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On-demand virtual research environments using microservices
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Spjuth)ORCID iD: 0000-0002-4851-759x
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Spjuth group)ORCID iD: 0000-0002-2096-8102
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Spjuth group)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab. (Spjuth group)ORCID iD: 0000-0002-2187-5426
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2019 (English)In: PeerJ Computer Science, ISSN 2376-5992, Vol. 5, article id e232Article in journal (Refereed) Published
Abstract [en]

The computational demands for scientific applications are continuously increasing. The emergence of cloud computing has enabled on-demand resource allocation. However, relying solely on infrastructure as a service does not achieve the degree of flexibility required by the scientific community. Here we present a microservice-oriented methodology, where scientific applications run in a distributed orchestration platform as software containers, referred to as on-demand, virtual research environments. The methodology is vendor agnostic and we provide an open source implementation that supports the major cloud providers, offering scalable management of scientific pipelines. We demonstrate applicability and scalability of our methodology in life science applications, but the methodology is general and can be applied to other scientific domains.

Place, publisher, year, edition, pages
PeerJ Inc. , 2019. Vol. 5, article id e232
National Category
Computer Sciences Bioinformatics and Systems Biology
Research subject
Computer Science
Identifiers
URN: urn:nbn:se:uu:diva-400586DOI: 10.7717/peerj-cs.232OAI: oai:DiVA.org:uu-400586DiVA, id: diva2:1381809
Funder
EU, Horizon 2020, 654241NordForsk, NeIC Glenna2Available from: 2019-12-27 Created: 2019-12-27 Last updated: 2019-12-27

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Capuccini, MarcoLarsson, AndersNovella, Jon AnderToor, SalmanSpjuth, Ola

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Capuccini, MarcoLarsson, AndersNovella, Jon AnderToor, SalmanSpjuth, Ola
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