GUBS, a Behavior-based Language for Open System Dedicated to Synthetic Biology

In this article, we propose a domain specific language, GUBS (Genomic Unified Behavior Specification), dedicated to the behavioral specification of synthetic biological devices, viewed as discrete open dynamical systems. GUBS is a rule-based declarative language. By contrast to a closed system, a program is always a partial description of the behavior of the system. The semantics of the language accounts the existence of some hidden non-specified actions possibly altering the behavior of the programmed device. The compilation framework follows a scheme similar to automatic theorem proving, aiming at improving synthetic biological design safety.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347

Gubs, un langage de description comportementale pour la biologie de synthèse: Conception d'un langage dédié à la conception de fonctions biologiques de synthèse par compilation de spécifications comportementales

The field of synthetic biology is looking forward engineering framework for safely designing reliable de-novo biological functions. In this undertaking, Computer-Aided-Design (CAD) environments should play a central role for facilitating the design. Although, CAD environment is widely used to engineer artificial systems the application in synthetic biology is still in its infancy. In this article we address the problem of the design of a high level language which at the core of CAD environment. More specifically the Gubs (Genomic Unified Behavioural Specification) language is a specification language used to describe the observations of the expected behaviour. The compiler appropriately selects components such that the observation of the synthetic biological function resulting to their assembly complies to the programmed behaviour.La biologie de synthèse est un domaine émergent en quête d’outils afin deformaliser et d’automatiser la caractérisation et la conception de systèmes biologiques.Dans ce cadre, nous proposons un langage de spécification comportementale dessystèmes biologiques, ainsi que la conception d’un compilateur traduisant cettespécification en un assemblage de composants biologiques.La première partie sera dédiée à un langage de description comportementalenommé Gubs (Genetic Unified Behaviour Specification) pour la spécification decomposants biologiques en les décrivant comme des systèmes ouverts dynamiques etdiscrets. Gubs est un langage déclaratif dont la syntaxe se fonde sur une descriptiondes comportements par un ensemble de relations causales. Contrairement à un systèmefermé, un programme est toujours une description partielle du comportement dusystème. La sémantique a été conçue afin de prendre en compte la présence d’actionsnon spécifiées qui pourraient potentiellement altérer le comportement des composantsprogrammés en l’exprimant sous forme d’une formule de logique hybride.En seconde partie, nous introduisons un système formel décrivant les principes decompilation d’une spécification en Gubs en un ensemble de composants biologiquessynthétisables. Ce système est implémenté par Ggc, un compilateur permettant desélectionner automatiquement les composants possédant les propriétés adéquatespour qu’une fois assemblés ils simulent le comportement décrit. La compilation d’unespécification Gubs s’appuie sur le principe d’ACI-Unification en utilisant un schémasimilaire au système de preuve automatique afin de sélectionner les composants dontl’assemblage est correct par rapport à la spécification. Dans le cadre d’une unificationavec une base de données de grande taille, l’algorithme d’ACI-Unification bascule surun algorithme évolutionnaire d’optimisation permettant la recherche des composantsen adéquation avec le programme afin d’obtenir une solution.Finalement, cette thèse se conclut sur un ensemble d’optimisations permettantde sélectionner des composants selon des propriétés biologiques afin d’obtenir unesélection plus fine dans le but d’assurer une synthèse des éléments in-silico en systèmesbiologiques viables in-vivo. Nous concluons aussi sur un traitement automatique desbases de données à disposition des chercheurs afin de les traduire en un ensemble decomposants Gubs

Genetic Diversity in Svaneti and Highland Western Georgia

This study investigates the genetic diversity and ethnohistory of Svaneti and its neighboring highland Georgian and breakaway regions in order to better understand the complex population history of the South Caucasus. The objectives of this project are to (1) document the biological diversity in contemporary settlements in the region of Svaneti; (2) compare patterns of gene diversity with Svaneti’s western and eastern neighbors, Abkhazia and South Ossetia, respectively; and (3) determine whether gene frequencies in Svaneti are evently distributed across geographic space by characterizing any village-level structuring. We will contextualize the findings within broader studies that address major regional population settlement events during the Upper Paleolithic, Neolithic, and Metal Ages, as well as the putative ‘Alan migration’ in the 4th century AD. To accomplish these goals, biological samples were collected from participants in Svaneti for genetic analysis, providing a more thorough coverage of village districts in Svaneti than has been achieved in previous studies. In addition, local-level ethnohistorical interviews were conducted in an effort to distinguish patterns of diversity resulting from long-term inhabitation versus those arising from recent immigration into the region. These DNA samples were characterized for mitochondrial DNA and Y-chromosome variation, and the resulting data analyzed with statistical and phylogenetic methods to define the biological affinities of highland Georgian populations, and reconstruct the migration and settlement history of the region. Data from published and unpublished sources on the genetic diversity of the greater Near East and Caucasus, specifically Abkhaz and Ossete populations, were used for phylogeographic and statistical comparison. The results revealed reduced Y-chromosome haplogroup diversity in Svans, with a predominance of G2a, although their paternal lineages occurred at frequencies comparable to those of neighboring highland populations. By contrast, mtDNA haplogroup diversity in Svans was both very high and reasonably similar in terms of frequency to other regional populations, with W6 and X2 occurring at unusually high frequencies. Interestingly, there was no geographic patterning of Y-chromosome or mitochondrial DNA diversity within Svaneti at the village level. Nevertheless, strong Y-chromosome affinities with eastern and western populations (i.e., Ossete and Abkhaz, respectively) living adjacent to the Svans indicated a common gene pool for these three ethno-linguistic groups in spite of linguistic differences at the language family level, and minimal contribution to the Ossete gene pool from Indo-European-speaking Alans

Problem space of modern society: philosophical-communicative and pedagogical interpretations. Part I

This collective monograph offers the description of philosophical bases of definition of communicative competence and pedagogical conditions for the formation of communication skills. The authors of individual chapters have chosen such point of view for the topic which they considered as the most important and specific for their field of study using the methods of logical and semantic analysis of concepts, the method of reflection, textual reconstruction and comparative analysis. The theoretical and applied problems of modern society are investigated in the context of philosophical, communicative and pedagogical interpretations

gubs, a behavior-based language for open system dedicated to synthetic biology

In this article, we propose a domain speci c language, GUBS (Genomic Uni ed Behavior Speci cation), dedicated to the behavioral speci cation of synthetic biological devices, viewed as discrete open dynamical systems. gubs is a rule-based declarative language. By contrast to a closed system, a program is always a partial description of the behavior of the system. The semantics of the language accounts the existence of some hidden non-speci ed actions possibly altering the behavior of the programmed device. The compilation framework follows a scheme similar to automatic theorem proving, aiming at improving synthetic biological design safety

Corpses revealed: The staging of the theatrical corpse in early modern drama

My dissertation examines the theatrical depiction of corpses as both stage-objects for theoretical speculation and as performance phenomena of the early modern English stage. Investigating popular drama on the London stage from 1587 -- 1683, I demonstrate that the performance of the dead body by the living actor (what I term the theatrical corpse ) is informed by early modern secular and religious polemics over the materiality of the body, the efficacy of performative behavior, and emerging theories of theatrical presence. Previously, literary scholars have approached the performance of death on the stage using the insights of psychoanalysis or medical science, arguing for a rise of the subject and a growing sense of the individual via the emergence of empirical science and anatomical dissection. By contrast, my dissertation focuses on the material realities of the performance event such as staging, sets, and performance objects. In so doing, my dissertation reveals the theatrical corpse on stage---much like the early modern corpse off stage---to function as an active narrative agent beyond its death

GVSU Press Releases, 2007

A compilation of press releases for the year 2007 submitted by University Communications (formerly News & Information Services) to news agencies concerning the people, places, and events related to Grand Valley State University