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This project has received funding from the European Union’s Horizon 2020 research
and innovation programme under grant agr...
Why MuG: The two genomics worlds
2
Structural biology
Genomics
...
Molecular Biology
Cell Biology
...
Output → structures
...
Why MuG: The dream
3
Why MuG: The Problems
4
Methods
developers
HPC
facilities
Biologists
Interoperability
Fast-evolving → Immature
Usability
L...
MuGVRE
→ 17 Tools & Visualizers
→ ~100 registered users
→ ~ 190GB of user’s data
→ 2 training workshops
→ 19 dissemination...
User perspective: Authentication
6
external ID providers
User perspective
7
GET DATA WORKSPACE TOOLS EXECUTION VISUALIZATION
from local file
from URL
from public data repository
8
GET DATA WORKSPACE TOOLS EXECUTION VISUALIZATION
User perspective
TOOLSGET DATA WORKSPACE
User perspective
EXECUTION VISUALIZATION
10
EXECUTION
User perspective
GET DATA WORKSPACE TOOLS VISUALIZATION
VISUALIZATION
User perspective:
GET DATA WORKSPACE TOOLS EXECUTION
User perspective
MuGVRE Backend - metadata driven
12
MuGVRE Backend - infrastructure
13
MuGVRE Backend - infrastructure
14
COMPSs → orchestrates tasks
→ dynamically scales resources
MuG-Tool API → standardize V...
MuGVRE Backend - infrastructure
15
SGE → enqueues to Tool VMs
→ oneFlow scales Tool VMs on demand
PMES → controls underlyi...
MuGVRE Backend - infrastructure
16
Linking to e-infrastructures
1717
Public
Repos
User interface
MuG @
MuG @ MuG
Repos
Data management (aim)
18
Single virtual data space
Public
Repos Tool’s execution
/ENA
PMES
/EBI_disk
PMES
NFS
/ENA
PMES
NFS
VRE
NFS
public
repository
API
public
repository
API
public
repositoryAPI
SGE
Da...
The MuG’s team
20
Genís Bayarri (IRB)
Marco Pasi (UNot)
Mark McDowall (EBI)
Modesto Orozco (IRB)
Josep Lluís Gelpí (BSC)
R...
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agr...
Register now!!
22
A joint MuG – BioExcel workshop
Multi-resolution Nucleic Acids Simulations
Date: 22nd
June 2018
Venue: B...
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Laia Codo: Multi Scale Genomics (MuG) project

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Laia Codo: Multi Scale Genomics (MuG) project
(EOSC hub week, Malaga, 16 - 20 April 2018)

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Laia Codo: Multi Scale Genomics (MuG) project

  1. 1. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 676556. e-Infrastructure for the Multi-Scale Complex Genomics VRE www.multiscalegenomics.eu/MuGVRE Laia Codó, Barcelona Supercomputing Center EOSC-hub week, Málaga 17th April
  2. 2. Why MuG: The two genomics worlds 2 Structural biology Genomics ... Molecular Biology Cell Biology ... Output → structures → ensembles → sequences Output → images → functions → chem. mechanisms
  3. 3. Why MuG: The dream 3
  4. 4. Why MuG: The Problems 4 Methods developers HPC facilities Biologists Interoperability Fast-evolving → Immature Usability Lack of standards No FAIR data Formats & types Unfriendly Undigested Disconnected
  5. 5. MuGVRE → 17 Tools & Visualizers → ~100 registered users → ~ 190GB of user’s data → 2 training workshops → 19 dissemination activities ….. and growing released Oct 17’ www.multiscalegenomics.eu/MuGVRE/
  6. 6. User perspective: Authentication 6 external ID providers
  7. 7. User perspective 7 GET DATA WORKSPACE TOOLS EXECUTION VISUALIZATION from local file from URL from public data repository
  8. 8. 8 GET DATA WORKSPACE TOOLS EXECUTION VISUALIZATION User perspective
  9. 9. TOOLSGET DATA WORKSPACE User perspective EXECUTION VISUALIZATION
  10. 10. 10 EXECUTION User perspective GET DATA WORKSPACE TOOLS VISUALIZATION
  11. 11. VISUALIZATION User perspective: GET DATA WORKSPACE TOOLS EXECUTION User perspective
  12. 12. MuGVRE Backend - metadata driven 12
  13. 13. MuGVRE Backend - infrastructure 13
  14. 14. MuGVRE Backend - infrastructure 14 COMPSs → orchestrates tasks → dynamically scales resources MuG-Tool API → standardize VRE communications → homogenize data access
  15. 15. MuGVRE Backend - infrastructure 15 SGE → enqueues to Tool VMs → oneFlow scales Tool VMs on demand PMES → controls underlying cloud via OCCI
  16. 16. MuGVRE Backend - infrastructure 16
  17. 17. Linking to e-infrastructures 1717 Public Repos User interface MuG @ MuG @ MuG Repos
  18. 18. Data management (aim) 18 Single virtual data space Public Repos Tool’s execution
  19. 19. /ENA PMES /EBI_disk PMES NFS /ENA PMES NFS VRE NFS public repository API public repository API public repositoryAPI SGE Data management (aim) NFS IRB_storage EBI_storage BSC_storage VM TOOL VM TOOL VM TOOL copy-on-read multiuser transparent (Fuse)
  20. 20. The MuG’s team 20 Genís Bayarri (IRB) Marco Pasi (UNot) Mark McDowall (EBI) Modesto Orozco (IRB) Josep Lluís Gelpí (BSC) Rosa Badia (BSC) Baptiste Grenier Enol Fernandez Lukasz Dutka Michal Orzechowski
  21. 21. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 676556. @MuG_genomics irbinfo.mug@irbbarcelona.org www.multiscalegenomics.eu Thank you!
  22. 22. Register now!! 22 A joint MuG – BioExcel workshop Multi-resolution Nucleic Acids Simulations Date: 22nd June 2018 Venue: Barcelona Supercomputing Center, Barcelona, SP | Multis-scale Genomics workshop for tool developers Tool integration into MuGVRE Date: September 2018 Venue: EMBL-EBI European Bioinformatics Institute, Hinxton, UK &

Laia Codo: Multi Scale Genomics (MuG) project (EOSC hub week, Malaga, 16 - 20 April 2018)

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