Building bridges between services and e-Infrastructure in - - PowerPoint PPT Presentation

Building bridges between services and e-Infrastructure in structural biology

Alexandre Bonvin

Utrecht University The Netherlands a.m.j.j.bonvin@uu.nl

European Open Science Cloud CC

Under EGI-Engage

The structural biology e-Infrastructure landscape over the years

European Open Science Cloud CC

Under EGI-Engage

The structural biology e-Infrastructure landscape over the years

Virtual Research Community

# Number of dimensions 2 # INAME 1 1H # INAME 2 1H 12 2.137 2.387 1 T 0.000e+00 0.00e+00 - 0 2756 2760 0 14 2.387 4.140 1 T 0.000e+00 0.00e+00 - 0 2760 2752 0 32 1.849 4.432 1 T 0.000e+00 0.00e+00 - 0 2259 2257 0 36 1.849 3.143 1 T 0.000e+00 0.00e+00 - 0 2259 2587 0 39 1.760 4.432 1 T 0.000e+00 0.00e+00 - 0 2260 2257 0 40 1.760 1.849 1 T 0.000e+00 0.00e+00 - 0 2260 2259 0 43 1.760 3.143 1 T 0.000e+00 0.00e+00 - 0 2260 2587 0 46 1.649 4.432 1 T 1.035e+05 0.00e+00 r 0 2583 2257 0 47 1.649 1.849 1 T 0.000e+00 0.00e+00 - 0 2583 2259 0 assign ( resid 501 and name OO ) ( resid 501 and name Z ) ( resid 501 and name X ) ( resid 501 and name Y ) ( resid 2 and name CA ) -0.1400 0.15000 assign ( resid 501 and name OO ) ( resid 501 and name Z ) ( resid 501 and name X ) ( resid 501 and name Y ) ( resid 3 and name CA ) -0.0100 0.15000

Data interpretation

Structure, dynamics & interactions è impact on research and health:

• origin of disease
• design of new experiments
• drug design…

Exploiting GRID resources in structural biology…

Computations

NMR data collection and processing SAXS data analysis

eScience hub for NMR and structural biology

Infrastructure Science Community Knowledge

The WeNMR VRC

www.wenmr.eu

WeNMR VRC (February 2018)

• enmr.eu: One of the largest (#users) VO in life sciences
• >830 users have registered so far(36% outside EU)
• Support from >40 sites for >200’000 CPU cores via EGI infrastructure
• User-friendly access to Grid via web portals
• Supported by an SLA (2016, updated in 2017) with EGI and NGIs

www.wenmr.eu

NMR SAXS

A worldwide e-Infrastructure for NMR and structural biology

Sustained growth of the WeNMR VRC

250 500 750 1000 1250 1500 1750 2000 2250 2500 2750 3000 3250 3500

2011-01 2011-04 2011-07 2011-10 2012-01 2012-04 2012-07 2012-10 2013-01 2013-04 2013-07 2013-10 2014-01 2014-04 2014-07 2014-10 2015-01 2015-04 2015-07 2015-10 2016-01 2016-04 2016-07 2016-10 2017-01 2017-04 2017-07 2017-10 2018-01

50000 100000 150000 200000 250000 300000 350000 400000 450000 500000

2009/1 2009/4 2009/7 2009/10 2010/1 2010/4 2010/7 2010/10 2011/1 2011/4 2011/7 2011/10 2012/1 2012/4 2012/7 2012/10 2013/1 2013/4 2013/7 2013/10 2014/1 2014/4 2014/7 2014/10 2015/1 2015/4 2015/7 2015/10 2016/1 2016/4 2016/7 2016/10 2017/1 2017/4 2017/7 2017/10

enmr.eu VO grid jobs

Operational since 10 years

End of WeNMR funding Start of EGI-Engage Start of West-Life End of eNMR

~2400 normalized CPU years over 2017

The West-Life VRE

west-life.eu

Challenges & e-Solutions

§ Attract users!

§ Offer them top of the line eScience solutions for their research ... which means top of the line software

The West-Life VRE

west-life.eu

Thematic services under EOSC-Hub

https://www.egi.eu/use-cases/scientific-applications-tools/

Challenges & e-Solutions

§ Attract users!

§ Offer them top of the line eScience solutions for their research ... which means top of the line software § Provide them training, tutorials and support

West-Life knowledge and support center

• Various online

tutorials aggregated in the support center

Challenges & e-Solutions

§ Attract users!

§ Offer them top of the line eScience solutions for their research ... which means top of the line softwares) § Provide them training, tutorials and support § Make their life easier è SSO mechanisms è Build bridges between applications and with e-infrastructure solutions

European Open Science Cloud CC

Under EGI-Engage

Building bridges

Building bridges between services

SCIPION cloud server in production

West-Life: Cryo-EM in the clouds

indigodatacloudapps/disvis indigodatacloudapps/powerfit

udocker (Userspace Container Support)

New grid, GPGPU-enabled web portals: DISVIS & POWERFIT

http://milou.science.uu.nl/enmr/services/DISVIS/ http://milou.science.uu.nl/enmr/services/POWERFIT/

• Hosted in Utrecht
• Implement INDIGO-Datacloud solutions
• Runs on GPGPU resources in Florence

Scipion – PowerFit workflow

FANTEN – HADDOCK workflow

Building bridges with “cloud” storage

The West-Life VRE

west-life.eu

The West-Life Virtual Folder

The West-Life Virtual Folder

SSO authentification via INSTRUCT-ERIC

The West-Life Virtual Folder

Allows to aggregate storage providers

The West-Life Virtual Folder

Allows to browse storage

West-Life VMs

West-Life VMs

Available from EGI AppDB

West-Life Virtual Folder

More on the West-Life GitHub repo

Implementation in a web portal

Implementation in a web portal

Implementation in a web portal

Conclusions

• Life of users made easier by offering direct

connections between portals (no need to download and upload data)

• West-Life Virtual Folder solution
• Aggregated view of data
• Direct transfer to portal via webdav
• Future: Direct upload of results to Virtual

Folder

Conclusions

• Life of users made easier by offering direct

connections between portals (no need to download and upload data)

• West-Life Virtual Folder solution
• Aggregated view of data
• Direct transfer to portal via webdav
• Present Future: Direct upload of results to

Virtual Folder

Implementation in a web portal

Acknowledgments:

the CSB group@UU

VICI TOP-PUNT WeNMR West-Life EGI-Engage INDIGO- Datacloud BioExcel CoE EOSC-Hub SURFSara

€€

Thank you for your attention!

http://bonvinlab.org