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BIOMED

BioMed: High Throughput Compute platform for image analysis in life sciences

Biomed is a large-scale international Virtual Organization (VO) supporting communities from the Life Sciences sector focusing on three main groups: medical image analysis, bioinformatics and drug discovery.

The challenge

One of the flagship science gateways of BioMed is the Virtual Imaging Platform (VIP). Through VIP, researchers can access multiple applications, as well as important amounts of storage and computing resources, without required technical skills beyond the use of a web browser. The model has proved to be successful: VIP currently counts more than 1300 registered users, accessing 20 applications. 

The challenge for VIP is now about interoperability and reproducibility, in the larger scope of a FAIR approach to scientific data analysis.

In the next few years, we can imagine a platform of platforms exchanging apps and data effortlessly. Re-usability of applications across platforms can be achieved with containers, which allow users to build applications on their desktops and run hundreds or even thousands of instances on remote CPUs.

The solution

The distributed infrastructure supporting biomed, and therefore VIP, consists of resources from the National Grid Initiatives (NGIs), EGI, supercomputing platforms (DEISA), infrastructures potentially provided by ESFRIs, and other possible resources (e.g. commercial/private cloud resources). 

From the EGI Infrastructure, more specifically, 14 HTC and cloud resource providers are supporting the biomed community allocating computing and storage resources to serve the European Life Sciences community.

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 Online Storage

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

EGI Check-in

Login with your own credentials.

Training and consultancy

Dedicated computing and storage for training and education and consultancy activities

Impact

>1,340 users

registered to the VIP portal (40% from outside Europe)

>202,598 of (Cloud) CPU hours

consumed over the last 2 years (Dec. 2019 – May 2021)

12,121,811 of (HTC) CPU hours

consumed over the last 2 years (Dec. 2019 – May 2021)

94 VMs

instantiated in the EGI Federated Cloud infrastructure

Highlights

Creating a digital hearth

Scientists from the University of Lyon used the VIP platform to develop a framework for generating virtual data to study heart diseases.
One 3D sequence took around 6 hours to generate on VIP. On a personal laptop, 280 hours would have been needed.

VIP tutorial

Check the documentations and tutorial about the VIP platform

Participating Partners

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