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Arteria :
Arteria : An automation system for a sequencing core facility
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- Dahlberg, Johan (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Hermansson, Johan (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Molekylär medicin
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- Sturlaugsson, Steinar (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Lysenkova, Mariya (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Smeds, Patrik (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för immunologi, genetik och patologi
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- Ladenvall, Claes, PhD, 1974- (author)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab
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- Valls Guimera, Roman (author)
- University of Melbourne Center for Cancer Research, University of Melbourne, Melbourne, Australia
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- Reisinger, Florian (author)
- University of Melbourne Center for Cancer Research, University of Melbourne, Melbourne, Australia
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- Hofmann, Oliver (author)
- University of Melbourne Center for Cancer Research, University of Melbourne, Melbourne, Australia
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- Larsson, Pontus (author)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2019-12-11
- 2019
- English.
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In: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 8:12
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Abstract
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- Background: In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an automation system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities.Findings: Arteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/.Conclusions: We describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.
Subject headings
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Elektroteknik och elektronik -- Datorsystem (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Electrical Engineering, Electronic Engineering, Information Engineering -- Computer Systems (hsv//eng)
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- ref (subject category)
- art (subject category)
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- By the author/editor
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Dahlberg, Johan
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Hermansson, Joha ...
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Sturlaugsson, St ...
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Lysenkova, Mariy ...
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Smeds, Patrik
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Ladenvall, Claes ...
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Valls Guimera, R ...
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Reisinger, Flori ...
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Hofmann, Oliver
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Larsson, Pontus
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Bioinformatics
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- ENGINEERING AND TECHNOLOGY
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ENGINEERING AND ...
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and Electrical Engin ...
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and Computer Systems
- Articles in the publication
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GigaScience
- By the university
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Uppsala University