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Arteria: An automation system for a sequencing core facility.

ABSTRACT: 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.

SUBMITTER: Dahlberg J

PROVIDER: S-EPMC6905352 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Arteria: An automation system for a sequencing core facility.

Dahlberg Johan J Hermansson Johan J Sturlaugsson Steinar S Lysenkova Mariya M Smeds Patrik P Ladenvall Claes C Guimera Roman Valls RV Reisinger Florian F Hofmann Oliver O Larsson Pontus P

GigaScience 20191201 12

<h4>Background</h4>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 a ...[more]

PMID: 31825479

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Project description:PurposeThe purpose of this study was to develop an auto-planning platform to be interfaced with a commercial treatment planning system (TPS). The main goal was to obtain robust and high-quality plans for different anatomic sites and various dosimetric requirements.MethodsMonaco (Elekta, St. Louis, US) was the TPS in this work. All input parameters for inverse planning could be defined in a plan template inside Monaco. A software tool called Robot Framework was used to launch auto-planning trials with updated plan templates. The template modifier external to Monaco was the major component of our auto-planning platform. For current implementation, it was a rule-based system that mimics the trial-and-error process of an experienced planner. A template was automatically updated by changing the optimization constraints based on dosimetric evaluation of the plan obtained in the previous trial, along with the data of the iterative optimization extracted from Monaco. Treatment plans generated by Monaco with all plan evaluation criteria satisfied were considered acceptable, and such plans would be saved for further evaluation by clinicians. The auto-planning platform was validated for 10 prostate and 10 head-and-neck cases in comparison with clinical plans generated by experienced planners.ResultsThe performance and robustness of our auto-planning platform was tested with clinical cases of prostate and head and neck treatment. For prostate cases, automatically generated plans had very similar plan quality with the clinical plans, and the bladder volume receiving 62.5 Gy, 50 Gy, and 40 Gy in auto-plans was reduced by 1%, 3%, and 5%, respectively. For head and neck cases, auto-plans had better conformity with reduced dose to the normal structures but slightly higher dose inhomogeneity in the target volume. Remarkably, the maximum dose in the spinal cord and brain stem was reduced by more than 3.5 Gy in auto-plans. Fluence map optimization only with less than 30 trials was adequate to generate acceptable plans, and subsequent optimization for final plans was completed by Monaco without further intervention. The plan quality was weakly dependent on the parameter selection in the initial template and the choices of the step sizes for changing the constraint values.ConclusionAn automated planning platform to interface with Monaco was developed, and our reported tests showed preliminary results for prostate and head and neck cases.

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Arteria: An automation system for a sequencing core facility.

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Arteria: An automation system for a sequencing core facility.

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