PhenoMeNal: processing and analysis of metabolomics data in the cloud.

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State: Public
Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_18192C20F501
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
PhenoMeNal: processing and analysis of metabolomics data in the cloud.
Journal
GigaScience
Author(s)
Peters K., Bradbury J., Bergmann S., Capuccini M., Cascante M., de Atauri P., Ebbels TMD, Foguet C., Glen R., Gonzalez-Beltran A., Günther U.L., Handakas E., Hankemeier T., Haug K., Herman S., Holub P., Izzo M., Jacob D., Johnson D., Jourdan F., Kale N., Karaman I., Khalili B., Emami Khonsari P., Kultima K., Lampa S., Larsson A., Ludwig C., Moreno P., Neumann S., Novella J.A., O'Donovan C., Pearce JTM, Peluso A., Piras M.E., Pireddu L., Reed MAC, Rocca-Serra P., Roger P., Rosato A., Rueedi R., Ruttkies C., Sadawi N., Salek R.M., Sansone S.A., Selivanov V., Spjuth O., Schober D., Thévenot E.A., Tomasoni M., van Rijswijk M., van Vliet M., Viant M.R., Weber RJM, Zanetti G., Steinbeck C.
ISSN
2047-217X (Electronic)
ISSN-L
2047-217X
Publication state
Published
Issued date
01/02/2019
Peer-reviewed
Oui
Volume
8
Number
2
Pages
giy149
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution.
PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm.
PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.
Keywords
Cloud Computing, Humans, Metabolomics/methods, Software, Workflow, NMR, cloud computing, computational workflows, data analysis, e-infrastructures, galaxy, mass spectrometry, metabolomics, standardization, statistics
Pubmed
Web of science
Open Access
Yes
Create date
05/01/2019 16:48
Last modification date
20/08/2019 13:48
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