publication in PNAS

Scientific Foundations

Rule-based Modeling Languages
Constraint Solving Techniques
Formal Methods for Systems Biology
Tight Integration of In Silico and In Vivo Approaches

Application Domains

Combinatorial optimization
Computational Systems Biology

Software

BIOCHAM, biochemical abstract machine
Nicotine
STSE, spatio-temporal simulation environment
YeastImageToolkit
SBMC, systems biology model-checker
FO-CTL( $R_{lin}$ ), first-order computation tree logic over the reals
Rules2CP
SiLCC, linear concurrent constraint programming
EMoP, existential modules for Prolog
CHRat, CHR with ask and tell
CLPGUI, constraint logic programming graphical user interface

New Results

Inferring Reaction Rule Models from Ordinary Differential Equations
Petri Net Analyses of Biochemical Networks using Constraint Logic Programming
Subgraph Epimorphisms
Parameter Search with Temporal Logic Constraints
Coupled Model of the Cell Cycle and Circadian Clock
STL-based Analysis of TRAIL-induced Apoptosis
Real-time Control of Gene Expression in Yeast
Genome Engineering of Mammalian Cells: Targeted and Efficient Integration of Multi-unit Genetic Payloads
Reifying Global Constraints
Railway Time Tabling Optimization

Bilateral Contracts and Grants with Industry

Dassault-Systèmes, BioIntelligence project
KLS-Optim, Rules2Optim project
General Electric Transportation, Cifre contract

Partnerships and Cooperations

National Initiatives
European Initiatives
International Initiatives
International Research Visitors

Dissemination

Scientific Animation
Teaching - Supervision - Juries
Popularization

Bibliography

Publications of the year

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Section: Software

SBMC, systems biology model-checker

Participant : Szymon Stoma.

Systems Biology Model Checker (SBMC) is a webservice allowing to verify biological models (e.g. signaling pathways stored in SBML files) against their specifications given in Signal Temporal Logics (STL). This project aims at providing to a large audience the methods described in [21] and used to analyse extrensic apoptosis pathway. Project webpage is: SBMC .

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