Cloud computing applications for biomedical science: A perspective

Navale, Vivek; Bourne, Philip E.

doi:10.1371/journal.pcbi.1006144

Cited by 81 publications

(56 citation statements)

References 37 publications

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“…Moreover, the EU ICT industrial ecosystem must be supported in order to alleviate the risks associated with storing and sharing data across cloud systems operated by non-EU companies. The EU has established a strict privacy and ethics policy through the implementation of the GDPR legislation, which is binding for all operators active in the EU territory [48][49][50][51].…”

Section: Need For Innovative Public-private Funding Initiativesmentioning

confidence: 99%

Towards a European health research and innovation cloud (HRIC)

Aarestrup

Albeyatti

Armitage³

et al. 2020

Genome Med

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The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action points to ensure that a European HRIC: i) is built on established standards and guidelines, providing cloud technologies through an open and decentralized infrastructure; ii) is developed and certified to the highest standards of interoperability and data security that can be trusted by all stakeholders; iii) is supported by a robust ethical and legal framework that is compliant with the EU General Data Protection Regulation (GDPR); iv) establishes a proper environment for the training of new generations of data and medical scientists; and v) stimulates research and innovation in transnational collaborations through public and private initiatives and partnerships funded by the EU through Horizon 2020 and Horizon Europe.

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Section: Need For Innovative Public-private Funding Initiativesmentioning

confidence: 99%

Towards a European health research and innovation cloud (HRIC)

Aarestrup

Albeyatti

Armitage³

et al. 2020

Genome Med

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show abstract

“…machine, software or human entry modes) to make data findable, accessible, interoperable and reusable (FAIR) 29 . In our opinion, a cloud-based data archive platform (shown in Figure 2 ) can provide a dynamic environment for managing research data life cycle along with capabilities for long-term preservation of biomedical data 30 .…”

Section: Archival Storagementioning

confidence: 99%

Long-term preservation of biomedical research data

Navale

McAuliffe

2018

F1000Res

Self Cite

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Genomics and molecular imaging, along with clinical and translational research have transformed biomedical science into a data-intensive scientific endeavor. For researchers to benefit from Big Data sets, developing long-term biomedical digital data preservation strategy is very important. In this opinion article, we discuss specific actions that researchers and institutions can take to make research data a continued resource even after research projects have reached the end of their lifecycle. The actions involve utilizing an Open Archival Information System model comprised of six functional entities: Ingest, Access, Data Management, Archival Storage, Administration and Preservation Planning. We believe that involvement of data stewards early in the digital data life-cycle management process can significantly contribute towards long term preservation of biomedical data. Developing data collection strategies consistent with institutional policies, and encouraging the use of common data elements in clinical research, patient registries and other human subject research can be advantageous for data sharing and integration purposes. Specifically, data stewards at the onset of research program should engage with established repositories and curators to develop data sustainability plans for research data. Placing equal importance on the requirements for initial activities (e.g., collection, processing, storage) with subsequent activities (data analysis, sharing) can improve data quality, provide traceability and support reproducibility. Preparing and tracking data provenance, using common data elements and biomedical ontologies are important for standardizing the data description, making the interpretation and reuse of data easier. The Big Data biomedical community requires scalable platform that can support the diversity and complexity of data ingest modes (e.g. machine, software or human entry modes). Secure virtual workspaces to integrate and manipulate data, with shared software programs (e.g., bioinformatics tools), can facilitate the FAIR (Findable, Accessible, Interoperable and Reusable) use of data for near- and long-term research needs.

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“…Growth of personal genomic data has been limited by bottlenecks in computational requirements and server capacity (O'Driscoll et al 2013). The NIH and several other institutions are moving toward cloud-computing-based services in order to overcome these bottlenecks (Patterson 2018;Navale and Bourne 2018;GovernmentCIO 2019). However, cloud-based storage and data analysis tools present security concerns, as they are based on a centralized architecture and are therefore vulnerable to single-point-of-failure losses (Ozercan et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Storing and analyzing a genome on a blockchain

Gürsoy

Brannon

Wagner

et al. 2020

Preprint

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The genomic characterization of individuals promises to be immensely useful for medical research. Moreover, sequencing, analysis, and interpretation of patients' genomes is projected to be a staple of healthcare in the future. A critical barrier to expanding personal genome sequencing is the ability to store genomic data securely and with high integrity. While cloud storage offers solutions to access such data from any place and device, the security, data integrity, and robustness vulnerabilities such as single-point-of failure losses have not yet been addressed. Here, we developed novel tools for decentralized storage, access, and analysis of genome sequencing data on private blockchain networks. Storing and analyzing large-scale data on a blockchain can be challenging because of the slow transaction speed and limitations on querying data stored on-chain. Hence, current genomic blockchain applications only log links to the data. We overcome this challenge by implementing data compression techniques and nested database indexing. Our tools provide open-source blockchain-based storage and access tools for advanced genomic analyses such as variant calling.

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Cloud computing applications for biomedical science: A perspective

Cited by 81 publications

References 37 publications

Towards a European health research and innovation cloud (HRIC)

Towards a European health research and innovation cloud (HRIC)

Long-term preservation of biomedical research data

Storing and analyzing a genome on a blockchain

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