"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

The Lifeware research team

© Inria / Photo C. Morel

Lifeware is a project-team of Inria, located in the Inria Saclay - Ile de France 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 and experimental settings 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 techniques in our research, we keep some activity purely dedicated to optimization problems, in particular on constraint programming methods for computing with partial information systems and solving NP-hard static analysis problems, and on continuous optimization methods for dealing with continuous parameters.

© Inria / Photo C. Morel

This project addresses fundamental research issues in computer science on the interplay between structure and dynamics in large interaction networks, and on mixed analog-discrete computation. We contribute to the theory of biochemical computation, and develop since 2002 a modelling, analysis and synthesis software, the Biochemical Abstract Machine, BIOCHAM. The reaction rule-based language of this system allows us to reason about biochemical reaction networks at different levels of abstraction, in the stochastic, differential, discrete, Boolean and hybrid semantics of reaction systems. 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 model building or network synthesis.

© Inria / Photo C. Morel

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 and experimentalists who deal with advanced microfluidic and synthetic biology technologies to perform accurate observations at "single cell" level, and also to implement biochemical programs in totally artificial vesicles.

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


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

Sarah M. Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger and Claudine Chaouiya, Frank T. Bergmann, Andrew Finney , Colin S. Gillespie, Tomávs Helikar and Stefan Hoops, Rahuman S. Malik-Sheriff, Stuart L. Moodie, Ion I. Moraru, Chris J. Myers and Aurélien Naldi, Brett G. Olivier, Sven Sahle , James C. Schaff, Lucian P. Smith, Maciej J. Swat, Denis Thieffry, Leandro Watanabe, Darren J. Wilkinson, Michael L. Blinov, Kimberly Begley , James R. Faeder, Harold F. Gómez, Thomas M. Hamm, Yuichiro Inagaki, Wolfram Liebermeister and Allyson L. Lister, Daniel Lucio, Eric Mjolsness and Carole J. Proctor, Karthik Raman, Nicolas Rodriguez , Clifford A. Shaffer, Bruce E. Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier-Schellersheim, Herbert M. Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C. Doyle, Michael Hucka, Richard R. Adams and Nicholas A. Allen, Bastian R. Angermann, Marco Antoniotti, Gary D. Bader, Jan vCerveny and Mélanie Courtot, Chris D. Cox, Piero Dalle Pezze, Emek Demir, William S. Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim , Johannes Eichner, Johan Elf, Lukas Endler and Chris T. Evelo, Christoph Flamm, Ronan MT Fleming , Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski , Alex Gutteridge, Damon Hachmeister, Leonard A. Harris, Benjamin D. Heavner, Ron Henkel, William S. Hlavacek, Bin Hu, Daniel R. Hyduke, Hidde Jong, Nick Juty, Peter D. Karp, Jonathan R. Karr , Douglas B. Kell, Roland Keller, Ilya Kiselev , Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause and Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M. Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T. Monteiro, Kedar Nath Natarajan and Poul MF Nielsen, Tramy Nguyen, Alida Palmisano and Jean-Baptiste Pettit, Thomas Pfau, Robert D. Phair , Tomas Radivoyevitch, Johann M. Rohwer, Oliver A. Ruebenacker, Julio Saez-Rodriguez, Martin Scharm , Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C. Sealfon and Kieran Smallbone, Sylvain Soliman, Melanie I. Stefan, Devin P. Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, 16(8):1–21, 2020. [ preprint ]

A paper published in Bioinformatics

Aghamiri, Sara Sadat, Singh, Vidisha, Naldi, Aurélien, Helikar, Tomas, Soliman, Sylvain and Niarakis, Anna. Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics, 2020. [ preprint ]

Two papers accepted at CMSB 2020

Mathieu Hemery, François Fages, Sylvain Soliman. On the Complexity of Quadratization for Polynomial Differential Equations. In CMSB'20: Proceedings of the eighteenth international conference on Computational Methods in Systems Biology, Lecture Notes in BioInformatics. Springer-Verlag, 2020. [ preprint ]

Elisabeth Degrand, François Fages, Sylvain Soliman. Graphical Conditions for Rate Independence in Chemical Reaction Networks. In CMSB'20: Proceedings of the eighteenth international conference on Computational Methods in Systems Biology, Lecture Notes in BioInformatics. Springer-Verlag, 2020. [ preprint ] [ slides ] [ video ]

Biomachines for real

Francisco Santos Schneider, Patrick Amar, Asma Bahri, Julien Espeut, Julie Baptiste, Mellis Alali, François Fages, Franck Molina. Biomachines for Medical Diagnosis. Advanced Materials Letters, 11(4):1535–1558, 2020.

Book chapter in French on Biomachines

François Fages, Franck Molina. La cellule, un calculateur analogique chimique. In Approches symboliques de la modélisation et de l'analyse des systèmes biologiques. ISTE, Ed Ltd, London, 2020. [ preprint ]

Book chapter in an encyclopedia of Artificial Intelligence

François Fages. Artificial Intelligence in Biological Modeling. In A Guided Tour of Artificial Intelligence Research, Volume III: Interfaces and Applications of AI. Springer-Verlag, 2020. [ preprint ]

Spin-off Inbio

© Inria / Photo C. Morel

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

Cepeda-Humerez, Sarah Anhala, Ruess, Jakob and Tkavcik, Gavsper. Estimating information in time-varying signals. PLoS Computational Biology, 15(9):e1007290, 2019. [ preprint ]

Ruess, Jakob, Plevska, Marovs, Guet, Cvalin C, Tkavcik, Gavsper. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology, 2019. [ preprint ]

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

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

Fages, François, Le Guludec, Guillaume and Bournez, Olivier, Pouly, Amaury. Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs. In CMSB'17: Proceedings of the fiveteen international conference on Computational Methods in Systems Biology, pages 108–127, volume 10545 of Lecture Notes in Computer Science. Springer-Verlag, 2017. [ preprint ]

A paper accepted in Science Advances

Meredith, Hannah, Andreani, Virgile, Ma, Helena , Lopatkin, Allison, Lee, Anna, Anderson, Deverick, Batt, Gregory, You, Lingchong. Applying ecological resistance and resilience to dissect bacterial antibiotic responses. Science Advances, 4(12):eaau1873, 2018. [ preprint ]

A paper published in the Journal of Theoretical Biology

Adrien Baudier, François Fages, Sylvain Soliman. Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels. Journal of Theoretical Biology, 459:79–89, 2018. [ preprint ]

A paper in cover page of Molecular Systems Biology

Alexis Courbet, Patrick Amar, François Fages, Eric Renard, Franck Molina. Computer-aided biochemical programming of synthetic microreactors as diagnostic devices. Molecular Systems Biology, 14(4), 2018. [ preprint ]

A paper in Scientific Reports

Lugagne, Jean-Baptiste, Jain, Srajan, Ivanovitch, Pierre, Ben Meriem, Zacchary, Vulin, Clément and Fracassi, Chiara, Batt, Grégory, Hersen, Pascal. Identification of individual cells from z-stacks of bright-field microscopy images. Scientific Reports, 8(1):11455, 2018.

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

François Fages, Thierry Martinez, David Rosenblueth, Sylvain Soliman. Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018. [ preprint ]

Two papers published in the same issue of Nature Communications !

Remy Chait, Jakob Ruess, Tobias Bergmiller and Gavsper Tkavcik, Cvalin Guet. Shaping bacterial population behavior through computer-interfaced control of individual cells. Nature Communications, 8(1):1535, 2017.

Jean-Baptiste Lugagne, Sebastian Sosa Carrillo and Melanie Kirch, Agnes Köhler, Gregory Batt and Pascal Hersen. Balancing a genetic toggle switch by real-time feedback control and periodic forcing. Nature Communications, 8(1):1671, 2017.

BIOCHAM v4.0 released

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

A paper accepted in Bioinformatics

Palaniappan, Sucheendra K., Bertaux, François and Pichené, Matthieu, Fabre, Eric, Batt, Gregory , Genest, Blaise. Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway. Bioinformatics, 33(13):1980–1986, 2017. [ preprint ]

A paper accepted in J. Chemical Physics

Jakob Ruess, Heinz Koeppl, Christoph Zechner. Sensitivity estimation for stochastic models of biochemical reaction networks in the presence of extrinsic variability. The Journal of Chemical Physics, 146(12):124122, 2017.

Best Paper Award at CMSB 2017 and second paper

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

Fages, François, Le Guludec, Guillaume and Bournez, Olivier, Pouly, Amaury. Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs. In CMSB'17: Proceedings of the fiveteen international conference on Computational Methods in Systems Biology, pages 108–127, volume 10545 of Lecture Notes in Computer Science. Springer-Verlag, 2017. [ preprint ]

Carcano, Arthur, Fages, François, Soliman, Sylvain. Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data. In CMSB'17: Proceedings of the fifteenth international conference on Computational Methods in Systems Biology, pages 74–90, volume 10545 of , 2017. [ preprint ]

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

Cristian Versari, Szymon Stoma, Kirill Batmatov , Artémis Llamosi, Filip Moroz, Adam Kaczmarek , Matt Deyell, Cédric Lhoussaine, P. Hersen and G. Batt. Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform. Royal Society Interface, 14, 2017.

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

Pauline Traynard, Céline Feillet, Sylvain Soliman, Franck Delaunay, François Fages. Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-alpha Up-Regulation during Mitosis. Biosystems, 149:59–69, 2016. [ preprint ]

A paper accepted at ECCB'16

Pauline Traynard, Adrien Fauré, François Fages, Denis Thieffry. Logical model specification aided by model- checking techniques: application to the mammalian cell cycle regulation. Bioinformatics, 32(17):i772-i780, 2016. [ preprint ]

A paper accepted at CMSB'16

François Fages, Thierry Martinez, David Rosenblueth, Sylvain Soliman. Influence Systems vs Reaction Systems. In CMSB'16: Proceedings of the fourteenth international conference on Computational Methods in Systems Biology, pages 98–115, volume 9859 of Lecture Notes in BioInformatics. Springer-Verlag, 2016. [ preprint ]

PhD Thesis defense of François Bertaux

Wednesday June 15th at Inria Paris.

A paper accepted in PLoS Computational Biology

A. Llamosi, A.M. Gonzales-Vargas, E. Cinquemani , G. Ferrari-Trecate, P. Hersen, G. Batt. What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast. PLOS Computational Biology, 9(12), 2016.

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

Tai-Yin Chiu, Hui-Ju K. Chiang, Ruei-Yang Huang , Jie-Hong R. Jiang, François Fages. Synthesizing Configurable Biochemical Implementation of Linear Systems from Their Transfer Function Specifications. PLoS ONE, 10(9):e0137442, 2015.

PhD Defense of Steven Gay

May 26, 2015, University Paris-DIderot.

A paper accepted in ACM TOMACS

Hui-Ju Chiang, François Fages, Jie-Hong Jiang, Sylvain Soliman. Hybrid Simulations of Heterogeneous Biochemical Models in SBML. ACM Transactions on Modeling and Computer Simulation (TOMACS), 25(2):14:1–14:22, 2015. [ preprint ]

A paper accepted in Constraints

Faten Nabli, Thierry Martinez, François Fages, Sylvain Soliman. On Enumerating Minimal Siphons in Petri nets using CLP and SAT solvers: Theoretical and Practical Complexity. Constraints, 21(2):251–276, 2016. [ preprint ]

Xavier Duportet laureate of Doctors-Entrepreneurs awards

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

A paper accepted in PLoS Computational Biology

F. Bertaux, S. Stoma, D. Drasdo, G. Batt. Modeling dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance. PLoS Computational Biology, 10(10):e1003893, 2014.

A paper accepted in Algorihms for Molecular Biology

Sylvain Soliman, François Fages, Ovidiu Radulescu. A constraint solving approach to model reduction by tropical equilibration. Algorithms for Molecular Biology, 9(24), 2014.

PhD Defense of David Fournier

November 27th 2014, University Paris-Diderot

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

Pauline Traynard, François Fages, Sylvain Soliman. Trace Simplifications preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock. In CMSB'14: Proceedings of the twelth international conference on Computational Methods in Systems Biology, pages 114–128, Lecture Notes in BioInformatics. Springer-Verlag, 2014. [ preprint ] [ slides ]

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:

François Fages. Cells as Machines: towards Deciphering Biochemical Programs in the Cell (Invited Talk). In Proc. 10th International Conference on Distributed Computing and Internet Technology ICDCIT'14, pages 50–67, volume 8337 of Lecture Notes in Computer Science. Springer-Verlag, 2014. [ preprint ]

A paper accepted in TCS

François Fages, Steven Gay, Sylvain Soliman. Inferring Reaction Systems from Ordinary Differential Equations. Theoretical Computer Science, 599:64–78, 2015. [ preprint ]

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

Steven Gay, François Fages, Thierry Martinez, Sylvain Soliman, Christine Solnon. On the subgraph Epimorphism Problem. Discrete Applied Mathematics, 162:214–228, 2014. [ preprint ]

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

Sylvain Soliman. A stronger necessary condition for the multistationarity of chemical reaction networks. Bulletin of Mathematical Biology, 75(11):2289–2303, 2013. [ preprint ]

A paper accepted in PLoS Computational Biology

Szymon Stoma, Alexandre Donzé, François Bertaux, Oded Maler, Grégory Batt. STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification. PLoS Computational Biology, 9(5):e1003056, 2013.

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

Faten Nabli, François Fages, Thierry Martinez, Sylvain Soliman. A Boolean Model for Enumerating Minimal Siphons and Traps in Petri-nets. In Proceedings of CP'2012, 18th International Conference on Principles and Practice of Constraint Programming, pages 798–814, volume 7514 of Lecture Notes in Computer Science. Springer-Verlag, 2012. [ preprint ] [ slides ] [ poster ]

A paper accepted in PNAS

Jannis Uhlendorf, Agnés Miermont, Thierry Delaveau, Gilles Charvin, François Fages and Samuel Bottani, Gregory Batt, Pascal Hersen. Long-term model predictive control of gene expression at the population and single-cell levels. Proceedings of the National Academy of Sciences USA, 109(35):14271–14276, 2012.

A paper accepted in MolSysBiol, with Robert Lefkowitz, Nobel Prize in Chemistry 2012

Domitille Heitzler, Guillaume Durand, Nathalie Gallay, Aurélien Rizk, Seungkirl Ahn, Jihee Kim, Jonathan D. Violin, Laurence Dupuy and Christophe Gauthier, Vincent Piketty, Pascale Crépieux, Anne Poupon, Frédérique Clément, François Fages, Robert J. Lefkowitz, Eric Reiter. Competing G protein-coupled receptor kinases balance G protein and β-arrestin signaling. Molecular Systems Biology, 8(590), 2012.

A paper accepted in Algorithms for Molecular Biology

Sylvain Soliman. Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem. Algorithms for Molecular Biology, 7(15), 2012.

Release of FO-CTL(ℝlin) in January 2012

FO-CTL(ℝlin) 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

Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. Continuous Valuations of Temporal Logic Specifications with applications to Parameter Optimization and Robustness Measures. Theoretical Computer Science, 412(26):2827–2839, 2011. [ preprint ]

Elisabetta De Maria, François Fages, Aurélien Rizk, Sylvain Soliman. Design, Optimization, and Predictions of a Coupled Model of the Cell Cycle, Circadian Clock, DNA Repair System, Irinotecan Metabolism and Exposure Control under Temporal Logic Constraints. Theoretical Computer Science, 412(21):2108–2127, 2011. [ preprint ]

A paper accepted at PPDP 2010

Thierry Martinez. Semantics-preserving translations between Linear Concurrent Constraint Programming and Constraint Handling Rules. In Proceedings of PPDP'10, International Conference on Principles and Practice of Declarative Programming, Edinburgh, UK, pages 57–66. ACM, 2010. [ preprint ]

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

Steven Gay, Sylvain Soliman, François Fages. A Graphical Method for Reducing and Relating Models in Systems Biology. Bioinformatics, 26(18):i575–i581, 2010.

A paper accepted at CP 2009

François Fages, Aurélien Rizk. From Model-Checking to Temporal Logic Constraint Solving. In Proceedings of CP'2009, 15th International Conference on Principles and Practice of Constraint Programming, pages 319–334, Lecture Notes in Computer Science. Springer-Verlag, 2009. [ preprint ]

A paper accepted in JTB

Sriram Krishnamachari, Sylvain Soliman, François Fages. Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans. Journal of Theoretical Biology, 258(1):71–88, 2009. [ preprint ]

A paper accepted at ISMB 2009 and in Bioinformatics

Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics, 12(25):il69–il78, 2009.

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

François Fages, Aurélien Rizk. On Temporal Logic Constraint Solving for the Analysis of Numerical Data Time series. Theoretical Computer Science, 408(1):55–65, 2008. [ preprint ]

A paper in a book chapter

François Fages, Sylvain Soliman. Model Revision from Temporal Logic Properties in Systems Biology. In Probabilistic Inductive Logic Programming, pages 287–304, volume 4911 of Lecture Notes in Computer Science. Springer-Verlag, 2008. [ preprint ]

A paper accepted in TCS

François Fages, Sylvain Soliman. Abstract Interpretation and Types for Systems Biology. Theoretical Computer Science, 403(1):52–70, 2008. [ preprint ]

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

François Fages, Sylvain Soliman. Formal Cell Biology in BIOCHAM. In 8th Int. School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology SFM'08, pages 54–80, volume 5016 of Lecture Notes in Computer Science. Springer-Verlag, 2008. [ preprint ]

A paper accepted at FMSB 2008

François Fages, Sylvain Soliman. From reaction models to influence graphs and back: a theorem. In Proceedings of Formal Methods in Systems Biology FMSB'08, Lecture Notes in Computer Science. Springer-Verlag, 2008. [ preprint ]

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).