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WeNMR

WeNMR is a Virtual Research Community (VRC) supported by EGI. WeNMR aims at bringing together complementary research teams in the structural biology and life science area into a virtual research community at a worldwide level and providing them with a platform integrating and streamlining the computational approaches necessary for data analysis and modelling. 

The challenge

Creating a worldwide e-Infrastructure for NMR and Structural Biology

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences.

Since 2010, the WeNMR project has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI.

For WeNMR, the challenge is to provide the community with valuable tools on the one hand, and means of executing them in a user-friendly, efficient and cost-effective distributed manner on the other.

The solution

Collaboration and Support from EGI

Starting from 2016, WeNMR collaborates with seven EGI data centres allowing the scientific communities to use High-Throughput Computing and Online Storage services needed to develop portals for life and brain scientists worldwide.

Community Support

WeNMR benefits from a dedicated Competence Centre across the NGIs, involving user experts in the scientific domain, resource centres, and technology providers of the EGI. This collaboration was set-up with the goal to further support the community needs. 

Technical support

Technical support was provided by EGI to extend COVID-19 related research in the US using the computing resources provided by Open Science Grid.  Additional consultancy and technical support was also offered to integrate the EGI Workload Manager in the WeNMR portals to facilitate the distribution of computing jobs.

EGI services used by WeNMR

The WeNMR services suite are based on a web page front-end to the service exposed to the user, and a backend consisting of a variety of software and scripts.

The EGI Workload Manager service is used for distributing compute jobs.

The EGI computing and storage resources such as the EGI High-Throughput Compute and the EGI Online Storage serve to distribute the computations.
The EGI check in enables user registration and authentication mechanisms. And last but not least, the INDIGO-Datacloud udocker solution is used on some portals.

Services provided by EGI

EGI Workload Manager

Manage computing workloads in an efficient way

EGI High-Throughput Compute

Execute thousands of computational tasks to analyse large datasets

EGI Check-in

Login with your own credentials

EGI Online Storage

Store, share and access your files and their metadata on a global scale

Training and consultancy

Dedicated computing and storage for training and education and consultancy activities

udocker

Execute simple Docker containers in user space without requiring root privileges

Impact

392 active users

registered in the EGI Operations Portal

>29100 researchers and students

registered across 135 countries

17M HTC and 3.5M Cloud CPU hours

over the last 5 years

>32 HTC providers

of the EGI Federation are supporting the WeNMR VRC 

Support from EGI-ACE

60 millions CPU hours (opportunistic access)

540 vCPU cores, up to 1.3TB of RAM and 8TB of block storage

Highlights

HADDOCK to support COVID-19 research

In 2020, EGI contributed to port the HADDOCK in the EGI cloud resources operated by the providers supporting the WeNMR SLA and the resources provided by Open Science Grid (OSG).

WeNMR demonstrator at the EOSC launch event

The WeNMR suite for structural biology was the focus of one of the demonstrators presented during the EOSC launch event in Vienna, on 23 November 2018.

Alexandre M.J.J. Bonvin,
Professor of Computational Structural Biology, Faculty of Science - Chemistry, Utrecht University, the Netherlands

“Without the continuous support of EGI over the years, we could not have grown the WeNMR user community and our services to the size, success and worldwide impact they have today. We are surely looking forward to many more years of symbiosis between WeNMR and EGI”.

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