During this workshop, we will present an end-to-end federated data analysis use case covering federated data discovery and access, bioinformatics analysis, and ethical and legal considerations for responsible and fair data sharing flow. The workshop will comprise a mix of lectures and demos with some hands-on tutorials if time permits. Lectures will introduce key concepts for federated data sharing and analysis, GA4GH Beacon API, GA4GH Passports and Visas, and the Data Use Ontology (DUO), followed by practical sessions on real-world research and clinical applications.

In this webinar, we will give an overview of the CINECA workflows for genotype imputation, gene expression and splicing quantification, data normalisation and association testing, and demonstrate how these workflows can be used in a federated setting without transferring identifiable personal data between partners.

As a part of the CINECA project we have been working on the development of a demonstrator of federated genetic analyses utilising a computational pipeline for PRS analysis. In this webinar, we will provide an overview of this PRS pipeline utilising the CINECA UK1 synthetic dataset, derived from the 1000 genomes project, as a demonstrator. 

In this webinar, we will give an overview of the CINECA workflows for genotype imputation, gene expression and splicing quantification, data normalisation and association testing, and demonstrate how these workflows can be used in a federated setting without transferring identifiable personal data between partners.

The CINECA webinar series continues with a presentation by Dr Melanie Courtot, from the Ontario Institute for Cancer Research (OICR).

The ability to integrate and harmonise diverse, large human cohort data at scale promises exciting research perspectives and applications. This webinar provides a high-level introduction to some current standards for data representation and access, and tools leveraging them. Finally, we explore how modular assembly of tools and standards enables deployment of Findable, Accessible, Interoperable and Reusable (FAIR) data and showcase applications that “bring it all together”.

The Beacon is a protocol for sharing information about the presence or absence of a specific mutation in a given dataset. The latest version (v2) of the Beacon also allows to: filter by variables or interest (e.g. gender or age), trigger the data access process, and consult clinical annotation about the variants found, among others.

At the end of this training session, participants will be familiarized with Beacon queries, using the UI as well as the API. This training session is part of the CINECA GA4GH Beacon series.

The Beacon v2 Reference Implementation (B2RI) is a free open source Linux-based software created by the Centre for Genomic Regulation (Barcelona, Spain) that allows lighting up a Beacon v2 out-of-the-box.In this training session, a B2RI developer will give an overview on how to use the software to “beaconize” your data (from the user’s perspective).

At the end of this training session, participants will be familiarized with the input and output requirements of the B2RI, as well as with the type of queries allowed. This training session is part of the CINECA GA4GH Beacon series.

The Beacon is a protocol for sharing information about the presence or absence of a specific mutation in a given dataset. The latest version (v2) of the Beacon also allows to: filter by variables or interest (e.g. gender or age), trigger the data access process, and consult clinical annotation about the variants found, among others.

At the end of the training session, participants should have the tools to get started with the implementation autonomously, and have identified the resource persons to answer their questions during the implementation process. This training session is part of the CINECA GA4GH Beacon series.

The Beacon is a protocol for sharing information about the presence or absence of a specific mutation in a given dataset. The latest version (v2) of the Beacon also allows to: filter by variables or interest (e.g. gender or age), trigger the data access process, and consult clinical annotation about the variants found, among others.

In this webinar, the Beacon team at CRG will introduce you to the Beacon v2, its features, address security considerations, and illustrate a few use cases. This webinar is part of the CINECA GA4GH Beacon series.

The seven projects making up the EUCAN ELSI Collaboratory (EUCANCan, euCanSHare, CINECA, iReceptor Plus, EUCAN-Connect, ReCoD-ID, and EuCanImage) will host a joint webinar about how fostering stakeholder engagement can improve transparency and accountability in international sharing of health data.

The two-hour webinar will consist of two parts. The first part will include four 15-minute presentations and conclude with a Q&A. The second part will be dedicated to horizon scanning, providing a space for researchers in the EUCAN ELSI projects to discuss a wide verity of themes concerning the future of international data sharing, including ongoing barriers to be remover; future research that needs to be conducted; and affirmation of certain already existing frameworks.

The event is free of charge and open to everyone interested in learning more about international data sharing in the health research space and beyond.

The training consists of one hour of presentations, followed by a hands-on exercise with a Virtual Machine. In the hand-on part the trainees integrate their VM to ELIXIR AAI as an OpenID Connect client to retrieve a GA4GH Passport. The client then presents the Passport to a Data API to authorise the API call and to stream a dataset. The VMs are available for the trainees for two weeks after the training.

This webinar will focus on how the CINECA project is applying FAIR (Findable, Accessible, Interoperable, Reusable) principles in practice. Enabling federated data discovery, data access, and research and analysis, by using open standards across the federated network, is crucial in order to fully exploit the potential of human cohorts to drive personalised medicine. CINECA is working in collaboration with other GA4GH driver projects developing and implementing the methods and infrastructure which will allow effective use of widely-dispersed data to improve the size and quality of datasets available for disease research.

The FAIR principles – standing for Findability, Accessibility, Interoperability, and Reusability – have become the guiding principles for the wider sharing of research data in the life sciences. While FAIR provides guidance for the management of data as well as tools and workflows, the institutional conditions and organizational challenges associated with data sharing need to be taken into account to ensure responsible and fair data practices. This requires considering the context of legal requirements, for instance the principle of fairness and transparency in GDPR, expectations of research participants/data subjects, societal aspects and the “ethics work” that is an integral part of data flows, as well as fairness, equity and benefit sharing within transnational collaborations, which is of utmost importance. This webinar will, from the perspective of ethical, legal and societal implications (ELSI), discuss this broader context of responsible and fair data sharing associated with FAIR.

During this webinar, we will give you some tips and suggestions on how you can make more of the training materials you produce and encourage others to do the same. FAIR is not just for data - we can make our training materials FAIR too. Join us to find out the benefits of sharing your FAIR materials and some simple ways you can make it easy for others to use your materials in their teaching, or as aids for individuals to learn more.

This webinar will focus on practical applications of the FAIR data principles, particularly in the context of clinical bioinformatics. We will highlight several example projects that have put the FAIR principles in practice, and discuss the advantages and some of the challenges involved. ELIXIR Galaxy community (elixir-europe.org/communities/galaxy) promotes the use of Galaxy projects that enhance the FAIRness in data analysis. We will demonstrate the Galaxy services that deliver practical FAIR data analysis with “Single Sign-On” capability provided by ELIXIR-AAI. The aim is to provide (medical) researchers with the practicalities of implementing and using FAIR principles in the context of the CINECA project as applied to translational research at Erasmus University Medical Center.

In this talk, I will discuss the importance of the FAIR principles for the software tools we use to process data. Ranging from small analysis scripts to full fledged data processing pipelines, software needs to be FAIR to enable other researchers to reproduce our own experiments and reuse our software. However software and data are fundamentally different – software is executable in nature and may have intricate dependencies. FAIR principles apply differently to software than they do to data and we must be aware of these differences. Existing initiatives such as the RDA FAIR for Research Software (FAIR4RS) working group (https://www.rd-alliance.org/groups/fair-4-research-software-fair4rs-wg) and http://fair-software.eu/ are already focused on addressing these differences and raising awareness of the importance of FAIR for software.

In this presentation, we will explore several informatics techniques, such as the use of ontology, to make cohort data more FAIR. We will also consider the implications of making cohort data more open and the ethical and governance issues associated with open science benefit sharing.

CINECA starts a "How FAIR are you" webinar series with a presentation by Kees van Bochove, founder of The Hyve. In this webinar, we will dive into the basics of FAIR health data, but also take stock of the current situation in health data networks: after a year of frantic research and collaborations and many open datasets and hackathons on COVID-19, has the situation actually improved? Are we sharing health data on a global scale to improve medical practice, or is quality medical data still only accessible to researchers with the right credentials and deep pockets?

The target group of the training is developers and administrators of services that want to integrate with some advanced functionality of the ELIXIR AAI for user authentication and authorisation.

We live in an era of cloud computing. Many of the services in the life sciences are keenly planning cloud transformations, seeking to create globally distributed ecosystems of harmonised data based on standards from organisations like GA4GH. CINECA faces similar challenges, gathering cohort datasets from all over the globe, many of which are pinned in place, due to their size, legal restrictions, or other considerations.

This hands-on workshop at IHCC 2020 aims to collect a variety of use cases for cohort interoperability and work towards practical steps to address them. This will include approaches for metadata harmonisation, querying/discovery, authentication, data retrieval and analysis. We propose to identify a subset of cohorts that will provide the relevant information for use case driven development.
We welcome any cohort with plans for prospective or retrospective metadata harmonisation, enthusiastic to share their experience and learn from CINECA’s perspective in the context of federated dataset discovery and analysis.

This webinar will be to present the first findings of the ELSI activities in the CINECA project, ranging from questions of ethics of data sharing across continents to legal basis of secondary processing of personal data, consent requirements and vulnerable groups or public and stakeholders’ attitudes toward sharing of genomic and health related data for research.

This webinar introduces the CINECA (Common Infrastructure for National Cohorts in Europe, Canada, and Africa) project, which aims to develop a federated cloud enabled infrastructure to make population scale genomic and biomolecular data accessible across international borders, to accelerate research, and improve the health of individuals across continents. CINECA will leverage international investment in human cohort studies from Europe, Canada, and Africa to deliver a paradigm shift of federated research and clinical applications.