A formal architecture-centric and model driven approach for the engineering of science gateways

From n-Tier client/server applications, to more complex academic Grids, or even the most recent and promising industrial Clouds, the last decade has witnessed significant developments in distributed computing. In spite of this conceptual heterogeneity, Service-Oriented Architecture (SOA) seems to have emerged as the common and underlying abstraction paradigm, even though different standards and technologies are applied across application domains. Suitable access to data and algorithms resident in SOAs via so-called ‘Science Gateways’ has thus become a pressing need in order to realize the benefits of distributed computing infrastructures.In an attempt to inform service-oriented systems design and developments in Grid-based biomedical research infrastructures, the applicant has consolidated work from three complementary experiences in European projects, which have developed and deployed large-scale production quality infrastructures and more recently Science Gateways to support research in breast cancer, pediatric diseases and neurodegenerative pathologies respectively. In analyzing the requirements from these biomedical applications the applicant was able to elaborate on commonly faced issues in Grid development and deployment, while proposing an adapted and extensible engineering framework. Grids implement a number of protocols, applications, standards and attempt to virtualize and harmonize accesses to them. Most Grid implementations therefore are instantiated as superposed software layers, often resulting in a low quality of services and quality of applications, thus making design and development increasingly complex, and rendering classical software engineering approaches unsuitable for Grid developments.The applicant proposes the application of a formal Model-Driven Engineering (MDE) approach to service-oriented developments, making it possible to define Grid-based architectures and Science Gateways that satisfy quality of service requirements, execution platform and distribution criteria at design time. An novel investigation is thus presented on the applicability of the resulting grid MDE (gMDE) to specific examples and conclusions are drawn on the benefits of this approach and its possible application to other areas, in particular that of Distributed Computing Infrastructures (DCI) interoperability, Science Gateways and Cloud architectures developments

Position Paper: Secure Infrastructure for Scientific Data Life Cycle Management

Abstract—Within the Austrian Grid project phase 2, three different groups, each allocated to a different workpackage, join their efforts to implement a grid infrastructure for the european research project “Breath Gas Analysis for molecular oriented diseases”. This position paper provides background on the task and the resulting requirements, a presentation on solutions developed during related projects in the application domain, identifies problems that have not yet been solved, and finally presents the intended solution to be developed. I. INTRODUCTION & CONTEXT This position paper describes the current state, the in-tended realisation and a discussion of the project Grid Breath Gas Analysis (BAMOD-Grid) carried out withi

Providing traceability for neuroimaging analyses

IntroductionWith the increasingly digital nature of biomedical data and as the complexity of analyses in medical research increases, the need for accurate information capture, traceability and accessibility has become crucial to medical researchers in the pursuance of their research goals. Grid- or Cloud-based technologies, often based on so-called Service Oriented Architectures (SOA), are increasingly being seen as viable solutions for managing distributed data and algorithms in the bio-medical domain. For neuroscientific analyses, especially those centred on complex image analysis, traceability of processes and datasets is essential but up to now this has not been captured in a manner that facilitates collaborative study. Purpose and MethodFew examples exist, of deployed medical systems based on Grids that provide the traceability of research data needed to facilitate complex analyses and none have been evaluated in practice. Over the past decade, we have been working with mammographers, paediatricians and neuroscientists in three generations of projects to provide the data management and provenance services now required for 21st century medical research. This paper outlines the finding of a requirements study and a resulting system architecture for the production of services to support neuroscientific studies of biomarkers for Alzheimer’s Disease.ResultsThe paper proposes a software infrastructure and services that provide the foundation for such support. It introduces the use of the CRISTAL software to provide provenance management as one of a number of services delivered on a SOA, deployed to manage neuroimaging projects that have been studying biomarkers for Alzheimer’s disease. ConclusionsIn the neuGRID and N4U projects a Provenance Service has been delivered that captures and reconstructs the workflow information needed to facilitate researchers in conducting neuroimaging analyses. The software enables neuroscientists to track the evolution of workflows and datasets. It also tracks the outcomes of various analyses and provides provenance traceability throughout the lifecycle of their studies. As the Provenance Service has been designed to be generic it can be applied across the medical domain as a reusable tool for supporting medical researchers thus providing communities of researchers for the first time with the necessary tools to conduct widely distributed collaborative programmes of medical analysis

Data, metadata, and workflow in healthcare informatics

This dissertation considers a number of interlinked concepts, propositions and relations, and puts forward a set of design theses, to support the role of informatics in the overall goal of knowledge-based, information-driven, integrated, patient-centred, collaborative healthcare and research. This rather ambitious scope may be delimited by exclusion: the work is not concerned explicitly with genomics or bioinformatics, but it does encompass certain aspects of trans- lational medicine and personalized healthcare, which I take to be subsumed in some sense under “knowledge-based” and “information-driven”. Although I do not exclude public health informatics, my exposure extends only to surveillance of infectious diseases, patient engagement, and the effectiveness of screening programmes. I do take ethical, legal, social and economic issues (ELSE) to be included, at least to the extent that I aim at an infrastructure that encompasses these issues and aims to incorporate them in technical designs in an effort to meet ethicists’, lawyers’, policy makers’, and economists’ concerns halfway. To a first approx- imation, the aim has been to integrate two strands of work over the last decade or more: the informatics of medical records on one hand and the distributed computational infrastructures for healthcare and biomedical research on the other.The papers assembled in this dissertation span a period of rapid growth in biomedical inform- atics (BMIi). Their unifying theme was not declared programmatically at the beginning of this period, but rather developed, along with individual pieces of work, as my engagement – and that of my students – with BMI became more focused and penetrated deeper into the issues. Nevertheless, I believe I have learned something from each project I have been involved in and have brought this cumulative experience to bear on the central theme of my present work. My thematic vision is of a scientifically literate and engaged community whose members – citizens, patients, caregivers, advocates – are sufficiently interested in medical progress and in their own health to take ownership of their medical records, to subscribe to a research service that informs them about progress and about current studies that may interest them, and so take responsibility for their own and the health of those close to them. This entails many things: agreements on what constitutes legitimate data sharing and when such sharing may be permitted or required by the patient as owner of the data. It calls for a means of recognizing the intellectual contribution, and in some healthcare economies, the economic interest of a physician who generates that record. Ethically, it requires a consenting policy that allows patients to control who may approach them for participation in a study, whether as a subject, as a co-investigator, as a patient advocate, or as a lay advisor. Educationally, it requires willingness on the part of physician- researchers and scientists to disseminate what they have discovered and what they have learned in terms that are comprehensible to the interested lay participant—but do not speak down to her

Doctor of Philosophy

dissertationPublic health surveillance systems are crucial for the timely detection and response to public health threats. Since the terrorist attacks of September 11, 2001, and the release of anthrax in the following month, there has been a heightened interest in public health surveillance. The years immediately following these attacks were met with increased awareness and funding from the federal government which has significantly strengthened the United States surveillance capabilities; however, despite these improvements, there are substantial challenges faced by today's public health surveillance systems. Problems with the current surveillance systems include: a) lack of leveraging unstructured public health data for surveillance purposes; and b) lack of information integration and the ability to leverage resources, applications or other surveillance efforts due to systems being built on a centralized model. This research addresses these problems by focusing on the development and evaluation of new informatics methods to improve the public health surveillance. To address the problems above, we first identified a current public surveillance workflow which is affected by the problems described and has the opportunity for enhancement through current informatics techniques. The 122 Mortality Surveillance for Pneumonia and Influenza was chosen as the primary use case for this dissertation work. The second step involved demonstrating the feasibility of using unstructured public health data, in this case death certificates. For this we created and evaluated a pipeline iv composed of a detection rule and natural language processor, for the coding of death certificates and the identification of pneumonia and influenza cases. The second problem was addressed by presenting the rationale of creating a federated model by leveraging grid technology concepts and tools for the sharing and epidemiological analyses of public health data. As a case study of this approach, a secured virtual organization was created where users are able to access two grid data services, using death certificates from the Utah Department of Health, and two analytical grid services, MetaMap and R. A scientific workflow was created using the published services to replicate the mortality surveillance workflow. To validate these approaches, and provide proofs-of-concepts, a series of real-world scenarios were conducted

Uma rede telemática para a prestação regional de cuidados de saúde

Doutoramento em Engenharia InformáticaAs tecnologias de informação e comunicação na área da saúde não são só um instrumento para a boa gestão de informação, mas antes um fator estratégico para uma prestação de cuidados mais eficiente e segura. As tecnologias de informação são um pilar para que os sistemas de saúde evoluam em direção a um modelo centrado no cidadão, no qual um conjunto abrangente de informação do doente deve estar automaticamente disponível para as equipas que lhe prestam cuidados, independentemente de onde foi gerada (local geográfico ou sistema). Este tipo de utilização segura e agregada da informação clínica é posta em causa pela fragmentação generalizada das implementações de sistemas de informação em saúde. Várias aproximações têm sido propostas para colmatar as limitações decorrentes das chamadas “ilhas de informação” na saúde, desde a centralização total (um sistema único), à utilização de redes descentralizadas de troca de mensagens clínicas. Neste trabalho, propomos a utilização de uma camada de unificação baseada em serviços, através da federação de fontes de informação heterogéneas. Este agregador de informação clínica fornece a base necessária para desenvolver aplicações com uma lógica regional, que demostrámos com a implementação de um sistema de registo de saúde eletrónico virtual. Ao contrário dos métodos baseados em mensagens clínicas ponto-a-ponto, populares na integração de sistemas em saúde, desenvolvemos um middleware segundo os padrões de arquitetura J2EE, no qual a informação federada é expressa como um modelo de objetos, acessível através de interfaces de programação. A arquitetura proposta foi instanciada na Rede Telemática de Saúde, uma plataforma instalada na região de Aveiro que liga oito instituições parceiras (dois hospitais e seis centros de saúde), cobrindo ~350.000 cidadãos, utilizada por ~350 profissionais registados e que permite acesso a mais de 19.000.000 de episódios. Para além da plataforma colaborativa regional para a saúde (RTSys), introduzimos uma segunda linha de investigação, procurando fazer a ponte entre as redes para a prestação de cuidados e as redes para a computação científica. Neste segundo cenário, propomos a utilização dos modelos de computação Grid para viabilizar a utilização e integração massiva de informação biomédica. A arquitetura proposta (não implementada) permite o acesso a infraestruturas de e-Ciência existentes para criar repositórios de informação clínica para aplicações em saúde.Modern health information technology is not just a supporting instrument to good information management but a strategic requirement to provide more efficient and safer health care. Health information technology is a cornerstone to build the future patient-centric health care systems in which a comprehensive set of patient data will be available to the relevant care teams, in spite of where (system or service point) it was generated. Such secure and efficient use of clinical data is challenged by the existing fragmentation of health information systems implementation. Several approaches have been proposed to address the limitations of the so called “information silos” in healthcare, ranging from full centralization (a single system) to full-decentralized clinical message exchange networks. In this work we advocate the use of a service-based unification layer, by federating distributed heterogeneous information sources. This clinical information hub provides the basis to build regional-level applications, which we have demonstrated by implementing a virtual Electronic Health Record system. Unlike the message-driven, point-to-point approaches popular in health care systems integration, we developed a middleware layer, using J2EE architectural patterns, in which the common information is represented as an object model, accessible through programming interfaces. The proposed architecture was instantiated in the Rede Telemática da Saúde network, a platform deployed in the region of Aveiro connecting eight partner institutions (two hospitals and six primary care units), covering ~ 350,000 citizens, indexing information on more than 19,000,000 episodes of care and used by ~350 registered professionals. In addition to the regional health information collaborative platform (RTSys), we introduce a second line of research towards bridging the care networks and the science networks. In the later scenario, we propose the use of Grid computing to enable the massive use and integration of biomedical information. The proposed architecture (not implemented) enables to access existing e-Science infrastructures to create clinical information repositories for health applications