The Contraintes research team
Contraintes is a project-team of Inria, located in the Paris-Rocquencourt research center. Created in March 2001, Contraintes investigates the theoretical foundations, design, implementation and applications of formal methods for mastering the complexity of complex systems in two domains: real-life combinatorial optimization problems and cell biology.
In combinatorial optimization, Contraintes develops declarative modeling languages and hybrid discrete-continuous constraint propagation algorithms for solving search problems in high dimension. We apply these techniques to bin packing, scheduling and graph problems.
In computational biology, Contraintes investigates, in collaboration with biologists, the tight integration of in silico and in vivo approaches, including the use of micro-fluidic and synthetic biology techniques. We build computational models of cell signaling, gene expression and cell cycle control.
In synergy in both domains, we develop logic-based modeling languages, abstraction and model reduction techniques, and inference and search algorithms.
Contraintes is associated to the PhD programs Sciences Mathématiques de Paris Centre and Frontiers in Life Sciences in Paris. Contraintes and the Weiss's lab for synthetic biology at MIT, USA collaborate via the TisHom associated team.
Positions available for PhD / internships / stages de Grandes Écoles et universités
A paper accepted at CP 2012
(biblio $key = 'NFMS12cp')
A paper accepted in PNAS
A paper accepted in MolSysBiol, with Robert Lefkowitz, Nobel Prize in Chemistry 2012
A paper accepted in Algorithms for Molecular Biology
Release of FO-CTL(lin) in January 2012
FO-CTL(lin) is a constraint solver for full First-Order Computation Tree Logic formulae with linear arithmetic over the reals in constrained transition systems (CTS). CTS are transition systems where both states and transitions are described with constraints.
Two papers accepted in TCS
(biblio $key = 'RBFS11tcs')
(biblio $key = 'DFRS11tcs')
A paper accepted at PPDP 2010
(biblio $key = 'Martinez10ppdp')
Release of Biocham 3 in June 2010
Biocham 3 is now available including a new SBGN graphical editor, new methods for model reduction, parameter optimization and robustness analyses w.r.t. temporal logic specifications.
A paper accepted at ECCB 2010 and in Bioinformatics
(biblio $key = 'GSF10bi')
A paper accepted at CP 2009
(biblio $key = 'FR09cp')
A paper accepted in JTB
(biblio $key = 'KSF09jtb')
A paper accepted at ISMB 2009 and in Bioinformatics
(biblio $key = 'RBFS09bi')
Release of Rules2CP and PKML in April 2009
Rules2CP is a general purpose rule-based modeling language for constraint programming. It aims at making constraint programming technology easier to use by non-programmers, by modeling combinatorial optimization problems with logical rules and elementary data structures. The Packing Knowledge Modeling Language (PKML) is a Rules2CP library dedicated to industrial bin packing problems.
A paper accepted in TCS
(biblio $key = 'FR08tcs')
A paper in a book chapter
(biblio $key = 'FS08pilp')
A paper accepted in TCS
(biblio $key = 'FS08tcs')
Release of CHRat in July 2008
The CHRat language is a modular version of the Constraint Handling Rules language CHR, called CHRat for modular CHR with ask and tell. Any constraint defined in a CHRat component can be reused both in rules and guards in another CHRat component to define new constraint solvers.
Release of Biocham 2.7 in April 2008
Biocham introduces a powerful parameter search procedures with respect to temporal logic quantitative properties, a stochastic simulator and a system for inferring conservation laws.
A paper accepted at FMSB 2008
(biblio $key = 'FS08fmsb')
IGEM 2007 foundational research prize
For its first participation to the iGEM 2007 competition organised by the MIT on synthetic biology, the French team with Aurélien Rizk was finalist and won the first prize of foundational research using Biocham.