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In this deliverable report, we highlight outreach and training achievements in the period of January 2022 to February 2023 and also summarise overall achievements for the entire CINECA project. In total, we have delivered 59 learning interventions (including staff visits, webinars, workshops and training events, short training videos, and an overarching self-paced learning pathway) and we have reached a large and diverse audience, through both training and dissemination activities and through our website and social media channels. Below we provide further detail in terms of the diverse activities that we have developed and delivered since the beginning of the project, the wide demographic we have engaged, our reach through dissemination and training activities, and the impact that our training has had in the longer term.

GA4GH Passport (a.k.a. GA4GH Researcher ID) is the GA4GH standard for expressing an authenticated researcher’s roles and data access permissions (a.k.a. passport visas). Together with the GA4GH Authentication and Authorisation Infrastructure (AAI) specification, it describes how passport visas are issued and delivered from their authority (such as a Data Access Committee) to the environment where the data access takes place (such as an analysis platform or cloud). The work package has contributed to the Passport and AAI standards which were approved by the GA4GH in October 2019. This deliverable provides an overview of the GA4GH Passport and AAI standards (version 1.0) in general. It then describes in detail how ELIXIR AAI has implemented the specification as a Passport broker service. Some directions of the next version of the GA4GH Passport and AAI standards, which are still in development in the GA4GH DURI workstream, are displayed. Finally, a hands-on experiment presents how passports could alternatively leverage self-sovereign identity, an emerging identity and access management paradigm in the industry.

In this deliverable document, we report on the activities in task 6.4 - Training Programme, describe the CINECA training activities that took place in months 25-36 of the project and provide the Training Plan for the final year. The CINECA training programme aims to train people within the CINECA consortium as well as external users. Different approaches have been employed, including face-to-face and online courses, hackathons, training videos and staff exchanges. While we waited for CINECA products to be completed, many of the training efforts for the year again focused on internal learning opportunities and knowledge exchanges, but some externally facing events were held to disseminate outputs. All the training and outreach events continued to be heavily impacted by COVID-19, which removed our ability to hold face-to-face workshops and staff exchanges. The staff exchanges were suspended and replaced with virtual meet-ups.

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. As with the first 12 months of the CINECA project, many of the training efforts for the second 12 months also focused on internal learning opportunities and knowledge exchanges. However, all the training and outreach events have been heavily impacted by COVID-19, which removed our ability to hold face-to-face workshops and staff exchanges. 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. To increase engagement, the short videos were submitted to ELIXIR’s training portal and disseminated via CINECA’s various communication channels.

CINECA aims to support the federated queries and analyses of distributed cohorts across continents. A vital component of this work is building a machine readable catalogue of cohorts and sites that support the efforts of Work Package 1 discovery and analysis APIs, which can be programmatically queried so that API calls can be made to relevant sites and results gathered and presented to the researcher. Deliverable D1.1, Discovery Service Catalogue, supports the work of dependent work packages by implementing and demonstrating an open-source extended implementation of the Service Registry standard of the Global Alliance for Genomics and Health (GA4GH) for WP1’s discovery queries, the GA4GH Beacon queries. The Service Registry standard is now supported by the ELIXIR Beacon Network that CINECA WP1 uses to federate discovery queries across cohorts, and this demonstrator deliverable demonstrates the use of the service registry and its open source implementation.

This deliverable demonstrates authentication and authorisation interoperability between the ELIXIR and CanDIG infrastructures. Users from one infrastructure can access services from the other. The interoperability covers user identification and authentication as well as the transfer of the authorisation claims following the GA4GH Passport and AAI OpenID Connect protocol (OIDC) profile specifications.

In this deliverable document, we report on the activities for Deliverable 4.1 - Report on trust model for partner sites, and between sites and controlled-access researchers. The Work Package 4 goals concern the development of a set of tools that can facilitate federated analyses of new and diverse genetic and genomic datasets, based on specific use cases. The tools selected will be using the common federated infrastructure established in earlier work packages, and the datasets will be described with metadata standards identified in Work Package 3. In our report we considered trust as the extent to which one party is willing to depend on the other party in a given situation with a feeling of relative security, even though negative consequences are possible. This work has contributed towards establishing a description of the trust model and four different levels of data access concerning specific cohort’s data, identifying use cases for the development of federated analysis workflows and describing existing data access models to inspire subsequent WP4 deliverables related to the implementation of the federated analysis workflow.

In this deliverable document, we report on the activities in task 6.2a - Training Programme and describe the CINECA training activities in the first 12 months of the project. In the first phase of the CINECA project, many of the training efforts are focused on internal learning opportunities and knowledge exchanges. There are many interdependencies between the different CINECA work packages, so to this end we have set up a staff exchange program.For training interventions targeted at a broader audience, we have set up a webinar series, providing online learning interventions. Feedback from these webinars is collected and is used to further increase the utility of the webinars going forward.We have disseminated a survey to identify the training needs of CINECA’s stakeholder community. Additionally, we ran our first stakeholder engagement session at the International Hundred Thousand Cohorts Consortium (IHCC) Meeting in Reykjavik, Iceland in April 2019. During this session, we gathered feedback on the challenges of managing cohorts and cohort data harmonisation. More extensive face-to-face workshops and training events are being planned for 2020.

In this deliverable document, we report on the activities in task 6.1 – Stakeholder analysis, with the outreach and dissemination plan, as well as the training plan presented in this report, we have completed this task. We have used a combination of surveys and face-to-face meetings to verify and extend or identify key stakeholder groups, understand their interest in the project, and identify bottlenecks that can be addressed by outreach and training. Outreach activities will be accomplished by task 6.2 and training by task 6.3.

In this deliverable document, we report on the activities in task 6.1 - Stakeholder analysis, with the outreach and dissemination plan, as well as the training plan presented in this report, we have completed this task. We have used a combination of surveys and face-to-face meetings to verify and extend or identify key stakeholder groups, understand their interest in the project, and identify bottlenecks that can be addressed by outreach and training. Outreach activities will be accomplished by task 6.2 and training by task 6.3. The stakeholder survey was developed and distributed within the CINECA stakeholder community; a total of 54 responses were received. While the response rate was on the low side, it is sufficient for the initial analysis, which is presented below. A CINECA competency framework was developed and validated through the survey. The competency framework has four areas of competence (generating data, finding and accessing data, analysis and clinical interpretation of data and sharing data), reflecting the research lifecycle. A total of 17 competencies have been defined. We consider both the stakeholder analysis and the competency profile to be living documents that will evolve over the course of the project. We plan to obtain additional feedback on both the competency profile as well as update the stakeholder analysis throughout the project through a range of methods, these could include interviews, discussion groups, conference workshops. A dissemination strategy was created aimed at the effective communication of CINECA activities and outcomes to all relevant partners and stakeholders. To this end, a range of dissemination channels have been set up, including a CINECA project webpage, various social media channels, a newsletter, and physical materials such as flyers and brochures. Furthermore, a set of conferences and events have been identified at which a CINECA presence (e.g. workshop, booth, talk) could benefit stakeholder engagement. Consistent branding across these different dissemination channels is achieved through the development of a logo, colour scheme, and the creation of templates for materials such as brochures, posters and slides. Furthermore, a number of CINECA areas of research and expertise have been identified that may be suitable for publication as peer-reviewed articles. A training plan was developed covering a variety of learning interventions, including webinars, staff visits, workshops and hackathons. In the early phase of the project (first ~18 months), training activities will be focused primarily on internal CINECA knowledge exchanges to allow work package interdepencies to be resolved. To this end, a regular webinar series has been started to inform CINECA project members and other interested parties of the various CINECA activities and outcomes. Furthermore, a staff exchange program was set up to allow knowledge exchanges between different interdependent work packages. CINECA members may submit staff visit requests via an online form, and after the visit a blog post about the outcomes will be posted on the CINECA website. As the project progresses, the focus of training activities will gradually shift to dissemination to a wider audience and will consist primarily of workshops (face-to-face or online) and hackathons.

Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community.H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis.Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training.For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa.

A shortage of practical skills and relevant expertise is possibly the primary obstacle to social upliftment and sustainable development in Africa. The "omics" fields, especially genomics, are increasingly dependent on the effective interpretation of large and complex sets of data. Despite abundant natural resources and population sizes comparable with many first-world countries from which talent could be drawn, countries in Africa still lag far behind the rest of the world in terms of specialized skills development. Moreover, there are serious concerns about disparities between countries within the continent. The multidisciplinary nature of the bioinformatics field, coupled with rare and depleting expertise, is a critical problem for the advancement of bioinformatics in Africa. We propose a formalized matchmaking system, which is aimed at reversing this trend, by introducing the Knowledge Transfer Programme (KTP). Instead of individual researchers travelling to other labs to learn, researchers with desirable skills are invited to join African research groups for six weeks to six months. Visiting researchers or trainers will pass on their expertise to multiple people simultaneously in their local environments, thus increasing the efficiency of knowledge transference. In return, visiting researchers have the opportunity to develop professional contacts, gain industry work experience, work with novel datasets, and strengthen and support their ongoing research. The KTP develops a network with a centralized hub through which groups and individuals are put into contact with one another and exchanges are facilitated by connecting both parties with potential funding sources.

Includes abstract., Includes bibliographical references., In this project, we review some existing pathway-based approaches for GWA study analyses, by exploring different implemented methods for combining effects of multiple modest genetic variants at gene and pathway levels. We then propose a graph-based method, ancGWAS, that incorporates the signal from GWA study, and the locus-specific ancestry into the human protein-protein interaction (PPI) network to identify significant sub-networks or pathways associated with the trait of interest. This network-based method applies centrality measures within linkage disequilibrium (LD) on the network to search for pathways and applies a scoring summary statistic on the resulting pathways to identify the most enriched pathways associated with complex diseases.