publication . Article . Preprint . 2019

On-demand virtual research environments using microservices

Marco Capuccini; Anders Larsson; Matteo Carone; Jon Ander Novella; Noureddin Sadawi; Jianliang Gao; Salman Toor; Ola Spjuth;
Open Access
  • Published: 01 Nov 2019 Journal: PeerJ Computer Science, volume 5, page e232 (eissn: 2376-5992, Copyright policy)
  • Publisher: PeerJ
Abstract
<jats:p> 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 scien...
Subjects
free text keywords: Data science, Resource allocation, Orchestration (computing), Ecology, Cloud computing, business.industry, business, On demand, Microservices, Biology, Computer Science - Distributed, Parallel, and Cluster Computing, Virtual research environments, Application containers, Orchestration, Electronic computers. Computer science, QA75.5-76.95
Related Organizations
Funded by
EC| PhenoMeNal
Project
PhenoMeNal
PhenoMeNal: A comprehensive and standardised e-infrastructure for analysing medical metabolic phenotype data
  • Funder: European Commission (EC)
  • Project Code: 654241
  • Funding stream: H2020 | RIA
43 references, page 1 of 3

[1] J. Tho¨ nes, “Microservices,” IEEE Software, vol. 32, no. 1, pp. 116-116, Jan 2015.

P. Emami Khoonsari, P. Moreno, S. Bergmann, J. Burman, M. Capuccini, M. Carone, M. Cascante, P. de Atauri, C. Foguet, A. GonzalezBeltran, T. Hankemeier, K. Haug, S. He, S. Herman, D. Johnson, N. Kale, A. Larsson, S. Neumann, K. Peters, L. Pireddu, P. RoccaSerra, P. Roger, R. Rueedi, C. Ruttkies, N. Sadawi, R. M. Salek, S.- A. Sansone, D. Schober, V. Selivanov, E. A. The´venot, M. van Vliet, G. Zanetti, C. Steinbeck, K. Kultima, and O. Spjuth, “Interoperable and scalable metabolomics data analysis with microservices,” bioRxiv, 2017.

D. D'Agostino, L. Roverelli, G. Zereik, A. D. Luca, R. Salvaterra, A. Belfiore, G. Lisini, G. Novara, and A. Tiengo, “A microservicebased portal for x-ray transient and variable sources,” PeerJ PrePrints, vol. 5, p. e2519, 2017.

C. Wu, R. Tobar, K. Vinsen, A. Wicenec, D. Pallot, B. Lao, R. Wang, T. An, M. Boulton, I. Cooper, R. Dodson, M. Dolensky, Y. Mei, and F. Wang, “Daliuge: A graph execution framework for harnessing the astronomical data deluge,” CoRR, vol. abs/1702.07617, 2017. [OpenAIRE]

Open Container Initiative, “The 5 principles of Standard Containers,” https://github.com/opencontainers/runtime-spec/blob/master/principles.

md, Dec. 2016, accessed 05-12-2017.

A. Shimel, “Docker becomes de facto Linux standard,” http://www.networkworld.com/article/2226751/opensource-subnet/ docker-becomes-de-facto-linux-standard.html, Apr. 2016, accessed 05-12-2017.

A. Khan, “Key characteristics of a container orchestration platform to enable a modern application,” IEEE Cloud Computing, vol. 4, no. 5, pp. 42-48, September 2017.

M. Asay, “Why Kubernetes is winning the container http://www.infoworld.com/article/3118345/cloud-computing/ why-kubernetes-is-winning-the-container-war.html, Sep.

accessed 05-12-2017.

war,” [9] “Kubespray,” https://github.com/kubernetes-incubator/kubespray, accessed 05-12-2017.

[10] M. Bayramusta and V. A. Nasir, “A fad or future of it?: A comprehensive literature review on the cloud computing research.” Int J. Information Management, vol. 36, no. 4, pp. 635-644, 2016. [OpenAIRE]

[11] I. A. Elia, N. Antunes, N. Laranjeiro, and M. Vieira, “An analysis of openstack vulnerabilities,” in 2017 13th European Dependable Computing Conference (EDCC), Sept 2017, pp. 129-134.

[12] “Amazon S3,” https://aws.amazon.com/s3/, accessed 09-01-2018.

[13] “Cloudflare,” https://www.cloudflare.com, accessed 05-12-2017.

43 references, page 1 of 3
Abstract
<jats:p> 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 scien...
Subjects
free text keywords: Data science, Resource allocation, Orchestration (computing), Ecology, Cloud computing, business.industry, business, On demand, Microservices, Biology, Computer Science - Distributed, Parallel, and Cluster Computing, Virtual research environments, Application containers, Orchestration, Electronic computers. Computer science, QA75.5-76.95
Related Organizations
Funded by
EC| PhenoMeNal
Project
PhenoMeNal
PhenoMeNal: A comprehensive and standardised e-infrastructure for analysing medical metabolic phenotype data
  • Funder: European Commission (EC)
  • Project Code: 654241
  • Funding stream: H2020 | RIA
43 references, page 1 of 3

[1] J. Tho¨ nes, “Microservices,” IEEE Software, vol. 32, no. 1, pp. 116-116, Jan 2015.

P. Emami Khoonsari, P. Moreno, S. Bergmann, J. Burman, M. Capuccini, M. Carone, M. Cascante, P. de Atauri, C. Foguet, A. GonzalezBeltran, T. Hankemeier, K. Haug, S. He, S. Herman, D. Johnson, N. Kale, A. Larsson, S. Neumann, K. Peters, L. Pireddu, P. RoccaSerra, P. Roger, R. Rueedi, C. Ruttkies, N. Sadawi, R. M. Salek, S.- A. Sansone, D. Schober, V. Selivanov, E. A. The´venot, M. van Vliet, G. Zanetti, C. Steinbeck, K. Kultima, and O. Spjuth, “Interoperable and scalable metabolomics data analysis with microservices,” bioRxiv, 2017.

D. D'Agostino, L. Roverelli, G. Zereik, A. D. Luca, R. Salvaterra, A. Belfiore, G. Lisini, G. Novara, and A. Tiengo, “A microservicebased portal for x-ray transient and variable sources,” PeerJ PrePrints, vol. 5, p. e2519, 2017.

C. Wu, R. Tobar, K. Vinsen, A. Wicenec, D. Pallot, B. Lao, R. Wang, T. An, M. Boulton, I. Cooper, R. Dodson, M. Dolensky, Y. Mei, and F. Wang, “Daliuge: A graph execution framework for harnessing the astronomical data deluge,” CoRR, vol. abs/1702.07617, 2017. [OpenAIRE]

Open Container Initiative, “The 5 principles of Standard Containers,” https://github.com/opencontainers/runtime-spec/blob/master/principles.

md, Dec. 2016, accessed 05-12-2017.

A. Shimel, “Docker becomes de facto Linux standard,” http://www.networkworld.com/article/2226751/opensource-subnet/ docker-becomes-de-facto-linux-standard.html, Apr. 2016, accessed 05-12-2017.

A. Khan, “Key characteristics of a container orchestration platform to enable a modern application,” IEEE Cloud Computing, vol. 4, no. 5, pp. 42-48, September 2017.

M. Asay, “Why Kubernetes is winning the container http://www.infoworld.com/article/3118345/cloud-computing/ why-kubernetes-is-winning-the-container-war.html, Sep.

accessed 05-12-2017.

war,” [9] “Kubespray,” https://github.com/kubernetes-incubator/kubespray, accessed 05-12-2017.

[10] M. Bayramusta and V. A. Nasir, “A fad or future of it?: A comprehensive literature review on the cloud computing research.” Int J. Information Management, vol. 36, no. 4, pp. 635-644, 2016. [OpenAIRE]

[11] I. A. Elia, N. Antunes, N. Laranjeiro, and M. Vieira, “An analysis of openstack vulnerabilities,” in 2017 13th European Dependable Computing Conference (EDCC), Sept 2017, pp. 129-134.

[12] “Amazon S3,” https://aws.amazon.com/s3/, accessed 09-01-2018.

[13] “Cloudflare,” https://www.cloudflare.com, accessed 05-12-2017.

43 references, page 1 of 3
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