Reflectance Transformation Imaging (RTI) System for Ancient Documentary Artefacts

This tutorial summarises our uses of reflectance transformation imaging in archaeological contexts. It introduces the UK AHRC funded project reflectance Transformation Imaging for Anciant Documentary Artefacts and demonstrates imaging methodologies

Workflow Provenance: from Modeling to Reporting

Workflow provenance is a crucial part of a workflow system as it enables data lineage analysis, error tracking, workflow monitoring, usage pattern discovery, and so on. Integrating provenance into a workflow system or modifying a workflow system to capture or analyze different provenance information is burdensome, requiring extensive development because provenance mechanisms rely heavily on the modelling, architecture, and design of the workflow system. Various tools and technologies exist for logging events in a software system. Unfortunately, logging tools and technologies are not designed for capturing and analyzing provenance information. Workflow provenance is not only about logging, but also about retrieving workflow related information from logs. In this work, we propose a taxonomy of provenance questions and guided by these questions, we created a workflow programming model 'ProvMod' with a supporting run-time library to provide automated provenance and log analysis for any workflow system. The design and provenance mechanism of ProvMod is based on recommendations from prominent research and is easy to integrate into any workflow system. ProvMod offers Neo4j graph database support to manage semi-structured heterogeneous JSON logs. The log structure is adaptable to any NoSQL technology. For each provenance question in our taxonomy, ProvMod provides the answer with data visualization using Neo4j and the ELK Stack. Besides analyzing performance from various angles, we demonstrate the ease of integration by integrating ProvMod with Apache Taverna and evaluate ProvMod usability by engaging users. Finally, we present two Software Engineering research cases (clone detection and architecture extraction) where our proposed model ProvMod and provenance questions taxonomy can be applied to discover meaningful insights

Reprodutibilidade e reuso de experimentos em eScience : workflows, ontologias e scripts

Orientadores: Claudia Maria Bauzer Medeiros, Yolanda GilTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Scripts e Sistemas Gerenciadores de Workflows Científicos (SGWfC) são abordagens comumente utilizadas para automatizar o fluxo de processos e análise de dados em experimentos científicos computacionais. Apesar de amplamente usados em diversas disciplinas, scripts são difíceis de entender, adaptar, reusar e reproduzir. Por esta razão, diversas soluções têm sido propostas para auxiliar na reprodutibilidade de experimentos que utilizam ambientes baseados em scripts. Porém, estas soluções não permitem a documentação completa do experimento, nem ajudam quando outros cientistas querem reusar apenas parte do código do script. SGWfCs, por outro lado, ajudam na documentação e reuso através do suporte aos cientistas durante a modelagem e execução dos seus experimentos, que são especificados e executados como componentes interconectados (reutilizáveis) de workflows. Enquanto workflows são melhores que scripts para entendimento e reuso dos experimentos, eles também exigem documentação adicional. Durante a modelagem de um experimento, cientistas frequentemente criam variantes de workflows, e.g., mudando componentes do workflow. Reuso e reprodutibilidade exigem o entendimento e rastreamento da proveniência das variantes, uma tarefa que consome muito tempo. Esta tese tem como objetivo auxiliar na reprodutibilidade e reuso de experimentos computacionais. Para superar estes desafios, nós lidamos com dois problemas de pesquisas: (1) entendimento de um experimento computacional, e (2) extensão de um experimento computacional. Nosso trabalho para resolver estes problemas nos direcionou na escolha de workflows e ontologias como respostas para ambos os problemas. As principais contribuições desta tese são: (i) apresentar os requisitos para a conversão de experimentos baseados em scripts em experimentos reprodutíveis; (ii) propor uma metodologia que guia o cientista durante o processo de conversão de experimentos baseados em scripts em workflow research objects reprodutíveis. (iii) projetar e implementar funcionalidades para avaliação da qualidade de experimentos computacionais; (iv) projetar e implementar o W2Share, um arcabouço para auxiliar a metodologia de conversão, que explora ferramentas e padrões que foram desenvolvidos pela comunidade científica para promover o reuso e reprodutibilidade; (v) projetar e implementar o OntoSoft-VFF, um arcabouço para captura de informação sobre software e componentes de workflow para auxiliar cientistas a gerenciarem a exploração e evolução de workflows. Nosso trabalho é apresentado via casos de uso em Dinâmica Molecular, Bioinformática e Previsão do TempoAbstract: Scripts and Scientific Workflow Management Systems (SWfMSs) are common approaches that have been used to automate the execution flow of processes and data analysis in scientific (computational) experiments. Although widely used in many disciplines, scripts are hard to understand, adapt, reuse, and reproduce. For this reason, several solutions have been proposed to aid experiment reproducibility for script-based environments. However, they neither allow to fully document the experiment nor do they help when third parties want to reuse just part of the code. SWfMSs, on the other hand, help documentation and reuse by supporting scientists in the design and execution of their experiments, which are specified and run as interconnected (reusable) workflow components (a.k.a. building blocks). While workflows are better than scripts for understandability and reuse, they still require additional documentation. During experiment design, scientists frequently create workflow variants, e.g., by changing workflow components. Reuse and reproducibility require understanding and tracking variant provenance, a time-consuming task. This thesis aims to support reproducibility and reuse of computational experiments. To meet these challenges, we address two research problems: (1) understanding a computational experiment, and (2) extending a computational experiment. Our work towards solving these problems led us to choose workflows and ontologies to answer both problems. The main contributions of this thesis are thus: (i) to present the requirements for the conversion of script to reproducible research; (ii) to propose a methodology that guides the scientists through the process of conversion of script-based experiments into reproducible workflow research objects; (iii) to design and implement features for quality assessment of computational experiments; (iv) to design and implement W2Share, a framework to support the conversion methodology, which exploits tools and standards that have been developed by the scientific community to promote reuse and reproducibility; (v) to design and implement OntoSoft-VFF, a framework for capturing information about software and workflow components to support scientists manage workflow exploration and evolution. Our work is showcased via use cases in Molecular Dynamics, Bioinformatics and Weather ForecastingDoutoradoCiência da ComputaçãoDoutor em Ciência da Computação2013/08293-7, 2014/23861-4, 2017/03570-3FAPES