Building bridges between services and e-Infrastructure in structural biology Alexandre Bonvin Utrecht University The Netherlands a.m.j.j.bonvin@uu.nl
The structural biology e-Infrastructure landscape over the years CC Under EGI-Engage European Open Science Cloud
The structural biology e-Infrastructure landscape over the years CC Under EGI-Engage European Open Science Cloud
Virtual Research Community
Exploiting GRID resources in structural biology… NMR data collection and processing SAXS data analysis # 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 Data 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 assign ( resid 501 and name OO ) 40 1.760 1.849 1 T 0.000e+00 0.00e+00 - 0 2260 2259 0 ( resid 501 and name Z ) 43 1.760 3.143 1 T 0.000e+00 0.00e+00 - 0 2260 2587 0 ( resid 501 and name X ) interpretation 46 1.649 4.432 1 T 1.035e+05 0.00e+00 r 0 2583 2257 0 ( resid 501 and name Y ) 47 1.649 1.849 1 T 0.000e+00 0.00e+00 - 0 2583 2259 0 ( 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 Computations Structure, dynamics & interactions è impact on research and health: - origin of disease - design of new experiments - drug design…
Community The WeNMR VRC Infrastructure Knowledge Science eScience hub for NMR and structural biology
www.wenmr.eu
NMR SAXS A worldwide e-Infrastructure for NMR and structural biology 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
Sustained growth of the WeNMR VRC 1000 1250 1500 1750 2000 2250 2500 2750 3000 3250 3500 250 500 750 0 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
100000 150000 200000 250000 300000 350000 400000 450000 500000 50000 0 2009/1 2009/4 2009/7 2009/10 2010/1 Operational since 10 years 2010/4 2010/7 eNMR End of 2010/10 2011/1 ~2400 normalized CPU years over 2017 2011/4 2011/7 enmr.eu VO grid jobs 2011/10 2012/1 2012/4 2012/7 2012/10 2013/1 2013/4 WeNMR funding 2013/7 End of Start of EGI-Engage 2013/10 2014/1 2014/4 2014/7 2014/10 2015/1 Start of West-Life 2015/4 2015/7 2015/10 2016/1 2016/4 2016/7 2016/10 2017/1 2017/4 2017/7 2017/10
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
Building bridges CC Under EGI-Engage European Open Science Cloud
Building bridges between services
West-Life: Cryo-EM in the clouds SCIPION cloud server in production
New grid, GPGPU-enabled web portals: DISVIS & POWERFIT indigodatacloudapps/ disvis indigodatacloudapps/ powerfit udocker (Userspace Container Support) 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
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