1,721,009 research outputs found
Notebooks, datasets and additional files for D-Xylose mechanistic modeling from Minipigs Datasets
No full text<p>PrmEstLOG.ipynb and PrmEst_LOG2_models.ipynb must be run with Julia 1.8.2 or 1.9.3 kernel. </p><p>Both extracting inputs from Inputs_PrmEst.ipynb <i>and</i> InputsPrmEst<i>_</i>2models.ipynb, respectively.</p><p>displayResults.ipynb displays the results to make it as readable as possible, stored in new_figs/</p>
The Hoare-fol Tool
No full textThis document presents the tool named "Application of Hoare Logic and Dijkstra's Weakest Proposition Calculus to Biological Regulatory Networks Using Path Programs with Branching First-Order Logic Operators" or Hoare-fol for short. This tool consists in an implementation of the theoretical work developed in [Bernot et al., 2019] and contains the following features: (1) computation of the weakest precondition of a Hoare triple, (2) simplification of this weakest precondition using De Morgan laws and partial knowledge on the initial state, and (3) translation into Answer Set Programming to allow a solving of all compatible solutions
The Hoare-fol Tool
No full textThis document presents the tool named "Application of Hoare Logic and Dijkstra's Weakest Proposition Calculus to Biological Regulatory Networks Using Path Programs with Branching First-Order Logic Operators" or Hoare-fol for short. This tool consists in an implementation of the theoretical work developed in [Bernot et al., 2019] and contains the following features: (1) computation of the weakest precondition of a Hoare triple, (2) simplification of this weakest precondition using De Morgan laws and partial knowledge on the initial state, and (3) translation into Answer Set Programming to allow a solving of all compatible solutions
Modélisation algébrique de la dynamique multi-échelles des réseaux de régulation biologique
Full text linkRepresenting and analyzing large biological regulatory networks arethe two main challenges of the understanding of the livingmachinery. The work we expose here focuses on discrete modeling,usually composed of graphs and sets of parameters, and especiallyon a previously developed framework called Process Hitting, whichallows to give an atomistic representation of some components andtheir combined dynamics. In this thesis, we propose several newframeworks that consist of alternatives to the Process Hitting. Theirhigher expressivity permits to integrate discrete constraints intomodels based on the knowledge of reaction durations orsynchronicity relationships. We also propose a new method toanalyze the dynamics of such models by abstract interpretationwhich allows to answer reachability questions and is well-suited tolarge-scale models (made of hundreds of components, andpotentially more). This method relies on an approximation of thedynamics that avoids the combinatorial explosion usually inherent tosuch analyses, thus answering in in tenths of a second at the priceof being sometimes inconclusive. At last, we discuss the formalbonds between the different formalisms developed in this thesis andthe link with some other widespread discrete modelings. Wepropose several translations from and to these other modelings, inorder to benefit from the high power of modeling and analysis ofthese different frameworks.La représentation et l’analyse des grands réseaux de régulationbiologique sont les deux défis majeurs dans la compréhension desmécanismes du vivant. Le travail exposé dans cette thèse seconcentre sur les modèles discrets, souvent représentés sous laforme de graphes et d’ensembles de paramètres. Il s’inspirenotamment d’un formalisme préalablement développé, appeléFrappes de Processus, qui repose sur une représentation atomiqued’un ensemble de composants et de leur dynamique. Nousproposons dans cette thèse plusieurs représentations alternatives àce formalisme, qui possèdent une plus grande expressivité. Cesreprésentations sont adaptées à l’intégration de contraintesdiscrètes dans les modèles provenant de durées relatives ou derelations de synchronisme entre certaines réactions. Nousproposons par ailleurs une méthode d’analyse de la dynamique parinterprétation abstraite qui permet de répondre à des questionsd’atteignabilité. Cette méthode est spécifiquement adaptée à l’étudedes modèles de grande taille, pouvant contenir plusieurs centainesde composants, et potentiellement davantage. Elle repose en effetsur une approximation de la dynamique qui évite ainsi l’explosioncombinatoire inhérente à ce type d’analyse, permettant de répondreen quelques dixièmes de secondes au prix d’être parfois nonconclusive. Enfin, nous traçons des liens formels entre les différentsformalismes développés dans cette thèse, ainsi qu’avec plusieursautres modélisations discrètes répandues. Nous permettons ainsi àun modèle de jouir des capacités de représentation et d’analyse deplusieurs formalismes à la fois
The Hoare-fol Tool
No full textThis document presents the tool named "Application of Hoare Logic and Dijkstra's Weakest Proposition Calculus to Biological Regulatory Networks Using Path Programs with Branching First-Order Logic Operators" or Hoare-fol for short. This tool consists in an implementation of the theoretical work developed in [Bernot et al., 2019] and contains the following features: (1) computation of the weakest precondition of a Hoare triple, (2) simplification of this weakest precondition using De Morgan laws and partial knowledge on the initial state, and (3) translation into Answer Set Programming to allow a solving of all compatible solutions
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
The Hoare-fol Tool
No full textThis document presents the tool named "Application of Hoare Logic and Dijkstra's Weakest Proposition Calculus to Biological Regulatory Networks Using Path Programs with Branching First-Order Logic Operators" or Hoare-fol for short. This tool consists in an implementation of the theoretical work developed in [Bernot et al., 2019] and contains the following features: (1) computation of the weakest precondition of a Hoare triple, (2) simplification of this weakest precondition using De Morgan laws and partial knowledge on the initial state, and (3) translation into Answer Set Programming to allow a solving of all compatible solutions
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Identifier et analyser les comportements dynamiques à long terme des réseaux de régulation génétique à l’aide de modélisation hybride
No full textUtiliser des modèles dynamiques pour révéler les propriétés dynamiques des réseaux de régulation des gènes peut nous aider à mieux comprendre la nature de ces systèmes biologiques et à développer nouveaux traitements médicaux. Dans cette thèse, nous nous concentrons sur une classe de systèmes dynamiques hybrides appelés réseaux de régulation des gènes hybrides (HGRN) et visons à analyser les propriétés dynamiques à long terme. Nous proposons des méthodes pour trouver des cycles limites et analyser leur stabilité, et pour analyser l’accessibilité dans HGRNs. Ceci est suivi d’une étude plus approfondie de certains réseaux d’intérêt pour la biologie des systèmes : Les répressilateurs, et nous trouvons des conditions pour l’existence d’oscillations soutenues dans le répressilateur canonique en dimension 3, et des conditions, décrites par les caractéristiques topologiques des réseaux, pour l’existence d’un attracteur périodique dans les répressilateurs discrets en dimension 4. En résumé, cette thèse propose de nouvelles méthodes pour analyser certaines propriétés des HGRNs qui n’ont pas été étudiées auparavant, par exemple la stabilité des cycles limites à N dimensions, l’accessibilité, etc. Les résultats pourront être développés à l’avenir pour étudier d’autres grands réseaux complexes.Using dynamical models to reveal dynamical properties of gene regulatory networks can help us better understand the nature of these biological systems and develop new medical treatments. In this thesis, we focus on a class of hybrid dynamical systems called Hybrid Gene Regulatory Network (HGRN) and aim to analyze long-term dynamical properties. We propose methods to find limit cycles and analyze their stability, and to analyze the reachability in HGRNs. This is followed by a deeper study of some networks of interest for Systems Biology: The repressilators, and we find conditions for the existenceof sustained oscillations in the 3-dimensional canonical repressilator, and conditions, which are described by topological features of the networks, for the existence of a periodic attractor in discrete 4-dimensional repressilators. In summary, this thesis proposes new methods to analyze some properties of HGRNs that were not investigated before, for instance, the stability of N-dimensional limit cycles, the reachability, etc. The results can be further developed in the future to study other large complex networks
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