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home members research publications software contact lifeware computational systems biology and optimization "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 in paris. 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. © inria / photo c. morel 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. 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 tight collaborations with biologists and experimentalists. furthermore, half of lifeware is in the inbio group at institut pasteur headed by grégory batt who develops an experimental platform for the closed-loop control of intracellular processes . this platform combines hardware (microfluidic device and microscope), software (cell tracking and model-based predictive control algorithms) and liveware (genetically modified living cells). the originality of this project thus also deals with the recourse to advanced microfluidic and synthetic biology technologies to perform accurate observations, modi fications and real-time control at both single cell and cell population levels. © inria / photo c. morel for this to work, collaborations with top international leaders of these techniques have been established, and consolidated with student exchange programs, especially in the framework of the doctorate school frontiers in life sciences to which we are affiliated, in addition to the doctorate school sciences et technologies de l'information et de la communication (stic) . highlights 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 y
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