On proving the absence of oscillations in models of genetic circuits

International audienceUsing computer algebra methods to prove that gene regulatory networks cannot oscillate appears to be easier than expected. We illustrate this claim on a family of models related to historical examples

Systems biology via redescription and ontologies (I): finding phase changes with applications to malaria temporal data

Biological systems are complex and often composed of many subtly interacting components. Furthermore, such systems evolve through time and, as the underlying biology executes its genetic program, the relationships between components change and undergo dynamic reorganization. Characterizing these relationships precisely is a challenging task, but one that must be undertaken if we are to understand these systems in sufficient detail. One set of tools that may prove useful are the formal principles of model building and checking, which could allow the biologist to frame these inherently temporal questions in a sufficiently rigorous framework. In response to these challenges, GOALIE (Gene ontology algorithmic logic and information extractor) was developed and has been successfully employed in the analysis of high throughput biological data (e.g. time-course gene-expression microarray data and neural spike train recordings). The method has applications to a wide variety of temporal data, indeed any data for which there exist ontological descriptions. This paper describes the algorithms behind GOALIE and its use in the study of the Intraerythrocytic Developmental Cycle (IDC) of Plasmodium falciparum, the parasite responsible for a deadly form of chloroquine resistant malaria. We focus in particular on the problem of finding phase changes, times of reorganization of transcriptional control

An Introduction to Mechanized Reasoning

Mechanized reasoning uses computers to verify proofs and to help discover new theorems. Computer scientists have applied mechanized reasoning to economic problems but -- to date -- this work has not yet been properly presented in economics journals. We introduce mechanized reasoning to economists in three ways. First, we introduce mechanized reasoning in general, describing both the techniques and their successful applications. Second, we explain how mechanized reasoning has been applied to economic problems, concentrating on the two domains that have attracted the most attention: social choice theory and auction theory. Finally, we present a detailed example of mechanized reasoning in practice by means of a proof of Vickrey's familiar theorem on second-price auctions

Twenty years of rewriting logic

AbstractRewriting logic is a simple computational logic that can naturally express both concurrent computation and logical deduction with great generality. This paper provides a gentle, intuitive introduction to its main ideas, as well as a survey of the work that many researchers have carried out over the last twenty years in advancing: (i) its foundations; (ii) its semantic framework and logical framework uses; (iii) its language implementations and its formal tools; and (iv) its many applications to automated deduction, software and hardware specification and verification, security, real-time and cyber-physical systems, probabilistic systems, bioinformatics and chemical systems

ALGEBRAIC AND COMBINATORIAL PROPERTIES OF CERTAIN TORIC IDEALS IN THEORY AND APPLICATIONS

This work focuses on commutative algebra, its combinatorial and computational aspects, and its interactions with statistics. The main objects of interest are projective varieties in Pn, algebraic properties of their coordinate rings, and the combinatorial invariants, such as Hilbert series and Gröbner fans, of their defining ideals. Specifically, the ideals in this work are all toric ideals, and they come in three flavors: they are defining ideals of a family of classical varieties called rational normal scrolls, cut ideals that can be associated to a graph, and phylogenetic ideals arising in a new and increasingly popular area of algebraic statistics

Contribution à la gestion de l'évolution des processus métiers

La gestion de l'évolution des processus métier exige une compréhension approfondie des cause des changements, de leurs niveaux d'application ainsi que de leurs impacts sur le reste du système. Dans cette thèse, nous proposons une approche de gestion et de contrôle de l'éolution des processus métier permettant d'analyser ces changements et de comprendre leurs impacts. Cela assistera les concepteurs et les chargés de l'évolution des processus métier à établir une évaluation a priori de l'impact pour réduire les risques et les coûts liés à ces changements et d'améliorer le service et la qualité des processus métier. Ce travail consiste à proposer un ensemble de contributions permettant une vérification de la cohérence et de la conformité des modèles de processus métier après chaque changement, mais aussi d'établir une éaluation a priori de l'impact structurel et qualificatif des modifications. Les différentes approches proposées sont en cours d'expérimentation et de validation à travers le développement d'une plate-forme basée sur l'environnement EclipseThe evolution management of the business processes requires an exhaustive understanding of the change. An evolution engineer needs to understand reasons of a change, its application levels, and subsequently its impact on the whole system. In this thesis, we propose an approach for an a priori change impact analysis, to better control the business process evolution. This may help the business experts and the process designers to evaluate change impact in order to reduce the associated risks and estimate the related costs. It may also help to improve the service and quality of the business processes. This work contributes an eventual improvement, in regard, to verify the coherence and the compliance of the business process models, after each change. It leads to evaluate an a priori change impact analysis in structural and qualitatie aspects. The multiple-perspectives of the proposed approach have been reviewed experimentally. The validation of the approach is evaluated by exteding the Eclipse Development Environment, with the help of a set of plug-ins, as a prototype plate-form.DUNKERQUE-SCD-Bib.electronique (591839901) / SudocSudocFranceF