VIP and the biomed community: achievements and new challenges

Sorina Camarasu Pop writes about a successful science gateway

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 biomed VO is operated on the EGI infrastructure and supported by more than 50 sites, delivering access to a large number of heterogeneous resources. In 2018, biomed users executed more than 2.5 million jobs corresponding to 439 years of CPU. 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.

VIP relies on the France Grilles DIRAC instance for job submission and data management on EGI biomed resources. The model has proved to be successful: VIP currently counts more than 1000 registered users, accessing 20 applications. Since 2011 we have logged dozens of peer-reviewed papers published with results computed through VIP.

Challenges for the future

VIP is now focusing on challenges concerning interoperability and reproducibility, in the larger scope of a FAIR approach to scientific data analysis. Through Boutiques, VIP is able to easily describe and integrate new applications, as well as publish them on open repositories, such as Zenodo, to make them findable and accessible. Through CARMIN (Common API for Research Medical Imaging Network), VIP fosters data integration and interoperability among platforms. In the next 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 biomed community has come a long way along with what is now the EGI Federation. Despite the multitude and diversity of our research topics and applications, we share similar challenges and we can join our efforts in order to reach goals surpassing our individual means.

We need to work together to build a FAIR and promising future.

VIP in practice: creating a digital heart

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.

Read the full use case.

More information:

Sorina Camarasu Pop is a CNRS research engineer working at the CREATIS laboratory in France.

VIP Platform

Issue 34

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