PhenoMeNal: processing and analysis of metabolomics data in the cloud

Authors	PETERS K BRADBURY J BERGMANN S CAPUCCINI M CASCANTE M DE Atauri P EBBELS TMD FOGUET C GLEN R GONZALEZ-BELTRAN A GUNTHER UL HANDAKAS E HANKEMEIER T HAUG K HERMAN S HOLUB Petr IZZO M JACOB D JOHNSON D JOURDAN F KALE N KARAMAN I KHALILI B KHONSARI PE KULTIMA K LAMPA S LARSSON A LUDWIG C MORENO P NEUMANN S NOVELLA JA C O Donovan PEARCE JTM PELUSO A PIRAS ME PIREDDU L REED MAC ROCCA-SERRA P ROGER P ROSATO A RUEEDI R RUTTKIES C SADAWI N SALEK RM SANSONE SA SELIVANOV V SPJUTH O SCHOBER D THEVENOT EA TOMASONI M VAN RIJSWIJK M VAN VLIET M VIANT MR WEBER RJM ZANETTI G STEINBECK C
Year of publication	2019
Type	Article in Periodical
Magazine / Source	GIGASCIENCE
Citation
Web	https://academic.oup.com/gigascience/article/8/2/giy149/5232984
Doi	http://dx.doi.org/10.1093/gigascience/giy149
Keywords	metabolomics; data analysis; e-infrastructures; NMR; mass spectrometry; computational workflows; galaxy; cloud computing; standardization; statistics
Description	Background 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. Findings 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. Conclusions 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.