PhenoMeNal: processing and analysis of metabolomics data in the cloud
Authors: Peters Kristian , Bradbury James , Bergmann Sven , Capuccini Marco , Cascante Marta , de Atauri Pedro , Ebbels Timothy M D , Foguet Carles , Glen Robert , Gonzalez-Beltran Alejandra , Günther Ulrich L , Handakas Evangelos , Hankemeier Thomas , Haug Kenneth , Herman Stephanie , Holub Petr , Izzo Massimiliano , Jacob Daniel , Johnson David , Jourdan Fabien , Kale Namrata , Karaman Ibrahim , Khalili Bita , Emami Khonsari Payam , Kultima Kim , Lampa Samuel , Larsson Anders , Ludwig Christian , Moreno Pablo , Neumann Steffen , Novella Jon Ander , O'Donovan Claire , Pearce Jake T M , Peluso Alina , Piras Marco Enrico , Pireddu Luca , Reed Michelle A C , Rocca-Serra Philippe , Roger Pierrick , Rosato Antonio , Rueedi Rico , Ruttkies Christoph , Sadawi Noureddin , Salek Reza M , Sansone Susanna-Assunta , Selivanov Vitaly , Spjuth Ola , Schober Daniel , Thévenot Etienne A , Tomasoni Mattia , van Rijswijk Merlijn , van Vliet Michael , Viant Mark R , Weber Ralf J M , Zanetti Gianluigi , Steinbeck Christoph 
Published: December 2018

Abstract

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.