PhenoMeNal Large Scale Computing for Medical Metabolomics

Antonio Rosato rosato@cerm.unifi.it

University of Florence, Italy

PhenoMeNal Consortium

•  14 partners

•  3 years

•  8 Mio Euros

•  841 PMs

•  H2020 Societal Challenge in Health, Demographic Change and Well being.

•  Led by EMBL-EBI

Horizon2020 EINFRA-1-2014 PhenoMeNal

654241 PhenoMeNal – Part B - 38

The PhenoMeNal participants were carefully selected to reflect the different areas of impact addressed by the call and the work programme.

Figure 8: Consortium as a whole

3.4 Resources to be committed

3.4.1 Computational Resources that complement the EC contribution

All partners will contribute computational resources for developing and providing services to the PhenoMeNal infrastructure.

The hardware includes multiple servers on which the various Grid services are running (including the web portals), storage space on RAID systems and compute clusters. This will ensure a minimum computing capacity dedicated to the project. In the following, we are outlining the minimal contributions from each partner to the PhenoMeNal Grid/Cloud infrastructure.

Partner 1 (EMBL-EBI) develops and maintains a number of databases that are relevant for the PhenoMeNal project, including the MetaboLights database - the first open access, general purpose database for Metabolomics. EMBL-EBI will contribute support and development for the PhenoMeNal infrastructure through supporting the salary of the MetaboLights and PhenoMeNal coordinator. It contributes significant resources from its two Tier 3+ data centres in London and will contribute a sizable portion of its compute cluster with 771 nodes comprising 30000 hyper-threaded CPU cores, with a minimum of 100 contributed cores.

h"p://phenomenal-h2020.eu/home/

PhenoMeNal - Context

Holmes,E.,Wilson,I.D.andNicholson,J.K.(2008)Metabolicphenotypinginhealthanddisease.Cell,134,714–717.

Scientific motivation

AlzheimerDisease–redMildCogniPveImpairment-blue

PhenoMeNal - Key objectives

•  Understand the computational needs of the Clinical & Medical Metabolomics Community –  Infrastructure survey: goo.gl/6kArwA

•  Integrate and scale existing Open Source tools into a well-tested e-infrastructure.

Metabolomics in the cloud

Main components

DataProducer

PackagedDataToolContainers

Toolmaker

ComputeInfrastructure

PhenoMeNal VREPortalh"p://portal.phenomenal-h2020.eu/

VRE Portal http://portal.phenomenal-h2020.eu/

-  Three usability rounds

-  80% functionality running.

-  Public instance access.

-  App Library, hooked to EGI AppDB.

-  Documentation.

•  Thank you!

Summary

•  Infrastructure survey: goo.gl/6kArwA

Year1 Year2 Year3

x2