This report details the development of a demonstration tool for CINECA Task T5.1, which integrates WP1-3 CINECA services to advance federated biobank search. UML diagrams and mockups were used to model the search process and create a user interface. The architecture of the system and strategies for accessing and storing data were also described. The report highlights efforts to integrate pre-analytical metadata, which are important for determining the quality of biospecimens, and a synthetic dataset was prepared to develop search services for accessing and visualizing such data. The evaluation of the robustness and search effectiveness of the implemented services is also discussed.
https://doi.org/10.5281/zenodo.6783295
The EUCAN Cluster consists of seven projects (CINECA, EUCANCan, EUCAN-Connect, euCanSHare, iReceptor Plus, and ReCoDID) that received funding under the same Horizon 2020 call, SC1-BHC-05-2018.
This document provides a high-level overview of each project in the cluster.
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This video provides an Overview of the FAIRsharing.org by Allyson Lister as part of the CINECA “How FAIR are you” webinar series and hackathon.
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Adrian Thorogood, Heidi L. Rehm, Peter Goodhand, Angela J.H. Page, Yann Joly, Michael Baudis, Jordi Rambla, Arcadi Navarro, Tommi H. Nyronen, Mikael Linden, Edward S. Dove, Marc Fiume, Michael Brudno, Melissa S. Cline, Ewan Birney
Thorogood et al. provide a guide to federated approaches to data sharing, which aim to connect independent, secure genomic medicine databases through common standards, enabling users to derive insights across multiple databases. The authors argue that a federated approach is feasible and necessary to connect national genomics initiatives into a global network to advance precision medicine.
Read MoreHeidi L. Rehm, Angela J.H. Page, Mélanie Courtot, Jonathan Dursi, Lauren A. Fromont, Thomas M. Keane, Mikael Linden, Isuru Udara Liyanage, Nicola Mulder, Jordi Rambla, Gary I. Saunders, et al.
Rehm et al. describe the Global Alliance for Genomics and Health (GA4GH), which develops technical standards and policy frameworks to enable responsible international human genomic and biomedical data sharing. Broad international participation in building, adopting, and deploying these standards is necessary to bridge research and healthcare and is critical to making the best use of genomic data to inform advances in medicine and human health.
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This video describes the FAIRplus fairification wizard by Fuqi Xu (EMBL-EBI) as part of the CINECA “How FAIR are you” webinar series and hackathon.
Read MoreThe CINECA project aims to develop a common infrastructure to support federated data analysis across national cohorts in Europe, Canada, and Africa. In this report, the progress made over the past four years is discussed, which involves the development of six modular workflows to quantify and normalize molecular traits, pre-process genotype data, and test for associations between molecular traits and genotypes. The approach improves on the previous state of the art by packaging software dependencies into Docker/Singularity containers, using the Nextflow language to orchestrate complex multi-step workflows, and using the HASE(1) framework to reduce the amount of data that needs to be transferred between cohorts. The project provides training materials and open access datasets to encourage adoption and demonstrates how the workflows can be used to perform federated analysis across multiple real cohorts located in Switzerland, Germany, the Netherlands, and Estonia.
https://doi.org/10.5281/zenodo.7464116
In this deliverable document, we report on the activities in task 6.4 - Training Programme, describe the CINECA training activities in the first 24 months of the project and provide the Training Plan for the next 12-24 months. For training interventions targeted at a broader audience, we have set up a webinar series, providing quarterly online learning interventions. We ran a total of 6 webinars (3 of these webinars in 2019, and 3 in 2020), with 23 attendees on average, 68% on average of those who registered. In addition, a series of short training videos (https://www.cineca-project.eu/short-videos) was created to facilitate the uptake of CINECA outputs. Eight short videos were produced by work packages on different topics. The short videos were submitted to ELIXIR’s training portal to increase engagement and disseminated via CINECA’s various communication channels.
https://doi.org/10.5281/zenodo.6223125