PhenoMeNal Large Scale Computing for Medical Metabolomics Antonio Rosato [email protected] University of Florence, Italy
Feb 23, 2019
PhenoMeNal Large Scale Computing for Medical Metabolomics
Antonio Rosato [email protected]
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.
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.
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.