Citation Context

...works often involves posing the question if the hypothesized structure of a regulatory network is consistent with the observed behavior, or if a proposed structure can generate a desired behavior. In =-=[3]-=-, we recast the above questions into a parameter search problem for qualitative models of regulatory networks. We develop a method based on symbolic model checking that avoids enumerating all possible...

Citation Context

...lance analysis, graphbased analyses, chemical organization theory, etc.). They do not rely on kinetic information but require a well-defined structure as stochastic analysis techniques equally do. In =-=[9]-=-, we look into the structure inference problem for a model described by a system of Ordinary Differential Equations and provide conditions for the uniqueness of its solution. We describe a method to e...

Citation Context

...race, and use it as a fitness function in continuous optimization methods 2 in order to find unknown parameter values in a model satisfying a set of biological properties formalized in temporal logic =-=[8]-=-. This approach is heavily used in BIOCHAM for inferring unknown kinetic parameter values, initial concentrations, and/or control parameters from a formalization of the global behavior of the system i...

Citation Context

...o monitor quantitatively and dynamically many cellular processes. In contrast, it is still a challenge to perturb cellular processes - such as gene expression - in a precise and controlled manner. In =-=[26]-=-, [27], [28], we propose a first step towards in vivo control of gene expression: in real-time, we dynamically control the activity of a yeast signaling cascade thanks to an experimental platform comb...

Citation Context

...s heavily used in BIOCHAM for inferring unknown kinetic parameter values, initial concentrations, and/or control parameters from a formalization of the global behavior of the system in temporal logic =-=[7]-=-, [6], [15]. Following this route, similar metrics and methods are currently developed for stochastic processes [35]. Consistency techniques for hybrid ODE-stochastic simulations are also studied in t...

Citation Context

...int entailment. In particular, the Constraint Simplification Rules (CSR) subset of CHR and the flat subset of LCC, where agent nesting is restricted, are very close syntactically and semantically. In =-=[13]-=-, we analyze these similarities by providing translations between CSR and flat-LCC, on the one hand, and a transformation from the full LCC language to flat-LCC, on the other hand. This transformation...

Citation Context

...vain Soliman. In Systems Biology, very few analyses permit to extract information about the dynamics of quantitative models lacking precise parameter values, when pure symbolic computations fails. In =-=[14]-=-, [25], we present a way to generalize well-known results about the steady-state analysis of some symbolic Ordinary Differential Equations systems by taking into account the structure of the reaction ...

Citation Context

...differents fields of activity like software engeneering, rule based systems and resolution, learning in context, or personal experience storing systems. The state of this work is regularly updated on =-=[40]-=-. We worked on two main points: the development of a versatile tracer of CHR v with several extensions, in the framework called CHROME-REF (see TODAS project) and an application field we called “exo-m...

Citation Context

... and deactivation through amplified enzymatic processes. These results convincingly illustrate the value of using computational modeling to decipher the complex signaling mechanisms elicited by 7TMRs =-=[1]-=-. This approach is applied more generally to G protein-coupled receptor signaling which is of great importance in pharmacology. 6.10. Control of the HOG signaling cascade Participants: Grégory Batt, F...

Citation Context

...I SISYPHE, and Eric Reiter, INRA Tours, aims at understanding the structure and the dynamics of FSH and angiotensine signal transduction in mammalian cells. Our article submitted to Science Signaling =-=[6]-=- concludes our fruitful interactions done in the INRA AgroBi project INSIGHT (2006-2009) and in the AE REGATE. Control of gene expression and synthetic biology. This research lead in the team by Grégo...

Citation Context

...used in BIOCHAM for inferring unknown kinetic parameter values, initial concentrations, and/or control parameters from a formalization of the global behavior of the system in temporal logic [7], [6], =-=[15]-=-. Following this route, similar metrics and methods are currently developed for stochastic processes [35]. Consistency techniques for hybrid ODE-stochastic simulations are also studied in this perspec...

Citation Context

...anguage is its capability to express complex search strategies, by defining search trees with logical formulae and heuristic choice criteria by pattern matching on rule lefthand sides’ derivation. in =-=[29]-=-, we study a new compilation scheme for Rules2CP which allows us to deal with dynapmic ordering criteria and to generate procedural constraint programming code instead of flattened constraints. The co...

Citation Context

...inez. Rules2CP [33] is a rule-based modeling language which allows easy modeling of constraint satisfaction problems, together with specifications for search strategies and heuristic choice criterias =-=[2]-=-. The expressiveness and effectiveness of Rules2CP have been illustrated through the development of the Packing Knowledge Modeling Language PKML as a library on top of Rules2CP, dedicated to bin packi...

Citation Context

...d separately. These techniques are however far too restrictive to be applied on a large scale in systems biology, and do not take into account abstractions other than time or phase decompositions. In =-=[5]-=-, we propose a general computational method for relating models together, by considering primarily the structure of the interactions and abstracting from their dynamics in a first step. We present a g...

Citation Context

... on two main points: the development of a versatile tracer of CHR v with several extensions, in the framework called CHROME-REF (see TODAS project) and an application field we called “exo-memory”. In =-=[10]-=- we present an experimentation with a continuously updated textual exo-memory used to assist the natural memory of a subject. It is shown how trace theory could be used to improve the device. Main cha...

Citation Context

...lowing this route, similar metrics and methods are currently developed for stochastic processes [35]. Consistency techniques for hybrid ODE-stochastic simulations are also studied in this perspective =-=[16]-=-. 6.7. Parameter Inference for Qualitative Models of Regulatory Networks Participant: Grégory Batt. Investigating the relation between the structure and behavior of complex biological networks often i...

Citation Context

...issue. 5.1. BIOCHAM Participants: François Fages, Dragana Jovanovska, Aurélien Rizk, Sylvain Soliman. The Biochemical Abstract Machine BIOCHAM [32] is a modeling environment for systems biology [39], =-=[17]-=-, under development since 2001, and distributed as open-source since 2003. Current version is v3.2. BIOCHAM uses a compositional rule-based language for modeling biochemical systems, allowing patterns...

Citation Context

... even reaction rules from temporal logic properties; automatic detection of invariants, through constraint-based analysis of the underlying Petri net; • an SBGN-compatible reaction graph editor [21], =-=[20]-=-. BIOCHAM is implemented in GNU-Prolog and interfaced to the symbolic model checker NuSMV and to the continuous optimization tool CMAES developed by the EPI TAO. 5.2. Rules2CP Participants: François F...

Citation Context

...ns and even reaction rules from temporal logic properties; automatic detection of invariants, through constraint-based analysis of the underlying Petri net; • an SBGN-compatible reaction graph editor =-=[21]-=-, [20]. BIOCHAM is implemented in GNU-Prolog and interfaced to the symbolic model checker NuSMV and to the continuous optimization tool CMAES developed by the EPI TAO. 5.2. Rules2CP Participants: Fran...

Citation Context

...atient characterictics. This is at the heart of our participation in the EraNet SysBio project C5Sys, follow up of the former EU STREP project TEMPO, in collaboration with the EPI BANG. In [7], [22], =-=[23]-=- we show how temporal logic constraints, and the new features of BIOCHAM for parameter search (running on a cluster of 10000 processors at the GENCI) can be used to couple dynamical models in high dim...

Citation Context

...oliman. In Systems Biology, very few analyses permit to extract information about the dynamics of quantitative models lacking precise parameter values, when pure symbolic computations fails. In [14], =-=[25]-=-, we present a way to generalize well-known results about the steady-state analysis of some symbolic Ordinary Differential Equations systems by taking into account the structure of the reaction networ...

Citation Context

...geometry constraints with rules to express physical, common sense and packing business constraints to solve packing problems in the context of warehouse management systems for the automotive industry =-=[30]-=-. In this context, we have developed a rule-based modeling language, called Rules2CP, to express requirements in a declarative and flexible manner. and compile them to efficient constraint programs us...

Citation Context

...rameters from a formalization of the global behavior of the system in temporal logic [7], [6], [15]. Following this route, similar metrics and methods are currently developed for stochastic processes =-=[35]-=-. Consistency techniques for hybrid ODE-stochastic simulations are also studied in this perspective [16]. 6.7. Parameter Inference for Qualitative Models of Regulatory Networks Participant: Grégory Ba...

Citation Context

...od is then illustrated on some models of the Biomodels repository. Some other links between Petri nets and various Systems Biology modelling formalisms are studied in the framework of the ANR CALAMAR =-=[36]-=- leading, among other things, to the definition of conditions for the uniqueness of the mapping from differential equations to a structured model. Indeed, structure-related qualitative analysis techni...

Citation Context

...s Fages (6h), Thierry Martinez (3h). M2 course C2-19 on Computational Methods for Systemic and Synthetic Biology, Master Parisien de Recherche en Informatique (MPRI) François Fages (responsible, 12h) =-=[41]-=-, Grégory Batt (12h), Denis Thieffry (12h). M2 course on Computational Biology, Master Approches Interdisciplinaires du Vivant (AIV), Grégory Batt (24h). Cell Systems Biology master curriculum at the ...