Fernanda Campos

CelOWS: An ontology based framework for the provision of semantic web services related to biological models

The amount of information generated by biological research has lead to an intensive use of models. Mathematical and computational modeling needs accurate description to share, reuse and simulate models as formulated by original authors. In this paper, we introduce the Cell Component Ontology (CelO), expressed in OWL-DL. This ontology captures both the structure of a cell model and the properties of functional components. We use this ontology in a Web project (CelOWS) to describe, query and compose CellML models, using semantic web services. It aims to improve reuse and composition of existent components and allow semantic validation of new models.

Composer-Science: A semantic service based framework for workflow composition in e-Science projects

An important element in e-Science research is scientific workflow which is, in general, very long and composed of many computations, and represents a scientific process. Generally, a scientific workflow is difficult to define. One way to define it is using tools that aggregate semantics to assist in composition. In this context, this paper presents a proposal that aims to make composition of scientific workflows possible, considering semantic search of Web services and incorporating them into workflow definition.

Towards pragmatic interoperability to support collaboration

Context: Many researchers have argued that providing interoperability support only considering the format and meaning (i.e. syntax and semantic) of data exchange is not enough to achieve complete, effective and meaningful collaboration. Pragmatic interoperability has been highlighted as a key requirement to enhance collaboration. However, fulfilling this requirement is not a trivial task and there is a lack of works discussing solutions to achieve this level of interoperability.Objectives: The aim of this study is to present a systematic review and mapping of the literature in order to identify, analyse and classify the published solutions to achieve pragmatic interoperability.Method: To conduct a systematic review and mapping in accordance with the guidelines proposed in the evidence-based software engineering literature.Results: Our study identified 13 papers reporting pragmatic interoperability computational solutions. The first paper in our set of selected papers was published in 2004; the main strategies used to address pragmatic interoperability issues were service discovery, composition and/or selection and ontologies. The application domain of the identified solutions was mainly e-business. In addition, most of the identified solutions were software architectures.Conclusion: Mature proposals addressing pragmatic interoperability are still rare in the literature. Although many works have discussed the importance of pragmatic interoperability, it is necessary that researchers report solutions that implement and evaluate pragmatic interoperability in order to make progress in this area.

A Scientific Software Product Line for the Bioinformatics domain

CONTEXT Most specialized users (scientists) that use bioinformatics applications do not have suitable training on software development. Software Product Line (SPL) employs the concept of reuse considering that it is defined as a set of systems that are developed from a common set of base artifacts. In some contexts, such as in bioinformatics applications, it is advantageous to develop a collection of related software products, using SPL approach. If software products are similar enough, there is the possibility of predicting their commonalities, differences and then reuse these common features to support the development of new applications in the bioinformatics area. OBJECTIVES This paper presents the PL-Science approach which considers the context of SPL and ontology in order to assist scientists to define a scientific experiment, and to specify a workflow that encompasses bioinformatics applications of a given experiment. This paper also focuses on the use of ontologies to enable the use of Software Product Line in biological domains. METHOD In the context of this paper, Scientific Software Product Line (SSPL) differs from the Software Product Line due to the fact that SSPL uses an abstract scientific workflow model. This workflow is defined according to a scientific domain and using this abstract workflow model the products (scientific applications/algorithms) are instantiated. RESULTS Through the use of ontology as a knowledge representation model, we can provide domain restrictions as well as add semantic aspects in order to facilitate the selection and organization of bioinformatics workflows in a Scientific Software Product Line. The use of ontologies enables not only the expression of formal restrictions but also the inferences on these restrictions, considering that a scientific domain needs a formal specification. CONCLUSIONS This paper presents the development of the PL-Science approach, encompassing a methodology and an infrastructure, and also presents an approach evaluation. This evaluation presents case studies in bioinformatics, which were conducted in two renowned research institutions in Brazil.

PL-Science: A Scientific Software Product Line☆

Abstract A way to improve reusability and maintainability of a family of software products is through the use of Software Product Line (SPL) approach. Software families, also named SPLs, are a set of software intensive systems sharing a common set of features which are managed to satisfy specific needs of a particular market segment or mission and that are developed from a common set of core assets in a prescribed way. This paper presents the PL-Science approach that considers the context of SPL and aims to assist scientists to define a scientific experiment, specifying a workflow that encompasses scientific applications of a given experiment. Using SPL concepts, scientists can reuse models that specify the scientific product line, and carefully can make decisions according to their needs. In the context of this paper, Scientific Software Product Lines (SSPL) differs from the Software Product Lines (SPL) due to the fact that SSPL uses an abstract scientific workflow model. This workflow is defined according to a scientific domain and, using this abstract workflow model, the products (scientific applications/algorithms) will be instantiated. This paper also focuses on the use of ontologies to facilitate the process of applying Software Product Line (SPL) to scientific domains. Through the use of ontology as a domain model, we can provide additional information as well as add more semantics in the context of Scientific Software Product Lines (SSPL).

SciProv: an architecture for semantic query in provenance metadata on e-science context

This article describes SciProv, an architecture that aims to interact with Scientific Workflow Management Systems in order to capture and manipulate provenance metadata. For this purpose, SciProv adopts an approach based on an abstract model for representing the lineage. This model, called Open Provenance Model (OPM), allows that SciProv can set up a homogeneous and interoperable infrastructure for handling provenance metadata. As a result, SciProv is able to provide a framework for query metadata provenance generated in an e-Science scenario. Moreover, the architecture uses semantic web technology in order to process provenance queries. In this context, using ontologies and inference engines, SciProv can make inferences about lineage and, based on these inferences, obtain important results based on extraction of information beyond those that are registered explicitly from the data managed.

A Framework for Provenance Analysis and Visualization

Abstract Data provenance is a fundamental concept in scientific experimentation. However, for their proper understanding and use, efficient and user-friendly mechanisms are needed. Research in software visualization, ontologies and complex networks can help in this process. This paper presents a framework to assist in the understanding and use of data provenance using visualization techniques, ontologies and complex networks. The framework capture the provenance data and generates new information using ontologies and provenance graph analysis. The graph is analyzed through complex networks techniques and provide some metrics to help in each node analyzes. The visualization presents and highlights the inferences and results. The framework was used in the E-SECO scientific ecosystem to support the scientific experimentation.

Rede de Ontologias: apoio semântico a linha de produtos de objetos de aprendizagem

The keynotes goal is to reflect on emergent opportunities for human Discovery (in science), Creativity (in art & industry), and Learning (in education) as processes often occurring serendipitously in individuals and in communities empowered by dynamic Web connections in the global village. These reflections seem to fit best with the mandate of the CBIE Conference: sustainable education.Este trabalho apresenta uma evolucao do assistente inteligente SAE para inferir e fornecer orientacao pedagogica coerente com varias metodologias educacionais, superando uma dificuldade tradicional para este tipo de software, alem de fornecer mais apoio ao ensino-aprendizagem personalizado.O artigo fundamenta-se nos resultados do processo de desenvolvimento de um ambiente web de aprendizagem, ja modelado em dissertacao de mestrado (CABRAL,2006). O sistema tem por objetivo facilitar o acompanhamento das atividades que envolvem a definicao e a elaboracao de pre-projetos de Trabalhos de Conclusao de Curso (TCC). Para atingir tal objetivo o sistema e baseado em uma camada de agentes inteligentes que atuam como colaboradores para execucao de todas as atividades necessarias ao desenvolvimento do TCC. Para que esses agentes atuem de forma satisfatoria no ambiente e necessario o estabelecimento de um processo de comunicacao que possibilite aos agentes agirem em um nivel conceitual mais proximo do ser humano. Dessa forma, este artigo expoe os resultados obtidos ao longo do desenvolvimento dos agentes computacioniais e seus mecanismos de comunicacao.Este artigo descreve o projeto de desenvolvimento de jogo educativo baseado em metodologias participativas, pelas quais estudantes da rede publica de ensino medio idealizam, projetam e desenvolvem prototipos de um jogo sobre Sistema Imunologico e virus da Dengue. O objetivo da pesquisa e verificar os impactos do processo sobre a aprendizagem dos estudantes.O objetivo deste artigo e apresentar resultados de estudo de um caso exploratorio, realizado junto aos alunos de uma Instituicao de Ensino Superior. Como resultados, foram levantados indicadores de avaliacao do Sistema de EaD e identificados problemas, segundo a percepcao dos alunos. A partir dos resultados destaca-se que a Universidade desconhece a metodologia ITIL® e que seria fundamental que fosse implantada uma estrategia do servico (fase inicial da ITIL®), conduzindo a melhoria continua do servico e da infra-estrutura da Universidade.O facil acesso as informacoes devido a difusao da internet possibilita o enriquecimento intelectual, mas por vezes acaba por ser um meio de usufruir do conhecimento de outrem sem mencionar seus creditos/direitos autorais, o que por fim acaba na configuracao do plagio. O plagio no meio academico e uma tarefa dificil de ser controlada, devido o grande numero de trabalhos que sao feitos por uma vasta quantidade de alunos e tambem pelo excesso de tarefas dos professores e pelo pouco tempo que conseguem dedicar para o controle da qualidade e autenticidade dos trabalhos. Com isso, e importante contar com softwares que auxiliem no processo de verificacao de indicios de plagio, desta maneira o presente trabalho vislumbra desenvolver uma nova ferramenta de analise de indicios de plagio bem como aprimorar o metodo DIP – Detector de Indicios de Plagio para auxiliar o docente na verificacao da autenticidade dos trabalhos.A Neuropedagogia promove o confronto sucessivo e simultâneo entre concepcoes tacitas, crencas e valores normativos com esquemas inovadores, criando um espaco entropico e poetico no âmbito da experiencia humana. A natureza da ciencia neuropedagogica exige um modelo fractal de construcao de mundo, sustentado pelo prazer da perplexidade. Busca-se a geratriz e as leis de formacao para atingir a unanimidade sobre o conceito de educacao de pessoas com alta dotacao humana, impossivel de se concretizar, sem o recurso das ideologias filosoficas, cientificas e tecnologias aliadas as eticas.In this talk I will elaborate on the development, implementation and evaluation of the use of online tools for learning, with special attention to games and gamification, sharing and collaboration.

SASAgent: An agent based architecture for search, retrieval and composition of scientific models

Scientific computing is a multidisciplinary field that goes beyond the use of computer as machine where researchers write simple texts, presentations or store analysis and results of their experiments. Because of the huge hardware/software resources invested in experiments and simulations, this new approach to scientific computing currently adopted by research groups is well represented by e-Science. This work aims to propose a new architecture based on intelligent agents to search, recover and compose simulation models, generated in the context of research projects related to biological domain. The SASAgent architecture is described as a multi-tier, comprising three main modules, where CelO ontology satisfies requirements put by e-science projects mainly represented by the semantic knowledge base. Preliminary results suggest that the proposed architecture is promising to achieve requirements found in e-Science projects, considering mainly the biological domain.

Information Extraction to improve Link Prediction in scientific social networks

Link Prediction is a classic social networks analysis problem. Knowing in advance future actions in social network can help, for example, agents decision. Link Prediction techniques are based on metrics that have different approaches. In this paper, we model a multi-relational scientific social network to assess the impact of content extraction on topological metrics. Thus, a metric composed of topological and semantic approach is proposed to solve link prediction problem. The results were compared with those presented by Katz metric.