Submitted by Caroline Xavier (caroline.xavier@pucrs.br) on 2017-06-05T14:58:52Z No. of bitstreams: 1 TES_RENATA_DE_PARIS_COMPLETO.pdf: 8873897 bytes, checksum: 43b2a883518fc9ce39978e816042ab5f (MD5) / Made available in DSpace on 2017-06-05T14:58:53Z (GMT). No. of bitstreams: 1 TES_RENATA_DE_PARIS_COMPLETO.pdf: 8873897 bytes, checksum: 43b2a883518fc9ce39978e816042ab5f (MD5) Previous issue date: 2016-10-28 / Conselho Nacional de Pesquisa e Desenvolvimento Cient?fico e Tecnol?gico - CNPq / O uso de conforma??es obtidas por trajet?rias da din?mica molecular nos experimentos de docagem molecular ? a abordagem mais precisa para simular o comportamento de receptores e ligantes em ambientes moleculares. Entretanto, tais simula??es exigem alto custo computacional e a sua completa execu??o pode se tornar uma tarefa impratic?vel devido ao vasto n?mero de informa??es estruturais consideradas para representar a expl?cita flexibilidade de receptores. Al?m disso, o problema ? ainda mais desafiante quando deseja-se utilizar modelos de receptores totalmente flex?veis (Fully-Flexible Receptor - FFR) para realizar a triagem virtual em bibliotecas de ligantes. Este estudo apresenta um m?todo inovador para otimizar a triagem virtual baseada em docagem molecular de modelos FFR por meio da redu??o do n?mero de experimentos de docagem e, da invoca??o escalar de workflows de docagem para m?quinas virtuais de plataformas em nuvem. Para esse prop?sito, o workflow cient?fico basedo em nuvem, chamado e-FReDock, foi desenvolvido para acelerar as simula??es da docagem molecular em larga escala. e-FReDock ? baseado em um m?todo seletivo sem param?tros para executar experimentos de docagem ensemble com m?ltiplos ligantes. Como dados de entrada do e-FReDock, aplicou-se seis m?todos de agrupamento para particionar conforma??es com diferentes caracter?sticas estruturais no s?tio de liga??o da cavidade do substrato do receptor, visando identificar grupos de conforma??es favor?veis a interagir com espec?ficos ligantes durante os experimentos de docagem. Os resultados mostram o elevado n?vel de qualidade obtido pelos modelos de receptores totalmente flex?veis reduzidos (Reduced Fully-Flexible Receptor - RFFR) ao final dos experimentos em dois conjuntos de an?lises. O primeiro mostra que e-FReDock ? capaz de preservar a qualidade do modelo FFR entre 84,00% e 94,00%, enquanto a sua dimensionalidade reduz em uma m?dia de 49,68%. O segundo relata que os modelos RFFR resultantes s?o capazes de melhorar os resultados de docagem molecular em 97,00% dos ligantes testados quando comparados com a vers?o r?gida do modelo FFR. / The use of conformations obtained from molecular dynamics trajectories in the molecular docking experiments is the most accurate approach to simulate the behavior of receptors and ligands in molecular environments. However, such simulations are computationally expensive and their execution may become an infeasible task due to the large number of structural information, typically considered to represent the explicit flexibility of receptors. In addition, the computational demand increases when Fully-Flexible Receptor (FFR) models are routinely applied for screening of large compounds libraries. This study presents a novel method to optimize docking-based virtual screening of FFR models by reducing the size of FFR models at docking runtime, and scaling docking workflow invocations out onto virtual machines from cloud platforms. For this purpose, we developed e-FReDock, a cloud-based scientific workflow that assists in faster high-throughput docking simulations of flexible receptors and ligands. e-FReDock is based on a free-parameter selective method to perform ensemble docking experiments with multiple ligands from a clustered FFR model. The e-FReDock input data was generated by applying six clustering methods for partitioning conformations with different features in their substrate-binding cavities, aiming at identifying groups of snapshots with favorable interactions for specific ligands at docking runtime. Experimental results show the high quality Reduced Fully-Flexible Receptor (RFFR) models achieved by e-FReDock in two distinct sets of analyses. The first analysis shows that e-FReDock is able to preserve the quality of the FFR model between 84.00% and 94.00%, while its dimensionality reduces on average 49.68%. The second analysis reports that resulting RFFR models are able to reach better docking results than those obtained from the rigid version of the FFR model in 97.00% of the ligands tested.

Dans la gestion des systèmes de soins, la maîtrise des flux hospitaliers et l’anticipation des tensions sont des enjeux majeurs. Le but de cette thèse est de contribuer à l’étude et au développement d’un Système Collaboratif d’Aide à l’Ordonnancement et à l’Orchestration (SysCAOO) des tâches de soins à compétences multiples pour gérer les tensions dans les Services d’Urgences Pédiatriques (SUP) afin d’améliorer la qualité de prise en charge des patients. Le SysCAOO intègre une approche Workflow collaboratif pour modéliser le parcours patient afin d’identifier les dysfonctionnements et les pics d’activités du personnel médical dans le SUP. L’aspect dynamique et incertain du problème nous a conduits à adopter une alliance entre les Systèmes Multi-Agent (SMA) et les Algorithmes Evolutionnaires (AE) pour le traitement et l’ordonnancement des tâches de soins en tenant compte du niveau d’expérience des acteurs du SUP et leurs disponibilités. En cas d’aléas dans le SUP, une coalition d’agents se forme pour collaborer et négocier afin de proposer des décisions d’orchestration du Workflow et minimiser le temps d’attente des patients en cours de leur prise en charge. Les résultats expérimentaux présentés dans cette thèse justifient l’intérêt de l’alliance entre les SMA et les Métaheuristiques afin de gérer les tensions dans le SUP. Les travaux de recherche présentés dans cette thèse s’intègrent dans le cadre du projet HOST (Hôpital : Optimisation, Simulation et évitement des tensions) (http://www.agence-nationale-recherche.fr/?Projet=ANR-11-TECS-0010). / Health care systems management and the avoidance of overcrowding phenomena are major issues. The aim of this thesis is to implement a Collaborative Support System for Scheduling and Orchestration (CSSystSO) of multi-skill health care tasks in order to avoid areas bottlenecks in the Pediatric Emergency Department (PED) and improve health care quality for patients. The CSSystSO integrates a collaborative Workflow approach to model patient journey in order to identify dysfunctions and peaks of activities of medical staff in the PED. The dynamic and uncertain aspect of the problem has led us to adopt an alliance between Multi-Agent Systems (MAS) and Evolutionary Algorithms (EA) for health care tasks treatment and scheduling taking into account the level of experience of the PED actors and their availabilities. In case of perturbations in the PED, a coalition of agents is formed to collaborate and negotiate in order to provide orchestration Workflow decisions to minimize the waiting time of patients during their treatment. The experimental results presented in this thesis justify the interest of the alliance between MAS and Metaheuristics to manage overcrowding phenomena in the PED. This work belongs to the project HOST (Hôpital: Optimisation, Simulation et évitement des tensions). (http://www.agence-nationale-recherche.fr/?Projet=ANR-11-TECS-0010).

<body>Users require flexibility when interacting with information systems to contend with changing business processes and to support diverse workflow. Model-based user interface design can accommodate flexible business processes by integrating workflow modelling with other modelling approaches. We present a workflow model, the progression model, to help in developing systems that support flexible business processes. <p> The progression model tracks a users interaction with an application as a set of data elements we refer to as a workflow transaction. The steps a user takes to create a workflow transaction and the state of the workflow transaction at each step is made explicit. By making the workflow status and workflow transaction state explicit, the user can change the order of the steps in a process, manage multiple workflow transactions, keep track of data as it is accumulated, and so on. The intent is to provide the user with a mechanism to deal with partial information, interrupted and concurrent workflow transaction entry, and the processing of multiple workflow transactions. <p> This thesis describes the progression model, an XML-compliant notation to specify the progression model, and a prototype system. </body>

<body>Users require flexibility when interacting with information systems to contend with changing business processes and to support diverse workflow. Model-based user interface design can accommodate flexible business processes by integrating workflow modelling with other modelling approaches. We present a workflow model, the progression model, to help in developing systems that support flexible business processes. <p> The progression model tracks a users interaction with an application as a set of data elements we refer to as a workflow transaction. The steps a user takes to create a workflow transaction and the state of the workflow transaction at each step is made explicit. By making the workflow status and workflow transaction state explicit, the user can change the order of the steps in a process, manage multiple workflow transactions, keep track of data as it is accumulated, and so on. The intent is to provide the user with a mechanism to deal with partial information, interrupted and concurrent workflow transaction entry, and the processing of multiple workflow transactions. <p> This thesis describes the progression model, an XML-compliant notation to specify the progression model, and a prototype system. </body>

No description available.

Configurable process models are integrated representations of multiple variants of a process model in a given domain, e.g. multiple variants of a shipment-to-delivery process in the logistics domain. Configurable process models provide a basis for managing variability and for enabling reuse of process models in Process-Aware Information Systems. Rather than designing process models from scratch, analysts can derive process models by configuring existing ones, thereby reusing proven practices. This thesis starts with the observation that existing approaches for capturing and managing configurable process models suffer from three shortcomings that affect their usability in practice. Firstly, configuration in existing approaches is performed manually and as such it is error-prone. In particular, analysts are left with the burden of ensuring the correctness of the individualized models. Secondly, existing approaches suffer from a lack of decision support for the selection of configuration alternatives. Consequently, stakeholders involved in the configuration of process models need to possess expertise both in the application domain and in the modeling language employed. This assumption represents an adoption obstacle in domains where users are unfamiliar with modeling notations. Finally, existing approaches for configurable process modeling are limited in scope to control-flow aspects, ignoring other equally important aspects of process models such as object flow and resource management. Following a design science research method, this thesis addresses the above shortcomings by proposing an integrated framework to manage the configuration of process models. The framework is grounded on three original and interrelated contributions: (i) a conceptual foundation for correctness-preserving configuration of process models; (ii) a questionnaire-driven approach for process model configuration, providing decision support and abstraction from modeling notations; (iii) a meta-model for configurable process models covering control-flow, data objects and resources. While the framework is language-independent, an embodiment of the framework in the context of a process modeling language used in practice is also developed in this thesis. The framework was formally defined and validated using four scenarios taken from different domains. Moreover, a comprehensive toolset was implemented to support the validation of the framework.

Made available in DSpace on 2014-12-17T15:47:50Z (GMT). No. of bitstreams: 1 JoseRSMJ.pdf: 1414617 bytes, checksum: 1d2d0cfcaa6654701268463c98f3c2e9 (MD5) Previous issue date: 2008-08-29 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico / Recently the focus given to Web Services and Semantic Web technologies has provided the development of several research projects in different ways to addressing the Web services composition issue. Meanwhile, the challenge of creating an environment that provides the specification of an abstract business process and that it is automatically implemented by a composite service in a dynamic way is considered a currently open problem. WSDL and BPEL provided by industry support only manual service composition because they lack needed semantics so that Web services are discovered, selected and combined by software agents. Services ontology provided by Semantic Web enriches the syntactic descriptions of Web services to facilitate the automation of tasks, such as discovery and composition. This work presents an environment for specifying and ad-hoc executing Web services-based business processes, named WebFlowAH. The WebFlowAH employs common domain ontology to describe both Web services and business processes. It allows processes specification in terms of users goals or desires that are expressed based on the concepts of such common domain ontology. This approach allows processes to be specified in an abstract high level way, unburdening the user from the underline details needed to effectively run the process workflow / O enfoque dado ultimamente ?s tecnologias de Servi?os Web e da Web Sem?ntica tem proporcionado o desenvolvimento de v?rios projetos de pesquisa abordando, de diferentes maneiras, o tema da composi??o de servi?os Web. Entretanto, o desafio de criar um ambiente que favore?a a especifica??o de um processo de neg?cio abstrato e que seja implementado automaticamente por servi?os compostos de forma din?mica ? considerado atualmente um problema em aberto. Os padr?es WSDL e BPEL providos pela a ind?stria de software suportam apenas a composi??o manual de servi?os, pois falta a eles a sem?ntica necess?ria para que os servi?os Web sejam descobertos, selecionados e combinados por agentes de software. As ontologias de servi?o providas pela Web Sem?ntica enriquecem as descri??es sint?ticas dos servi?os Web de modo a facilitar a automa??o de tarefas, como a descoberta e a composi??o. Este trabalho prop?e um ambiente para a especifica??o e execu??o ad-hoc de processos de neg?cio baseados em servi?os Web chamado WebFlowAH. Este ambiente emprega uma ontologia de dom?nio comum para descrever tanto os servi?os Web e quanto os processos de neg?cio. Ele permite a especifica??o de processos em termos de desejos ou objetivos do usu?rio que s?o expressos por conceitos da ontologia de dom?nio comum. Tal abordagem permite que processos de neg?cio sejam especificados de maneira abstrata e de alto n?vel, liberando o usu?rio de detalhes necess?rios para executar eficazmente o workflow do processo

La qualité de service est devenue aujourd'hui une notion incontournable dans le développement des applications logicielles, en particulier dans le cadre des architectures orientées services. Les travaux de cette thèse se focalisent sur la supervision de la qualité de service des applications orientées services, définies sous forme d'orchestrations de services. L'approche de supervision proposée dans ce contexte est générique. Elle repose sur des patrons de flux de contrôle des orchestrations de services pouvant être implémentés en intégralité ou en partie par tout langage d'orchestration de services. D'autre part, elle ne pose aucune restriction, ni sur les attributs qualité à surveiller par le système de supervision, ni sur leurs représentations. Cette approche de supervision se distingue des approches existantes par l'exploitation d'un modèle de préférences orienté utilisateur, permettant de représenter fidèlement la satisfaction de ce dernier. Le degré de satisfaction, issu du modèle de préférences, constitue une information de haut niveau représentant la qualité globale de l'orchestration étudiée. Sur la base de ce degré de satisfaction, de nouvelles stratégies de surveillance sont proposées afin de satisfaire les attentes de l'utilisateur. L'élaboration du modèle de préférences exploite la méthode d'aide à la décision multi-critères MACBETH étendue avec l'opérateur d'agrégation de l'intégrale de Choquet 2-additive. Une illustration de l'approche de supervision a été réalisée sur une orchestration de services, représentant un processus industriel dans le domaine du pilotage d'atelier de production. Les travaux de cette thèse ont été réalisés dans le cadre d'un projet R&D regroupant sept éditeurs de progiciels dans le domaine du MES (Manufacturing Execution System). / Quality of Service (QoS) is an important issue today in the developement of software applications, especially in the context of Service-Oriented Architectures (SOA). The work of this thesis focuses on QoS supervision of service-oriented applications, defined as service orchestrations. The proposed supervision approach is generic. It is based on workflow control-flow patterns, which can be entirety or partillay implemented by any service orchestration language. On the other hand, it does not make any restrictions, neither on the monitored QoS attributes , nor on their representations. This supervision approach is based on a user-oriented preferences model, that represents faithfully the user satisfaction. The satisfaction degree derived from the preferences model is a high-level information representing the overall quality of the orchestration. New monitoring strategies are proposed on the basis of this satisfaction degree in order to satisfy user expectations. The elaboration of the preferences model uses the MACBETH method extended to the 2-additive Choquet integral operator as a multi criteria decision aiding method. An illustration of the approach is carried out on a service orchestration representing a Manufacturing Execution System (MES) process. This work was realized in a R&D project involving seven software vendors in the field of MES.STAR

Este trabalho descreve a avaliação do Processo Unificado Rational (RUP) realizada com base no Modelo de Maturidade da Capacitação (CMM ou SW-CMM), e a utilização de um sistema de gerência de workflow comercial, Exchange 2000 Server, na implementação de um protótipo de um ambiente de apoio a este processo, chamado de Ambiente de Gerenciamento de Projetos (AGP). O Processo Unificado Rational (RUP) foi avaliado com relação às práticas-chave descritas pelo Modelo de Maturidade da Capacitação (CMM) do Software Engineering Institute (SEI), da Carnegie Mellon University. A avaliação identificou o suporte fornecido por este modelo de processo às organizações que desejam alcançar níveis 2 e 3 do CMM. A avaliação resultou na elaboração de propostas para complementar as macro-atividades (Core Workflows) do RUP, visando satisfazer as práticas-chave do CMM. O CMM apresenta um modelo de avaliação de processo que busca atingir a maturidade dos processos da organização, é específico para o desenvolvimento de software, os aspectos de melhoria contínua são fortemente evidenciados e várias organizações já estão utilizando-o com sucesso. O RUP surgiu como uma proposta de unificar as melhores práticas de desenvolvimento de software. Foi experimentada a utilização de um sistema de gerência de workflow, de fato um servidor de colaboração, para apoiar o processo de desenvolvimento de software. A ferramenta desenvolvida foi avaliada com base em requisitos considerados, por alguns autores da área, desejáveis em um ambiente de apoio ao processo de desenvolvimento. O protótipo do ambiente de gerenciamento de projetos é uma ferramenta de suporte baseada na Web, que visa auxiliar os gerentes de projeto de software nas atividades de gerenciamento e controle, e ajudar na interação e troca de informações entre os membros da equipe de desenvolvimento. O Processo Unificado apresenta uma abordagem bem-definida dos processos de engenharia de software e de gerenciamento de projetos de software, mas não se concentra em atividades de gerenciamento de sistemas. Ele apresenta lacunas em atividades envolvendo gerenciamento de recursos humanos, gerenciamento de custos e gerenciamento de aquisição. AGP é uma ferramenta flexível que pode ser acessada pela Internet, suporta a colaboração entre os membros de uma equipe, e oferece os benefícios da Web, como navegação intuitiva através de links e páginas. Esta ferramenta ajuda no suporte ao gerenciamento, fornecendo opções para planejar e monitorar o projeto, e suporta eventos, como mudança de estados, e comunicação aos usuários de suas novas tarefas. / This master dissertation describes the assessment of the Rational Unified Process (RUP) based on the Capability Maturity Model for Software (SW-CMM or CMM), and the implementation of a prototype tool to support this process based on of-the-shelf Workflow Management System, Exchange 2000 Server. The prototype developed is called Project Management Environment (PME). Rational Unified Process (RUP) was assessed based on the key practices described for the Capability Maturity Model (CMM) at the Carnegie Mellon Software Engineering Institute. The assessment identified the facilities that RUP offers to support an organization aiming at CMM levels 2 and 3. The assessment resulted in the elaboration of propositions to complement the Rational Unified Process in order to satisfy the key process areas of CMM. CMM shows a process model that is far fetched to reach the process maturity of an organization, is specific for the software development, and strongly emphasizes the aspects of continuous improvement and several organizations already used it with success. RUP describes how to apply best practices of software engineering. It was experimented the use of a Workflow Management System, in fact a collaboration server, to support the software development process. The experimental environment was assessed considering the requirements identified by various researchers for an environment to effectively support a software development process. The prototype software development environment is a web-based process support system, which provides means to assist the management of software development projects and help the interaction and exchange of information between disperse members of a development. The Rational Unified Process presents a well defined approach on software project management and software engineering processes, but it is not an approach centered on systems management concerns. Therefore it lacks activities involving issues as cost management, human resource management, communications management, and procurement management. PME is a flexible tool that can be accessed through the Internet, supporting the collaboration between team members, and offering the benefits of the Web, with intuitive navigation through of links and pages. It helps to support management control, providing options to plan and monitor the project, and supports events of the process, as changing states, and communicates users of their attributed tasks.

Este trabalho descreve a avaliação do Processo Unificado Rational (RUP) realizada com base no Modelo de Maturidade da Capacitação (CMM ou SW-CMM), e a utilização de um sistema de gerência de workflow comercial, Exchange 2000 Server, na implementação de um protótipo de um ambiente de apoio a este processo, chamado de Ambiente de Gerenciamento de Projetos (AGP). O Processo Unificado Rational (RUP) foi avaliado com relação às práticas-chave descritas pelo Modelo de Maturidade da Capacitação (CMM) do Software Engineering Institute (SEI), da Carnegie Mellon University. A avaliação identificou o suporte fornecido por este modelo de processo às organizações que desejam alcançar níveis 2 e 3 do CMM. A avaliação resultou na elaboração de propostas para complementar as macro-atividades (Core Workflows) do RUP, visando satisfazer as práticas-chave do CMM. O CMM apresenta um modelo de avaliação de processo que busca atingir a maturidade dos processos da organização, é específico para o desenvolvimento de software, os aspectos de melhoria contínua são fortemente evidenciados e várias organizações já estão utilizando-o com sucesso. O RUP surgiu como uma proposta de unificar as melhores práticas de desenvolvimento de software. Foi experimentada a utilização de um sistema de gerência de workflow, de fato um servidor de colaboração, para apoiar o processo de desenvolvimento de software. A ferramenta desenvolvida foi avaliada com base em requisitos considerados, por alguns autores da área, desejáveis em um ambiente de apoio ao processo de desenvolvimento. O protótipo do ambiente de gerenciamento de projetos é uma ferramenta de suporte baseada na Web, que visa auxiliar os gerentes de projeto de software nas atividades de gerenciamento e controle, e ajudar na interação e troca de informações entre os membros da equipe de desenvolvimento. O Processo Unificado apresenta uma abordagem bem-definida dos processos de engenharia de software e de gerenciamento de projetos de software, mas não se concentra em atividades de gerenciamento de sistemas. Ele apresenta lacunas em atividades envolvendo gerenciamento de recursos humanos, gerenciamento de custos e gerenciamento de aquisição. AGP é uma ferramenta flexível que pode ser acessada pela Internet, suporta a colaboração entre os membros de uma equipe, e oferece os benefícios da Web, como navegação intuitiva através de links e páginas. Esta ferramenta ajuda no suporte ao gerenciamento, fornecendo opções para planejar e monitorar o projeto, e suporta eventos, como mudança de estados, e comunicação aos usuários de suas novas tarefas. / This master dissertation describes the assessment of the Rational Unified Process (RUP) based on the Capability Maturity Model for Software (SW-CMM or CMM), and the implementation of a prototype tool to support this process based on of-the-shelf Workflow Management System, Exchange 2000 Server. The prototype developed is called Project Management Environment (PME). Rational Unified Process (RUP) was assessed based on the key practices described for the Capability Maturity Model (CMM) at the Carnegie Mellon Software Engineering Institute. The assessment identified the facilities that RUP offers to support an organization aiming at CMM levels 2 and 3. The assessment resulted in the elaboration of propositions to complement the Rational Unified Process in order to satisfy the key process areas of CMM. CMM shows a process model that is far fetched to reach the process maturity of an organization, is specific for the software development, and strongly emphasizes the aspects of continuous improvement and several organizations already used it with success. RUP describes how to apply best practices of software engineering. It was experimented the use of a Workflow Management System, in fact a collaboration server, to support the software development process. The experimental environment was assessed considering the requirements identified by various researchers for an environment to effectively support a software development process. The prototype software development environment is a web-based process support system, which provides means to assist the management of software development projects and help the interaction and exchange of information between disperse members of a development. The Rational Unified Process presents a well defined approach on software project management and software engineering processes, but it is not an approach centered on systems management concerns. Therefore it lacks activities involving issues as cost management, human resource management, communications management, and procurement management. PME is a flexible tool that can be accessed through the Internet, supporting the collaboration between team members, and offering the benefits of the Web, with intuitive navigation through of links and pages. It helps to support management control, providing options to plan and monitor the project, and supports events of the process, as changing states, and communicates users of their attributed tasks.