Unifying European Biodiversity Informatics (BioUnify)

In order to preserve the variety of life on Earth, we must understand it better. Biodiversity research is at a pivotal point with research projects generating data at an ever increasing rate. Structuring, aggregating, linking and processing these data in a meaningful way is a major challenge. The systematic application of information management and engineering technologies in the study of biodiversity (biodiversity informatics) help transform data to knowledge. However, concerted action is required to be taken by existing e-infrastructures to develop and adopt common standards, provisions for interoperability and avoid overlapping in functionality. This would result in the unification of the currently fragmented landscape that restricts European biodiversity research from reaching its full potential. The overarching goal of this COST Action is to coordinate existing research and capacity building efforts, through a bottom-up trans-disciplinary approach, by unifying biodiversity informatics communities across Europe in order to support the long-term vision of modelling biodiversity on earth. BioUnify will: 1. specify technical requirements, evaluate and improve models for efficient data and workflow storage, sharing and re-use, within and between different biodiversity communities; 2. mobilise taxonomic, ecological, genomic and biomonitoring data generated and curated by natural history collections, research networks and remote sensing sources in Europe; 3. leverage results of ongoing biodiversity informatics projects by identifying and developing functional synergies on individual, group and project level; 4. raise technical awareness and transfer skills between biodiversity researchers and information technologists; 5. formulate a viable roadmap for achieving the long-term goals for European biodiversity informatics, which ensures alignment with global activities and translates into efficient biodiversity policy

Automated, Systematic and Parallel Approaches to Software Testing in Bioinformatics

Software quality assurance becomes especially critical if bioinformatics tools are to be used in a translational medical setting, such as analysis and interpretation of biological data. We must ensure that only validated algorithms are used, and that they are implemented correctly in the analysis pipeline – and not disrupted by hardware or software failure. In this thesis, I review common quality assurance practice and guidelines for bioinformatics software testing. Furthermore, I present a novel cloud-based framework to enable automated testing of genetic sequence alignment programs. This framework performs testing based on gold standard simulation data sets, and metamorphic testing. I demonstrate the effectiveness of this cloudbased framework using two widely used sequence alignment programs, BWA and Bowtie, and some fault-seeded ‘mutant’ versions of BWA and Bowtie. This preliminary study demonstrates that this type of cloud-based software testing framework is an effective and promising way to implement quality assurance in bioinformatics software that is used in genomic medicine

Small fish in a big pond: an architectural approach to users privacy, rights and security in the age of big data

We focus on the challenges and issues associated with Big Data, and propose a novel architecture that uses the principles of Separation of Concerns and distributed computing to overcome many of the challenges associated with storage, analysis and integrity. We address the issue of asymmetrical distribution of power between the originators of data and the organizations and institutions that make use of that data by taking a systemic perspective to include both sides in our architectural design, shifting from a customer-provider relationship to a more symbiotic one in which control over access to customer data resides with the customer. We illustrate the affordances of the proposed architecture by describing its application in the domain of Social Networking Sites, where we furnish a mechanism to address problems of privacy and identity, and create the potential to open up online social networking to a richer set of possible applications

Protecting the Privacy of Canadians\u27 Health Information in the Cloud

This article presents results from a year-long research project reviewing health privacy issues in the cloud, funded by the Contributions Program of the Office of the Privacy Commissioner of Canada (OPC). Section I provides a brief primer on cloud computing and its applications in data-centric health research and health care. Section II reviews Canadian privacy and health privacy laws and how they apply to CSPs. Section III identifies privacy risks arising from the technological, organizational, and jurisdictional complexity of cloud computing. Section IV argues that Canadian health privacy laws fail to address difficulties custodians face in balancing responsibilities with CSPs, determining whether foreign laws offer comparable protection, and ensuring transparency is maintained as data migrates to the cloud. In Section V, we survey standard agreements (Terms of Service) and privacy policies of leading CSPs, arguing that cloud contracts do not sufficiently address gaps in legislative protection for privacy and security. In Section VI, we identify the discrepancies in Canadian laws that apply to PHI which threaten interoperability of cloud contracts across provinces. This review is the first comprehensive review of legal and contractual privacy protections in the Canadian health sector. By identifying potential gaps in protection, we aim to inform the business decisions and contractual practices of both custodians and CSPs in Canada. By identifying discrepancies across provinces, we also aim to stimulate cooperative reform and harmonization of health privacy governance across Canada