Provenance-based Validation of E-Science Experiments

E-Science experiments typically involve many distributed services maintained by different organisations. After an experiment has been executed, it is useful for a scientist to verify that the execution was performed correctly or is compatible with some existing experimental criteria or standards, not necessarily anticipated prior to execution. Scientists may also want to review and verify experiments performed by their colleagues. There are no existing frameworks for validating such experiments in today's e-Science systems. Users therefore have to rely on error checking performed by the services, or adopt other ad hoc methods. This paper introduces a platform-independent framework for validating workflow executions. The validation relies on reasoning over the documented provenance of experiment results and semantic descriptions of services advertised in a registry. This validation process ensures experiments are performed correctly, and thus results generated are meaningful. The framework is tested in a bioinformatics application that performs protein compressibility analysis.

The First Provenance Challenge

The first Provenance Challenge was set up in order to provide a forum for the community to understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a Functional Magnetic Resonance Imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarise the participants contributions.

Recycling workflows and services through discovery and reuse

Scientific workflows are becoming a valuable tool for scientists to capture and automate e-Science procedures. Their success brings the opportunity to publish, share, reuse and repurpose this explicitly captured knowledge. Within the myGrid project, we have identified key resources that can be shared including complete workflows, fragments of workflows and constituent services. We have examined the alternative ways these can be described by their authors (and subsequent users), and developed a unified descriptive model to support their later discovery. By basing this model on existing standards, we have been able to extend existing Web Service and Semantic Web Service infrastructure whilst still supporting the specific needs of the e-Scientist. myGrid components enable a workflow life-cycle that extends beyond execution, to include discovery of previous relevant designs, reuse of those designs, and subsequent publication. Experience with example groups of scientists indicates that this cycle is valuable. The growing number of workflows and services mean more work is needed to support the user in effective ranking of search results, and to support the repurposing process.

Provenance: The Bridge Between Experiments and Data

Current scientific applications are often structured as workflows and rely on workflow systems to compile abstract experiment designs into enactable workflows that utilise the best available resources. The automation of this step and of the workflow enactment, hides the details of how results have been produced. Knowing how compilation and enactment occurred allows results to be reconnected with the experiment design. We investigate how provenance helps scientists to connect their results with the actual execution that took place, their original experiment and its inputs and parameters.

Workflows in Paradise: E-books, Acquisitions, and Cataloging

This article explores libraries’ technical workflow design and strategic considerations as various e-books business models and mobile devices and their management become a growing part of the information landscape.

Independência entre aplicações e processos modelados

O presente trabalho expõe uma análise sobre duas arquiteturas disponíveis para o desenvolvimento de sistemas que utilizam a tecnologia de workflow. Estas arquiteturas são: a Arquitetura Baseada em Modelagem e Execução em um ùnico Ambiente e a Arquitetura Baseada em Modelagem e Execução e Ambientes Distintos. São expostas: características, vantagens e desvantagens destas arquiteturas. A Aquitetura Baseada em Modelagem e Expressões em Ambientes Distintos é analisada em seu principal ponto negativo: a falta de independência existente entre as apliciações e os processos modelados, bem como são discutidos os problemas que esta falta de independência gera no desenvolvimemto e manutenção das aplicações. Uma alternativa à dependência entre o motor de workflow (engine) e as aplicações é proposta para a Arquitetura Baseada na Modelagem e Execução em Ambientes Distintos. Esta proposta é baseada em um modelo que consiste de uma Camada Intermediária, armazenada em um banco de dados relacional, capaz de extender as funcionalidades do motor de workflow. Este banco de dados armazena toda a estrrutura dos processos modelados, sendo responsável pela função que atualmente é repassada às aplicações: o controle da lógica dos processos. Estes trabalho produziu de uma Camada Intermediária, dividida em Camada de Independência (suportando a independência) e Camada de Integrgação (responsável pela comunicação com o motor de workflow). O estudo apresentada as estruturas do banco de dados, as funções disponibilizadas pela API da Camada Intermediária e um pequeno protótipo para dedmonstrar a arquitetura proposta.

Qualidade em Ambiente de Burocracia: O caso da Justiça Federal do Estado do Amazonas

The necessity to be efficient and effective has long shifted from the private to the public sector. New philosophies have appeared with the aim to supply better performance in both private and public organisms. One of those theories is Quality. It stresses that people who are part of an organisation must realise that they are customers and suppliers within a workflow. The aim of this study was to identify to what extent quality theory can be found in bureaucratic management. The hypothesis was that, despite of the Federal Justice in Amazonas State ─ JF-AM ─ being a bureaucratic organisation, quality parameters are present in the tasks conduction and practice execution. This study was descriptive and explicative. It was a case with bibliographical and field research. As for the means, this research was limited due to both a reduced bibliographical archive pertaining to the comparison between bureaucratic and quality theories, and the uncertainty about the veracity from the questionnaires answers to be answered by members of the sample organisation, the JF-AM. Another limitation factor was the fact that the sample organisation is under the federal judiciary power which excluded views from a State and municipal orbit and from other areas of public power, such as the legislative and the executive. Therefore it seems interesting to gather from this locus another view of quality, mainly as reforms to the judiciary system are in question, which lent a special meaning to this research. The final conclusion was that quality parameters were found in the bureaucratic sample organisation.

Qualidade em ambiente de burocracia: o caso da Justiça Federal do Estado do Amazonas

The necessity to be efficient and effective has long shifted from the private to the public sector. New philosophies have appeared with the aim to supply better performance in both private and public organisms. One of those theories is Quality. It stresses that people who are part of an organisation must realise that they are customers and suppliers within a workflow. The aim of this study was to identify to what extent quality theory can be found in bureaucratic management. The hypothesis was that, despite of the Federal Justice in Amazonas State ─ JF-AM ─ being a bureaucratic organisation, quality parameters are present in the tasks conduction and practice execution. This study was descriptive and explicative. It was a case with bibliographical and field research. As for the means, this research was limited due to both a reduced bibliographical archive pertaining to the comparison between bureaucratic and quality theories, and the uncertainty about the veracity from the questionnaires answers to be answered by members of the sample organisation, the JF-AM. Another limitation factor was the fact that the sample organisation is under the federal judiciary power which excluded views from a State and municipal orbit and from other areas of public power, such as the legislative and the executive. Therefore it seems interesting to gather from this locus another view of quality, mainly as reforms to the judiciary system are in question, which lent a special meaning to this research. The final conclusion was that quality parameters were found in the bureaucratic sample organisation.

Processos de gerenciamento de projetos de gestão: uma análise comparativa com o guia PMBOK

O objetivo deste trabalho é identificar e descrever os processos de gerenciamento dos projetos de ajuste na estrutura organizacional, processos e governança de uma grande empresa brasileira. Os processos de gerenciamento de projetos são o encadeamento das ações e atividades que permitem atingir os objetivos do projeto, constituindo o objeto de estudo do Guia PMBOK e outras bases de conhecimento em gestão de projetos. A pesquisa identificou e descreveu o fluxo de gerenciamento dos projetos de gestão de uma das gerências da Empresa “X” a partir de análise documental, entrevistas e observação participativa. Os resultados foram analisados à luz do referencial teórico sobre processos de gerenciamento de projetos, processos de gerenciamento “front-end” e governança de projetos. A pesquisa concluiu que, comparado ao processo de gerenciamento previsto no Guia PMBOK, o gerenciamento dos projetos de gestão analisados coloca ênfase relativamente maior nos processos que antecedem o início formal do projeto (processos front-end), responsáveis por garantir seu alinhamento aos direcionadores e variáveis organizacionais.

Chemical Composition of Lipids Present in Cat and Dog Oocyte by Matrix-Assisted Desorption Ionization Mass Spectrometry (MALDI- MS)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Uma plataforma de integração de middleware para computação ubíqua

One of the current challenges of Ubiquitous Computing is the development of complex applications, those are more than simple alarms triggered by sensors or simple systems to configure the environment according to user preferences. Those applications are hard to develop since they are composed by services provided by different middleware and it is needed to know the peculiarities of each of them, mainly the communication and context models. This thesis presents OpenCOPI, a platform which integrates various services providers, including context provision middleware. It provides an unified ontology-based context model, as well as an environment that enable easy development of ubiquitous applications via the definition of semantic workflows that contains the abstract description of the application. Those semantic workflows are converted into concrete workflows, called execution plans. An execution plan consists of a workflow instance containing activities that are automated by a set of Web services. OpenCOPI supports the automatic Web service selection and composition, enabling the use of services provided by distinct middleware in an independent and transparent way. Moreover, this platform also supports execution adaptation in case of service failures, user mobility and degradation of services quality. The validation of OpenCOPI is performed through the development of case studies, specifically applications of the oil industry. In addition, this work evaluates the overhead introduced by OpenCOPI and compares it with the provided benefits, and the efficiency of OpenCOPI s selection and adaptation mechanism

Um ambiente para especificação e execução AD-HOC de processos de negócio baseados em serviços Web

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

Uma abordagem dirigida por modelos para gerência de variabilidade e execução de processos de software

This dissertation presents a model-driven and integrated approach to variability management, customization and execution of software processes. Our approach is founded on the principles and techniques of software product lines and model-driven engineering. Model-driven engineering provides support to the specification of software processes and their transformation to workflow specifications. Software product lines techniques allows the automatic variability management of process elements and fragments. Additionally, in our approach, workflow technologies enable the process execution in workflow engines. In order to evaluate the approach feasibility, we have implemented it using existing model-driven engineering technologies. The software processes are specified using Eclipse Process Framework (EPF). The automatic variability management of software processes has been implemented as an extension of an existing product derivation tool. Finally, ATL and Acceleo transformation languages are adopted to transform EPF process to jPDL workflow language specifications in order to enable the deployment and execution of software processes in the JBoss BPM workflow engine. The approach is evaluated through the modeling and modularization of the project management discipline of the Open Unified Process (OpenUP)

Optimal clone identifier based on dynamic rules and process algebra

The rule creation to clone selection in different projects is a hard task to perform by using traditional implementations to control all the processes of the system. The use of an algebraic language is an alternative approach to manage all of system flow in a flexible way. In order to increase the power of versatility and consistency in defining the rules for optimal clone selection, this paper presents the software OCI 2 in which uses process algebra in the flow behavior of the system. OCI 2, controlled by an algebraic approach was applied in the rules elaboration for clone selection containing unique genes in the partial genome of the bacterium Bradyrhizobium elkanii Semia 587 and in the whole genome of the bacterium Xanthomonas axonopodis pv. citri. Copyright© (2009) by the International Society for Research in Science and Technology.

Algebraic approach to optimal clone selection applied in metagenomic projects

Due to the wide diversity of unknown organisms in the environment, 99% of them cannot be grown in traditional culture medium in laboratories. Therefore, metagenomics projects are proposed to study microbial communities present in the environment, from molecular techniques, especially the sequencing. Thereby, for the coming years it is expected an accumulation of sequences produced by these projects. Thus, the sequences produced by genomics and metagenomics projects present several challenges for the treatment, storing and analysis such as: the search for clones containing genes of interest. This work presents the OCI Metagenomics, which allows defines and manages dynamically the rules of clone selection in metagenomic libraries, thought an algebraic approach based on process algebra. Furthermore, a web interface was developed to allow researchers to easily create and execute their own rules to select clones in genomic sequence database. This software has been tested in metagenomic cosmid library and it was able to select clones containing genes of interest. Copyright 2010 ACM.