"Computer Science is no more about computers than astronomy is about telescopes." Edsger Dijkstra	"C'est aux algorithmes du monde vivant que s'intéresse aujourd'hui la biologie." François Jacob
"Le contraire de la recherche fondamentale ce n'est pas la recherche appliquée, c'est la recherche superficielle." Gilles Kahn

The Lifeware research team

Lifeware is a project-team of Inria, located in the Inria Saclay Center (formerly in Paris-Rocquencourt until January 2016) on the campus of Ecole Polytechnique in Palaiseau (and at Pasteur Institute until the creation of EPC Inbio at Inria Paris in January 2020).

Created in January 2014, as a follow-up of the Contraintes project-team, Lifeware aims at developing formal methods for understanding the cell machinery and establishing computational paradigms in cell biology. It is based on the vision of cells as machines, biochemical reaction networks as programs, and on the use of concepts and tools from computer science to master the complexity of cell processes.

Because of the importance of optimization problems in our research, we keep some research and teaching activity on Constraint Logic Programming for computing with partial information systems and practically solving NP-hard problems.

This project addresses fundamental research issues in computer science on the interplay between structure and dynamics in chemical reaction networks, and on their automated design. We contribute to a computational theory of chemical reaction networks (CRN), and develop since 2002 a CRN modelling, analysis and synthesis software, the Biochemical Abstract Machine, BIOCHAM (see also Inria Saclay showroom). The reaction rule-based language of this system allows us to reason about CRNs at different levels of abstraction, in their stochastic, differential, discrete, Boolean and graphical interpretations. We develop a variety of static analysis methods before going to simulations and dynamical analyses. We use quantitative temporal logics as a mean to formalise biological behaviours with imprecise data and to constrain CRN model building.

A tight integration between dry lab and wet lab efforts is also essential for the success of the project. This is achieved through long-term collaborations with biologists, pharmacologists and physicians who deal with advanced robotic, microfluidic and synthetic biology technologies to perform accurate observations at "single cell" level, and also to implement CRN programs in artificial devices for medical purposes.

Collaborations with top international leaders are established, and consolidated with student exchange programs, especially in the framework of the Institut Polytechnique de Paris.

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Highlights

Paper published in Mathematical BIosciences

The place to be: our favourite conference CMSB we organised this year in Lyon CMSB 2025

next year CMSB 2026 will be associated to FLOC 2026, LIsbon, Portugal, July 2026.

François Fages recipient of the Skolem award of the 30th CADE conference 2025

Test of time award for his paper

La thèse d'Alexandre Tan -Lhernould en 180s

c'est sur https://youtu.be/rotHmlgq9DU?t=2286

Computational Systems Biology results based on Constraint Logic Programming

Back to Logic Programming future

Workshop for the HDR defense of Jakob Ruess on March 18-19th 2024

Three articles in TCS's special issue on Foundational Methods in Systems Biology:

Paper in Journal of Chemical Physics

Marine Collery PhD thesis public defence, October 12th 2023, 2pm, Amphi Sophie Germain, Build. Alan Turing, Inria Saclay

Expressive classification rule learning with an emphasis on learning from sequential data.

Sahar Aghakhani PhD thesis public defence, September 22nd 2023 2pm, G2 Building, CEA Évry

Computational modeling of metabolic reprogramming in rheumatoid arthritis synovial fibroblasts and cancer-associated fibroblasts

Back to Constraint Programming conference

PhD graduation ceremony at Institut Polytechnique de Paris

to which we contributed for 3/251 PhD theses in 2022 with Dr Eléa Thibault-Greugny, Dr Jeremy Grignard and Dr Julien Martinelli

Three weeks meeting on Building Immune Digital Twin co-organized by Anna Niaraki

a fantastic exchange forum between life sciences and computational science at Institut Pascal, University Paris Saclay.

A paper presented at ICLR 2023

Mathieu Hemery at SIAM Computational Science in Engineering

presenting our approach to quadratization problems and their implementation in BIOCHAM

Jakob Ruess back to Lifeware !

where Jakob will develop his ERC starting grant BridgingScales project, welcome back !

Prolog 50th anniversary Symposium Paris Nov 10th 2022 small video

Document on the history of ISO Standard of Prolog to which our ancestor Inria project-teams Loco and Contraintes participated at Inria Rocquencourt.

As an example of current use of Prolog, it is worth noting that our cutting-edge CRN modelling, analysis and synthesis software BIOCHAM is implemented in Prolog, for several good reasons (rapid prototyping, constraint solving libraries, symbolic computation, easy parsing and syntax tree manipulation).

Paper published in PLOS computational biology

Elea Thibault-Greugny PhD thesis public defence, October 4th 2022 2pm,

3 papers accepted at our favourite conference CMSB

Best Paper Award given to the first:

Jeremy Grignard PhD thesis public defence, June 17th 2022 2pm

A paper with Servier accepted at PLOS Computational Biology

Julien Martinelli PhD thesis defense, Feb 18th 2022

Jeremy Grignard on France Culture, Jan12th 2021.

 Genomique et IA (from 40mn48s)

The COVID19 disease map: a Bioinformatics feat ! published in Mol. Sys. Biol.

An article presented at ECCB 2021, published in Bioinformatics

A paper accepted at CMSB 2021 and CASC 2021

A paper published in Cancers

An article on SBML 3, the latest version of the Systems Biology Markup Language standard

A paper published in Bioinformatics

Two papers accepted at CMSB 2020

Biomachines for real

Book chapter on Biomachines

Book chapter in an encyclopedia of Artificial Intelligence

Spin-off Inbio

Inbio has now officially left our group to create a new research group of the Inria Paris research centre at Pasteur Institute

Two papers in PLOS Computational Biology from InBIo group

Prix La Recherche 2019 F. Fages with O. Bournez LIX next floor

We are very honoured to receive the 2019 Prix La Recherche - science de l'information for our article (best paper award CMSB 2017) [slides]:

A paper accepted in Science Advances

A paper published in the Journal of Theoretical Biology

A paper in cover page of Molecular Systems Biology

A paper in Scientific Reports

A paper accepted in IEEE/ACM Transactions on Computational Biology and Bioinformatics

Two papers published in the same issue of Nature Communications !

BIOCHAM v4.0 released

complete rewriting of BIOCHAM with online notebooks, short tutorial and historical tutorial

A paper accepted in Bioinformatics

A paper accepted in J. Chemical Physics

Best Paper Award at CMSB 2017 and second paper

The first one solving a long standing open problem in chemical reaction network theory

InBio starts!

InBio is an Inria/Pasteur research group created in Feb 2017 and headed by Grégory Batt.

CellStar paper published in Royal Society Interface

PhD Thesis of Jean-Baptiste Lugagne

13 Dec 2016 in Paris

HDR of Sylvain Soliman

7 Dec 2016 in Palaiseau

A paper accepted in Biosystems

A paper accepted at ECCB'16

A paper accepted at CMSB'16

PhD Thesis defense of François Bertaux

Wednesday June 15th at Inria Paris.

A paper accepted in PLoS Computational Biology

PhD Thesis defense of Pauline Traynard

Tuesday May 10th at ENS.

PhD Theses season

Artemis Llamosi on Tuesday 15 December and Thierry Martinez on Thursday 17 December will defend their PhD thesis !

A paper accepted in PLoS ONE

PhD Defense of Steven Gay

May 26, 2015, University Paris-DIderot.

A paper accepted in ACM TOMACS

A paper accepted in Constraints

Xavier Duportet laureate of Doctors-Entrepreneurs awards

for his PhageX project, the antibiotics of the future, congrats !!!

A paper accepted in PLoS Computational Biology

A paper accepted in Algorihms for Molecular Biology

PhD Defense of David Fournier

November 27th 2014, University Paris-Diderot

Best student paper prize at CMSB'14, congratulations Pauline !

Exceptional PhD Defense of Xavier Duportet

November 14th 2014, Pasteur Institute

Release of Biocham 3.6

New release of Biocham with new features for hybrid simulation, improved SBML-3 interface and new version of biocham-web

Keynote talk at ECAI'14

Slides (pdf, pptx), see also invited talk paper at ICDCIT'14:

A paper accepted in TCS

Laureate of the French Academy of Sciences

François Fages is very honoured to receive the Michel Monpetit prize 2014 of the French Academy of Sciences for his contributions to fundamental computer science (unification theory and constraint logic programming) and computational systems biology (modeling of biochemical networks and design and supervision of the implementation of the BIOCHAM software).

Slides (pdf, pptx) and talk in French at College de France.

A paper accepted in Discrete Applied Mathematics

HDR defense of Grégory Batt

Grégory Batt brightly defended his ''Habilitation à Diriger des Recherches" (manuscript, slides,)

An article in the Bulletin of Mathematical Biology

refining the 10 years old result of C. Soulé on feedback circuits and multistationarity

A paper accepted in PLoS Computational Biology

PhD Defense of Faten Nabli

July 10th 2013, Univ. Paris-Diderot

Release of Biocham-web in May 2013

Biocham-Web provides you access to the latest version of Biocham as a web service.

A paper accepted at CP 2012

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(ℝ_lin) in January 2012

FO-CTL(ℝ_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

A paper accepted at PPDP 2010

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

A paper accepted at CP 2009

A paper accepted in JTB

A paper accepted at ISMB 2009 and in Bioinformatics

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

A paper in a book chapter

A paper accepted in TCS

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 2.7 releases a powerful parameter search procedure with respect to temporal logic quantitative properties, a stochastic simulator and an inference system for conservation laws.

A tutorial paper at SFM 2008

A paper accepted at FMSB 2008

Grand Prize Finalist + First Place Foundational Research at iGEM 2007

For the first participation of a French team to the iGEM competition organised by the MIT on synthetic biology, the Paris team, with Aurélien Rizk using BIOCHAM, was Grand Prize Finalist plus First Place - Foundational Research (slides).