From the Elementary to the Circuitous: Digital Processing Workflows at FIU

This presentation was given at the FLVC regional conference at Broward College on May 7, 2015 and introduced scanning, processing, record creation, dissemination, and preservation in FIU Libraries' Digital Collections Center. The main focus was on processing, specifically employing OCR technology with difficult sources.

Free software and free culture in Higher Education: pipelines and workflows for creative purposes

OpenLab ESEV is a project of the School of Education of the Polytechnic Institute of Viseu (ESEV), Portugal, that aims to promote, foster and support the use of Free/Libre Software and Open Source Software, Open Educational Resources, Free Culture, Free file formats and more flexible copyright licenses for creative and educational purposes in the ESEV's domains of activity (education, arts, media). Most of the OpenLab ESEV activities are related to the teacher education and arts and multimedia programs, with a special focus on the later. In this paper, the project and some activities are presented, starting with its origins and its conceptual framework. The presented overview is intended as background for the examination of the use of Free/Libre Software and Free Culture in educational settings, specially at the higher education level, and for creative purposes. The activities developed with students and professionals generated pipelines and workflows implemented for different creative purposes, software packages used for different tasks, choices for file formats and copyright licenses. Finished and ongoing multimedia and arts projects will be presented as real case scenarios.

Integrating structural variant calling, annotation and prioritization into whole genome analysis workflows: a practical application in the molecular diagnosis of neurodevelopmental disorders

Background: WGS is increasingly used as a first-line diagnostic test for patients with rare genetic diseases such as neurodevelopmental disorders (NDD). Clinical applications require a robust infrastructure to support processing, storage and analysis of WGS data. The identification and interpretation of SVs from WGS data also needs to be improved. Finally, there is a need for a prioritization system that enables downstream clinical analysis and facilitates data interpretation. Here, we present the results of a clinical application of WGS in a cohort of patients with NDD. Methods: We developed highly portable workflows for processing WGS data, including alignment, quality control, and variant calling of SNVs and SVs. A benchmark analysis of state-of-the-art SV detection tools was performed to select the most accurate combination for SV calling. A gene-based prioritization system was also implemented to support variant interpretation. Results: Using a benchmark analysis, we selected the most accurate combination of tools to improve SV detection from WGS data and build a dedicated pipeline. Our workflows were used to process WGS data from 77 NDD patient-parent families. The prioritization system supported downstream analysis and enabled molecular diagnosis in 32% of patients, 25% of which were SVs and suggested a potential diagnosis in 20% of patients, requiring further investigation to achieve diagnostic certainty. Conclusion: Our data suggest that the integration of SNVs and SVs is a main factor that increases diagnostic yield by WGS and show that the adoption of a dedicated pipeline improves the process of variant detection and interpretation.

A performance analysis of mesh models for cloud-based workflows

Nell'ambito della loro trasformazione digitale, molte organizzazioni stanno adottando nuove tecnologie per supportare lo sviluppo, l'implementazione e la gestione delle proprie architetture basate su microservizi negli ambienti cloud e tra i fornitori di cloud. In questo scenario, le service ed event mesh stanno emergendo come livelli infrastrutturali dinamici e configurabili che facilitano interazioni complesse e la gestione di applicazioni basate su microservizi e servizi cloud. L’obiettivo di questo lavoro è quello di analizzare soluzioni mesh open-source (istio, Linkerd, Apache EventMesh) dal punto di vista delle prestazioni, quando usate per gestire la comunicazione tra applicazioni a workflow basate su microservizi all’interno dell’ambiente cloud. A questo scopo è stato realizzato un sistema per eseguire il dislocamento di ognuno dei componenti all’interno di un cluster singolo e in un ambiente multi-cluster. La raccolta delle metriche e la loro sintesi è stata realizzata con un sistema personalizzato, compatibile con il formato dei dati di Prometheus. I test ci hanno permesso di valutare le prestazioni di ogni componente insieme alla sua efficacia. In generale, mentre si è potuta accertare la maturità delle implementazioni di service mesh testate, la soluzione di event mesh da noi usata è apparsa come una tecnologia ancora non matura, a causa di numerosi problemi di funzionamento.

Using workflow technology to manage flexible e-learning services

Workflow technology provides a suitable platform to define and manage the coordination of business process activities. We introduce a flexible e-learning environment – called Flex-eL – that has been built upon workflow technology. The workflow functionality of Flex-eL manages the coordination of learning and assessment activities of the course process between students and teaching staff. It provides a unique environment for teachers to design and develop process-centric courses and to monitor student progress. It allows students to learn at their own pace while observing the learning guidelines and checkpoints modeled into the course process by teaching staff. We also report on the successful deployment of the concept and system for university courses and our experiences from the implementation.

Digital radiology and Picture Archiving and Communication System (PACS)

Plain radiography still accounts for the vast majority of imaging studies that are performed at multiple clinical instances. Digital detectors are now prominent in many imaging facilities and they are the main driving force towards filmless environments. There has been a working paradigm shift due to the functional separation of acquisition, visualization, and storage with deep impact in the imaging workflows. Moreover with direct digital detectors images are made available almost immediately. Digital radiology is now completely integrated in Picture Archiving and Communication System (PACS) environments governed by the Digital Imaging and Communications in Medicine (DICOM) standard. In this chapter a brief overview of PACS architectures and components is presented together with a necessarily brief account of the DICOM standard. Special focus is given to the DICOM digital radiology objects and how specific attributes may now be used to improve and increase the metadata repository associated with image data. Regular scrutiny of the metadata repository may serve as a valuable tool for improved, cost-effective, and multidimensional quality control procedures.

Dominant set approach to ECG biometrics

Electrocardiographic (ECG) signals are emerging as a recent trend in the field of biometrics. In this paper, we propose a novel ECG biometric system that combines clustering and classification methodologies. Our approach is based on dominant-set clustering, and provides a framework for outlier removal and template selection. It enhances the typical workflows, by making them better suited to new ECG acquisition paradigms that use fingers or hand palms, which lead to signals with lower signal to noise ratio, and more prone to noise artifacts. Preliminary results show the potential of the approach, helping to further validate the highly usable setups and ECG signals as a complementary biometric modality.

Informal learning recognition through a cloud ecosystem

Learning and teaching processes, like all human activities, can be mediated through the use of tools. Information and communication technologies are now widespread within education. Their use in the daily life of teachers and learners affords engagement with educational activities at any place and time and not necessarily linked to an institution or a certificate. In the absence of formal certification, learning under these circumstances is known as informal learning. Despite the lack of certification, learning with technology in this way presents opportunities to gather information about and present new ways of exploiting an individual’s learning. Cloud technologies provide ways to achieve this through new architectures, methodologies, and workflows that facilitate semantic tagging, recognition, and acknowledgment of informal learning activities. The transparency and accessibility of cloud services mean that institutions and learners can exploit existing knowledge to their mutual benefit. The TRAILER project facilitates this aim by providing a technological framework using cloud services, a workflow, and a methodology. The services facilitate the exchange of information and knowledge associated with informal learning activities ranging from the use of social software through widgets, computer gaming, and remote laboratory experiments. Data from these activities are shared among institutions, learners, and workers. The project demonstrates the possibility of gathering information related to informal learning activities independently of the context or tools used to carry them out.

Autonomic workflow activities: the award framework

Workflows have been successfully applied to express the decomposition of complex scientific applications. This has motivated many initiatives that have been developing scientific workflow tools. However the existing tools still lack adequate support to important aspects namely, decoupling the enactment engine from workflow tasks specification, decentralizing the control of workflow activities, and allowing their tasks to run autonomous in distributed infrastructures, for instance on Clouds. Furthermore many workflow tools only support the execution of Direct Acyclic Graphs (DAG) without the concept of iterations, where activities are executed millions of iterations during long periods of time and supporting dynamic workflow reconfigurations after certain iteration. We present the AWARD (Autonomic Workflow Activities Reconfigurable and Dynamic) model of computation, based on the Process Networks model, where the workflow activities (AWA) are autonomic processes with independent control that can run in parallel on distributed infrastructures, e. g. on Clouds. Each AWA executes a Task developed as a Java class that implements a generic interface allowing end-users to code their applications without concerns for low-level details. The data-driven coordination of AWA interactions is based on a shared tuple space that also enables support to dynamic workflow reconfiguration and monitoring of the execution of workflows. We describe how AWARD supports dynamic reconfiguration and discuss typical workflow reconfiguration scenarios. For evaluation we describe experimental results of AWARD workflow executions in several application scenarios, mapped to a small dedicated cluster and the Amazon (Elastic Computing EC2) Cloud.

Enabling Global Experiments With Interactive Reconfiguration And Steering By Multiple Users

In global scientific experiments with collaborative scenarios involving multinational teams there are big challenges related to data access, namely data movements are precluded to other regions or Clouds due to the constraints on latency costs, data privacy and data ownership. Furthermore, each site is processing local data sets using specialized algorithms and producing intermediate results that are helpful as inputs to applications running on remote sites. This paper shows how to model such collaborative scenarios as a scientific workflow implemented with AWARD (Autonomic Workflow Activities Reconfigurable and Dynamic), a decentralized framework offering a feasible solution to run the workflow activities on distributed data centers in different regions without the need of large data movements. The AWARD workflow activities are independently monitored and dynamically reconfigured and steering by different users, namely by hot-swapping the algorithms to enhance the computation results or by changing the workflow structure to support feedback dependencies where an activity receives feedback output from a successor activity. A real implementation of one practical scenario and its execution on multiple data centers of the Amazon Cloud is presented including experimental results with steering by multiple users.

Plataforma de interoperabilidade da Universidade da Beira Interior

Comunicação apresentada no 8º Congresso Nacional de Administração Pública - Desafios e Soluções, em Carcavelos de 21 a 22 de Novembro de 2011.

Sistema de Informação como suporte ao Sistema de Gestão da Qualidade

Dissertação de Mestrado em Engenharia Informática

Impacto clínico da tecnologia em ultra-sonografia

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Avaliação de Riscos para a Segurança da Informação no ISEP Aplicação ao Processo de Notas

Desde que existe informação, há necessidade de criar um sistema que permita gerir e garantir que a informação está segura e que cumpre os requisitos básicos de segurança. Como tal, é necessário desenvolver técnicas e mecanismos para que os requisitos sejam testados e melhorados continuamente. Com esta necessidade em vista, apareceram padrões que dão resposta a um conjunto vasto de problemas, em diferentes sistemas e aplicações diversas. Estes tornaram-se guias de reflexão para quem os analisava, de arquitetura para quem os implementava e modelos para quem os geria. O padrão ISO 27001 dá resposta aos cuidados a ter para se conseguir um sistema de gestão da segurança da informação eficaz e eficiente. Esta norma preocupa-se com os detalhes de aplicação até à forma como é implementado e arquitetado o sistema. Os processos, atividades, fluxos de trabalho são essenciais para que esta norma seja cumprida. É necessário um bom escrutínio dos processos e suas atividades, assim como um fluxo de trabalho bem definido com papéis e responsabilidades de cada ator. É necessário também assegurar a forma como é gerido, a sua verificação e melhoria contínua. Foi aplicado no ISEP um exercício com o qual se pretendeu verificar se os processos e outros aspetos seguiam estes cuidados e se estavam de acordo com a norma. Durante o exercício foram verificados processos dentro de um certo âmbito, todas as suas atividades, papéis e responsabilidades, verificação de recursos, aplicação de controlos e aplicação de uma análise de risco. Esta análise tem como objetivo verificar o nível de segurança dos recursos, algo que a norma ISO 27001 propõe mas não especifica em que moldes. No final deste exercício pretendeu-se melhorar o sistema de gestão de informação do ISEP em vertentes tais como a documentação, a qual especifica quais os passos realizados no decorrer do mesmo.

Impacto clínico da tecnologia em ultra-sonografia

Recentemente, a tecnologia em Ultra-sons (US) tem sofrido grandes avanços tecnológicos e, como resultado, novas técnicas e aplicações clínicas são introduzidas frequentemente. Estas técnicas inovadoras apresentam o potencial de assistir os médicos na caracterização de entidades clínicas e de melhorar a qualidade do diagnóstico clínico. No entanto, a implementação destas técnicas requer uma avaliação objectiva das suas potencialidade e limitações, assim como da sua performance clínica para permitir a sua adopção na prática clínica. Este projecto aborda duas patologias particulares: a Cardiomiopatia Cirrótica (CC) e lesões oncológicas mamárias. Considerando a primeira, é aplicada a tecnologia disponível, em especial a Aplicação Clínica VVI de modo a detectar anormalidades que possam não ser visíveis com recurso à ecocardiografia convencional, com o objectivo de definir critérios de diagnóstico precisos. Para a segunda, pretende-se efectuar uma avaliação da performance clínica de um novo método de quantificação em Elastografia - o Strain Ratio (SR) - que analisa a rigidez das lesões mamárias, permitindo assim um diagnóstico clínico mais completo e rigoroso. Para atingir estes objectivos, é efectuada uma análise extensiva, utilizando testes estatísticos como a One-Way ANOVA, permitindo que diferenças estatisticamente relevantes sejam encontradas nos parâmetros considerados. Outros testes foram usados em cada estudo clínico, tendo em conta as suas características específicas – a análise ROC é utilizada para quantificar o acréscimo que o SR poderá potencialmente trazer em relação às técnicas convencionais. Embora não tenha sido possível reunir todas as condições necessárias para validar a contribuição dos US para o diagnóstico da CC, foi possível encontrar evidências que corroboram tratar-se uma patologia clinicamente latente. Os resultados do segundo estudo evidenciam que o SR poderá ser introduzido nos workflows clínicos a curto prazo, tendo no entanto em consideração que este produz resultados mais fidedignos quando utilizado como ferramenta complementar de apoio à decisão clínica do que como um método de quantificação absoluta.