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

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. Why MuG: The two genomics worlds
2
Structural biology
Genomics
...
Molecular Biology
Cell Biology
...
Output → structures
→ ensembles
→ sequences
Output → images
→ functions
→ chem. mechanisms

3. Why MuG: The dream
3

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. 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. User perspective: Authentication
6
external ID providers

7. User perspective
7
GET DATA WORKSPACE TOOLS EXECUTION VISUALIZATION
from local file
from URL
from public data repository

8. 8
GET DATA WORKSPACE TOOLS EXECUTION VISUALIZATION
User perspective

9. TOOLSGET DATA WORKSPACE
User perspective
EXECUTION VISUALIZATION

10. 10
EXECUTION
User perspective
GET DATA WORKSPACE TOOLS VISUALIZATION

11. VISUALIZATION
User perspective:
GET DATA WORKSPACE TOOLS EXECUTION
User perspective

12. MuGVRE Backend - metadata driven
12

13. MuGVRE Backend - infrastructure
13

14. MuGVRE Backend - infrastructure
14
COMPSs → orchestrates tasks
→ dynamically scales resources
MuG-Tool API → standardize VRE communications
→ homogenize data access

15. MuGVRE Backend - infrastructure
15
SGE → enqueues to Tool VMs
→ oneFlow scales Tool VMs on demand
PMES → controls underlying cloud via OCCI

16. MuGVRE Backend - infrastructure
16

17. Linking to e-infrastructures
1717
Public
Repos
User interface
MuG @
MuG @ MuG
Repos

18. Data management (aim)
18
Single virtual data space
Public
Repos Tool’s execution

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. 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. 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. 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
&