Les expériences bioinformatiques sont généralement effectuées à l'aide de workflows scientifiques dans lesquels les tâches sont enchaînées les unes aux autres pour former des structures de graphes très complexes et imbriquées. Les systèmes de workflows scientifiques ont ensuite été développés pour guider les utilisateurs dans la conception et l'exécution de workflows. Un avantage de ces systèmes par rapport aux approches traditionnelles est leur capacité à mémoriser automatiquement la provenance (ou lignage) des produits de données intermédiaires et finaux générés au cours de l'exécution du workflow. La provenance d'un produit de données contient des informations sur la façon dont le produit est dérivé, et est cruciale pour permettre aux scientifiques de comprendre, reproduire, et vérifier les résultats scientifiques facilement. Pour plusieurs raisons, la complexité du workflow et des structures d'exécution du workflow est en augmentation au fil du temps, ce qui a un impact évident sur la réutilisation des workflows scientifiques.L'objectif global de cette thèse est d'améliorer la réutilisation des workflows en fournissant des stratégies visant à réduire la complexité des structures de workflow tout en préservant la provenance. Deux stratégies sont introduites. Tout d'abord, nous proposons une approche de réécriture de la structure du graphe de n'importe quel workflow scientifique (classiquement représentée comme un graphe acyclique orienté (DAG)) dans une structure plus simple, à savoir une structure série-parallèle (SP) tout en préservant la provenance. Les SP-graphes sont simples et bien structurés, ce qui permet de mieux distinguer les principales étapes du workflow. En outre, d'un point de vue plus formel, on peut utiliser des algorithmes polynomiaux pour effectuer des opérations complexes fondées sur les graphiques (par exemple, la comparaison de workflows, ce qui est directement lié au problème d’homomorphisme de sous-graphes) lorsque les workflows ont des SP-structures alors que ces opérations sont reliées à des problèmes NP-hard pour des graphes qui sont des DAG sans aucune restriction sur leur structure. Nous avons introduit la notion de préservation de la provenance, conçu l’algorithme de réécriture SPFlow et réalisé l’outil associé.Deuxièmement, nous proposons une méthodologie avec une technique capable de réduire la redondance présente dans les workflow (en supprimant les occurrences inutiles de tâches). Plus précisément, nous détectons des « anti-modèles », un terme largement utilisé dans le domaine de la conception de programme, pour indiquer l'utilisation de formes idiomatiques qui mènent à une conception trop compliquée, et qui doit donc être évitée. Nous avons ainsi conçu l'algorithme DistillFlow qui est capable de transformer un workflow donné en un workflow sémantiquement équivalent «distillé», c’est-à-dire, qui est libre ou partiellement libre des anti-modèles et possède une structure plus concise et plus simple. Les deux principales approches de cette thèse (à savoir, SPFlow et DistillFlow) sont basées sur un modèle de provenance que nous avons introduit pour représenter la structure de la provenance des exécutions du workflowl. La notion de «provenance-équivalence» qui détermine si deux workflows ont la même signification est également au centre de notre travail. Nos solutions ont été testées systématiquement sur de grandes collections de workflows réels, en particulier avec le système Taverna. Nos outils sont disponibles à l'adresse: https://www.lri.fr/~chenj/. / Bioinformatics experiments are usually performed using scientific workflows in which tasks are chained together forming very intricate and nested graph structures. Scientific workflow systems have then been developed to guide users in the design and execution of workflows. An advantage of these systems over traditional approaches is their ability to automatically record the provenance (or lineage) of intermediate and final data products generated during workflow execution. The provenance of a data product contains information about how the product was derived, and it is crucial for enabling scientists to easily understand, reproduce, and verify scientific results. For several reasons, the complexity of workflow and workflow execution structures is increasing over time, which has a clear impact on scientific workflows reuse.The global aim of this thesis is to enhance workflow reuse by providing strategies to reduce the complexity of workflow structures while preserving provenance. Two strategies are introduced.First, we propose an approach to rewrite the graph structure of any scientific workflow (classically represented as a directed acyclic graph (DAG)) into a simpler structure, namely, a series-parallel (SP) structure while preserving provenance. SP-graphs are simple and layered, making the main phases of workflow easier to distinguish. Additionally, from a more formal point of view, polynomial-time algorithms for performing complex graph-based operations (e.g., comparing workflows, which is directly related to the problem of subgraph homomorphism) can be designed when workflows have SP-structures while such operations are related to an NP-hard problem for DAG structures without any restriction on their structures. The SPFlow rewriting and provenance-preserving algorithm and its associated tool are thus introduced.Second, we provide a methodology together with a technique able to reduce the redundancy present in workflows (by removing unnecessary occurrences of tasks). More precisely, we detect "anti-patterns", a term broadly used in program design to indicate the use of idiomatic forms that lead to over-complicated design, and which should therefore be avoided. We thus provide the DistillFlow algorithm able to transform a workflow into a distilled semantically-equivalent workflow, which is free or partly free of anti-patterns and has a more concise and simpler structure.The two main approaches of this thesis (namely, SPFlow and DistillFlow) are based on a provenance model that we have introduced to represent the provenance structure of the workflow executions. The notion of provenance-equivalence which determines whether two workflows have the same meaning is also at the center of our work. Our solutions have been systematically tested on large collections of real workflows, especially from the Taverna system. Our approaches are available for use at https://www.lri.fr/~chenj/.

Este trabalho objetiva uma revisão da recepção crítica e literária de Noite na Taverna, de Álvares de Azevedo. Com sua Noite na Taverna, esse poeta romântico criou uma peça singular em nossas letras, que gozou de grande popularidade desde então. Busco, a partir disso, elencar e comentar os mais relevantes estudos críticos sobre a obra, além de relacionar uma série de emulações da novela, produzidas sob sua inspiração e dividindo com ela o mesmo clima macabro e de espírito de grupo. Cumbre lembrar que, apesar do seu sucesso literário, Noite na Taverna não foi suficiente para criar entre nós uma tradição de literatura fantástica. Cabe ainda, ao apontar influxos (ainda que indiretos) da literatura de horror no romantismo brasileiro, apresentar uma reflexão sobre os motivos góticos no projeto estético de Álvares de Azevedo. / The aim of this research is to review the critical and literary reception of Noite na Taverna, de Álvares de Azevedo. With that book, this romantic poet created a unique piece in brazilian letters, which enjoyed great popularity since 1855. For this, I list and comment on the most relevant critical studies on the work, further relates a series of \"emulation\" of the novel, produced under his inspiration and sharing the same macabre atmosphere and group spirit. Although their literary success, Noite na Taverna was not enough to create among us a great tradition of fantastic literature. It also point to inflows (albeit indirect) of horror literature in Brazilian Romanticism, provide a reflection on the reasons for the Gothic themes in the Alvares de Azevedo\'s aesthetic project.

Este trabalho objetiva uma revisão da recepção crítica e literária de Noite na Taverna, de Álvares de Azevedo. Com sua Noite na Taverna, esse poeta romântico criou uma peça singular em nossas letras, que gozou de grande popularidade desde então. Busco, a partir disso, elencar e comentar os mais relevantes estudos críticos sobre a obra, além de relacionar uma série de emulações da novela, produzidas sob sua inspiração e dividindo com ela o mesmo clima macabro e de espírito de grupo. Cumbre lembrar que, apesar do seu sucesso literário, Noite na Taverna não foi suficiente para criar entre nós uma tradição de literatura fantástica. Cabe ainda, ao apontar influxos (ainda que indiretos) da literatura de horror no romantismo brasileiro, apresentar uma reflexão sobre os motivos góticos no projeto estético de Álvares de Azevedo. / The aim of this research is to review the critical and literary reception of Noite na Taverna, de Álvares de Azevedo. With that book, this romantic poet created a unique piece in brazilian letters, which enjoyed great popularity since 1855. For this, I list and comment on the most relevant critical studies on the work, further relates a series of \"emulation\" of the novel, produced under his inspiration and sharing the same macabre atmosphere and group spirit. Although their literary success, Noite na Taverna was not enough to create among us a great tradition of fantastic literature. It also point to inflows (albeit indirect) of horror literature in Brazilian Romanticism, provide a reflection on the reasons for the Gothic themes in the Alvares de Azevedo\'s aesthetic project.

<p>In silico experiments in the field of bioinformatics generate large amounts of data since most of the tasks are done in an exploratory fashion. Workflows are one of the many tools used by scientists to model complex tasks.The interoperability of data generated from these tools plays an important role in improving the efficiency of such tools and also in verifying results from other experiments.We aim to compare workflow systems by integrating bioinformatics data in Vistrails and Taverna. We also look at how the two systems use the open provenance model that has been developed to bring provenance interoperability. We developed web services to perform similar functions of some workflows in Vistrails. With the services we were able to perform most of the tasks we planned using both systems. Differences in how lists of items are processed in the two systems results in differences in how workflows are composed in the two systems. In Taverna there is implicit iteration and Vistrails requires the use of additional modules to perform iteration.There are also differences in the execution times of workflows using web services, with workflows in Taverna taking longer than their counterparts in Vistrails. There are some similarities in the execution pattern of workflows if same workflow is invokedmultiple times, with the first invocation taking longer time than the subsequent ones.</p>

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Diversos críticos enfatizaram a vertente de Noite na taverna, de Álvares de Azevedo, obra que se consagrou, portanto, como uma narrativa pertencente ao gênero fantástico, apesar de não corresponder plenamente à concepção do gênero desenvolvida por Tzvetan Todorov, em Introdução à literatura fantástica subsídio fundamental para os estudos da ficção insólita. "Fantástica"!, "sobrenatural", "de horror", "tétrica", "sombria", "macabra", "monstruosa", "dantesca", "simbolista avant la lettre", "gótica", "satanista", "byroniana" são alguns dos termos empregados pela crítica nos principais estudos publicados acerca da obra. Trata-se de uma multiplicidade de classificações que, no entanto, não a caracterizam adequadamente e só demonstram a dificuldade de definir-lhe o gênero. Refletindo sobre tais aspectos e partindo dos principais estudos críticos produzidos sobre a obra desde sua primeira edição, consideramos a pertinência de a classificarmos como integrante do gênero fantástico. Procura-se ainda, após minuciosa leitura destes estudos, identificar os momentos da história e da crítica literária brasileira em que Noite na taverna foi classificada com termos que a associaram a uma forma de literatura incomum no Brasil nacionalista do século XIX. / Many critics have emphasized that part fantastic of the Noite na taverna, by Álvares de Azevedo, work that is devoted, therefore, as a narrative of the fantastic although not fully correspond to the conception of the genre developed by Tzvetan Todorov, in Introduction to fantasy literature, basic allowance for studies of unusual fiction. "Fantastic," "supernatural," "horror," "gloomy," "dark," "macabre," "monstrous,""Dantesque", "Symbolist avant la lettre", "Gothic," "Satanist", "Byronic" are some of the terms used by critics in the main published studies about the work. It is a plurality of classifications not adequately characterize, and only demonstrate the difficulty of defining his gender. Reflecting on these aspects and building on the main critical studies on the work produced since its first edition, we consider the appropriateness of classifying as a member of the fantastic. Search is still, after careful reading of these studies, identify the moments of history and literary criticism in which Brazilian Night at the tavern was classified with the terms associated with a rare form of literature in Brazil's nationalist nineteenth century.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Diversos críticos enfatizaram a vertente de Noite na taverna, de Álvares de Azevedo, obra que se consagrou, portanto, como uma narrativa pertencente ao gênero fantástico, apesar de não corresponder plenamente à concepção do gênero desenvolvida por Tzvetan Todorov, em Introdução à literatura fantástica subsídio fundamental para os estudos da ficção insólita. "Fantástica"!, "sobrenatural", "de horror", "tétrica", "sombria", "macabra", "monstruosa", "dantesca", "simbolista avant la lettre", "gótica", "satanista", "byroniana" são alguns dos termos empregados pela crítica nos principais estudos publicados acerca da obra. Trata-se de uma multiplicidade de classificações que, no entanto, não a caracterizam adequadamente e só demonstram a dificuldade de definir-lhe o gênero. Refletindo sobre tais aspectos e partindo dos principais estudos críticos produzidos sobre a obra desde sua primeira edição, consideramos a pertinência de a classificarmos como integrante do gênero fantástico. Procura-se ainda, após minuciosa leitura destes estudos, identificar os momentos da história e da crítica literária brasileira em que Noite na taverna foi classificada com termos que a associaram a uma forma de literatura incomum no Brasil nacionalista do século XIX. / Many critics have emphasized that part fantastic of the Noite na taverna, by Álvares de Azevedo, work that is devoted, therefore, as a narrative of the fantastic although not fully correspond to the conception of the genre developed by Tzvetan Todorov, in Introduction to fantasy literature, basic allowance for studies of unusual fiction. "Fantastic," "supernatural," "horror," "gloomy," "dark," "macabre," "monstrous,""Dantesque", "Symbolist avant la lettre", "Gothic," "Satanist", "Byronic" are some of the terms used by critics in the main published studies about the work. It is a plurality of classifications not adequately characterize, and only demonstrate the difficulty of defining his gender. Reflecting on these aspects and building on the main critical studies on the work produced since its first edition, we consider the appropriateness of classifying as a member of the fantastic. Search is still, after careful reading of these studies, identify the moments of history and literary criticism in which Brazilian Night at the tavern was classified with the terms associated with a rare form of literature in Brazil's nationalist nineteenth century.

In silico experiments in the field of bioinformatics generate large amounts of data since most of the tasks are done in an exploratory fashion. Workflows are one of the many tools used by scientists to model complex tasks.The interoperability of data generated from these tools plays an important role in improving the efficiency of such tools and also in verifying results from other experiments.We aim to compare workflow systems by integrating bioinformatics data in Vistrails and Taverna. We also look at how the two systems use the open provenance model that has been developed to bring provenance interoperability. We developed web services to perform similar functions of some workflows in Vistrails. With the services we were able to perform most of the tasks we planned using both systems. Differences in how lists of items are processed in the two systems results in differences in how workflows are composed in the two systems. In Taverna there is implicit iteration and Vistrails requires the use of additional modules to perform iteration.There are also differences in the execution times of workflows using web services, with workflows in Taverna taking longer than their counterparts in Vistrails. There are some similarities in the execution pattern of workflows if same workflow is invokedmultiple times, with the first invocation taking longer time than the subsequent ones.

PINTO, Polyanna Ervedosa. O feminino e a fragmentação em Noite na Taverna. 2009. 133 f. Dissertação (Mestrado em Letras) – Universidade Federal do Ceará, Departamento de Literatura, Programa de Pós-Graduação em Letras, Fortaleza-CE, 2009. / Submitted by Liliane oliveira (morena.liliane@hotmail.com) on 2012-07-06T12:28:53Z No. of bitstreams: 1 2009_DIS_PEPINTO.pdf: 773130 bytes, checksum: 3970d2b8b1827d48aef518002ae43c16 (MD5) / Approved for entry into archive by Maria Josineide Góis(josineide@ufc.br) on 2012-07-17T12:10:34Z (GMT) No. of bitstreams: 1 2009_DIS_PEPINTO.pdf: 773130 bytes, checksum: 3970d2b8b1827d48aef518002ae43c16 (MD5) / Made available in DSpace on 2012-07-17T12:10:34Z (GMT). No. of bitstreams: 1 2009_DIS_PEPINTO.pdf: 773130 bytes, checksum: 3970d2b8b1827d48aef518002ae43c16 (MD5) Previous issue date: 2009 / The analysis of the line of research on affective imaginary in the novel by Álvares de Azevedo, Night at the Tavern, part of the statement of understanding of emotional memory and female romantic. Will pay-the understanding of disruptive conflicts that develop in the work, investigating the emotions of the characters and their way of story telling in this particular book. Interested teased the plans of Taverna Night, showing that the female is always the main impetus of writing because of the connection between women, nature and mythical, promoted by the Romantic Movement. Then it will analyze the reflection of the relationship disharmonize the fragmentation of the discourse in order to study the environment and its connection with infernal Macário to ultimately understand the relationship of life and death on each count. The narratives, though linked by Taverna, have its merits in the quest for oblivion because of the disappointments of frustrated love and the passions as an object, either through the sympathetic imagination, of symbolism, history or other possible readings that can provide grants to this dissertation. The primary purpose is to see Night at the Tavern in the sphere of human, yet assuring it literary value and evil atmosphere that encourages the natural extravagance azevediana, proving the existence of a female rescued from primitive times. It is expected to give room for a new look at the criticism on the work azevediana, not forgetting the many previous studies, but guaranteeing their continuity / A análise da linha de pesquisa sobre o imaginário afetivo, no romance de Álvares de Azevedo, Noite na Taverna, parte do entendimento da enunciação da memória sentimental e do feminino romântico. Dedicar-nos-emos ao entendimento dos conflitos perturbadores que se desenvolvem na obra, investigando as emoções das personagens e seu modo de contar histórias neste livro específico. Interessa esmiuçar os planos de Noite da Taverna, mostrando que o feminino é sempre o impulso principal da escrita devido à ligação entre a mulher, a natureza e o mítico, promovido pelo Movimento Romântico. Em seguida, analisaremos o reflexo das relações desarmonizadas na fragmentação do discurso, a fim de estudar o ambiente infernal e sua conexão com Macário para, finalmente, compreendermos a relação de vida e morte em cada conto. As narrativas, embora ligadas pela Taverna, possuem suas particularidades na busca do esquecimento em virtude das decepções de amores frustrados e das paixões como objeto, seja através do imaginário dos afetos, da simbologia, da História ou de outras possíveis leituras que possam dar subsídios a esta dissertação. O intuito principal é ver Noite na Taverna dentro da esfera do humano, mas ainda assim garantindo-lhe valor literário e atmosfera diabólica que favorece a natural extravagância azevediana, atestando a existência de um feminino resgatado de tempos primitivos. Esperamos dar margem a um novo olhar da crítica sobre a obra azevediana, não esquecendo os diversos estudos anteriores, mas garantindo-lhes continuidade