The document summarizes 10 years of the WeNMR thematic services which provide structural biology tools and resources powered by cloud computing infrastructure. Key points include:
- The services have over 13,000 registered users and served over 210,000 runs since 2008, with over 40% using grid resources.
- Continued growth has been enabled by high-throughput computing resources from successive EU projects over 10 years.
- Tools include the HADDOCK web portal for protein-protein docking and DISVIS/POWERFIT for GPU-accelerated analysis.
- Containerization using Docker and integration with the European Open Science Cloud help modernize services and ensure sustainability.
Driving Behavioral Change for Information Management through Data-Driven Gree...
Structural biology in the cloud powered by the WeNMR thematic services
1. Structural biology in the cloud
powered by the WeNMR thematic
services:
A success story of 10 years
Brian Jiménez-García – Alexandre M.J.J. Bonvin
Utrecht University
The Netherlands
b.jimenezgarcia@uu.nl
@irrati0nal
4. Haddock web portal
• > 13,000 registered users
• > 210,000 served runs since
June 2008
• > 40% on the GRID
Visit bonvinlab.org/softwareDe Vries et al. Nature Prot. 2010
Van Zundert et al. J.Mol.Biol. 2016
5. 10 years of serving the research
community
Made possible via HTC resources
provided by H2020 e-Infrastructure
projects over the years
6. European Open Science Cloud
CC
Under EGI-Engage
The eInfrastructure landscape over the years
bioexcel.eu
12. 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
§ Make their life easier
13. 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
§ Make their life easier
§ Develop software and maintain and operate a
complex infrastructure
15. HADDOCK development’s highlights
15
• New beta version of the server
https://wenmr.science.uu.nl/haddock2.4/
• Support for cryo-EM data1, cyclic peptides, etc.
M.E. Trellet et al. Protein-protein modelling using cryo-EM
restraints. Methods in Molecular Biology: Protein NMR Humana
Press, New York, NY, In Press (2019).
16. Automated deployment of the HADDOCK server
16
Migration from local provisioning to provisioning via docker-compose
• Improves portability and development
• Separation of the different components
• Important configuration stored in docker compose file
• Easy to switch between development/production configuration
• Easy scaling by deploying to a docker swarm
• Used in HelixNebula pilot project
• User database• Web portal• Static content
• SSL
20. GPGPU, GRID-enabled web portals
http://milou.science.uu.nl/enmr/services/DISVIS/ http://milou.science.uu.nl/enmr/services/POWERFIT/
21. Pre-processing
+
Input files
packaging
Architecture behind the portals
User DB
User not found
Input error
WEB CLIENT WEB SERVER MASTER NODE WORKING NODE
GPU-
calculation
Validation
Submission
to local
nodes
Submission
to grid
node
CPU-
calculation
Chimera
image
generation
Post-processing
+
Results formatting
Output files
packaging
+
submission of
image generation
OR
24. Conclusions & perspective
§ Successful operation of an e-infrastructure for structural
biology for > 10 years
§ WeNMR as early adopter / driver of new technology
(e.g. access to grid GPGPU resources with docker
containers)
§ Migration of servers to containers to facilitate
deployment and operation
