Connecting ELIXIR’s technical ambitions

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Plenary - 11 June | 9:00-10:30

Chair - Elaine Harrison (ELIXIR Hub)

Agenda

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#ELIXIR24

ELIXIR’s technical themes and their interactions

Jonathan Tedds, ELIXIR Hub

Scientific and technical priorities - Technology

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Technology tier - detailed ambitions

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What we are building on - 2019-2023

Packaging, Containerisation & Deployment

AAI Engagement

ELIXIR Hybrid Cloud

Container Orchestration

Training Toolkit

Consolidating quality and impact of the TeSS training resources

Training Capacity Building

FAIR underpinning standards and services

Interoperability Knowledge Hub with RDMkit and FAIR Cookbook

CDR, EDD, & Community Databases

Scalable Curation

Data Integration

Community and Data Management Network Engagement

Performance Benchmarking & Technical Monitoring

Gap analysis, training materials development and training delivery

Software Best Practices

The bio.tools Registry and EDAM Ontology

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ELIXIR’s Technical Platforms

Platforms are expert groups aligned around families of technologies and services

ELIXIR Programme 2019-2023

Through Programme funding we addressed specific foundational capabilities and problems

Recommended Interoperability Resources

Impact and alignment 2019-2023

Packaging, Containerisation & Deployment

AAI Engagement

ELIXIR Hybrid Cloud

Container Orchestration

Training Toolkit

Consolidating quality and impact of the TeSS training resources

Training Capacity Building

CDR, EDD, & Community Databases

Scalable Curation

Data Integration

Community and Data Management Network Engagement

Performance Benchmarking & Technical Monitoring

Gap analysis, training materials development and training delivery

Software Best Practices

The bio.tools Registry and EDAM Ontology

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Capabilities support EU Projects

Our core Services and capabilities prepared us to participate in major EU programmes - providing core data resources to BY-COVID, and AAI expertise to EOSC-Life

EU Projects deliver new Services

Projects deliver innovation - RDMKit, FAIR Cookbook, and WorkflowHub were all developed in EU Projects and are now ELIXIR Services

FAIR underpinning standards and services

Interoperability Knowledge Hub with RDMkit and FAIR Cookbook

Recommended Interoperability Resources

Train-the-Trainer programme consolidation

Establishing best practices for interoperable data management and use

Recognition and credit attribution of research contributions to data resources

Consolidating ELIXIR Training standards and best practices for Open science and Open education

Scalable curation support from the long tail of biological data

Standardising processes for FAIR data management

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The Platforms will continue to support development of capabilities in 2024-2028

Research Data Management is a key strength of ELIXIR and a focus in several Platforms

Machine-actionable data management plans

Train-the-Trainer programme consolidation

Establishing best practices for interoperable data management and use

Recognition and credit attribution of research contributions to data resources

Consolidating ELIXIR Training standards and best practices for Open science and Open education

Scalable curation support from the long tail of biological data

ELIXIR Research Data Management

Community

STEERS

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Again EU Projects will play a role in broadening our impact

ELIXIR Communities will also contribute - including the ELIXIR RDM Community developed through ELIXIR-CONVERGE

Standardising processes for FAIR data management

Machine-actionable data management plans

Software Management, Stewardship and Standards

Multi Cloud Infrastructure Deployment

Sustainability, Accounting and Provenance for Federated Analytics

Democratised access to reusable complex workflows

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Platforms will have to work together to deliver the new Priorities.

Tools and Compute together cover the landscape from software creation to distributed deployment and operation.

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Improving Software Quality for reproducible and distributed analysis

Software Management, Stewardship and Standards

Multi Cloud Infrastructure Deployment

Sustainability, Accounting and Provenance for Federated Analytics

Improving Software Quality for reproducible and distributed analysis

Democratised access to reusable complex workflows

ELIXIR Galaxy

Community

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The software and analysis ecosystems are requirements of the European Open Science Cloud

Through e.g. the ELIXIR Galaxy Community, our impact goes beyond EOSC to influence international strategy

STEERS

The ELIXIR Research Software Ecosystem

Advanced Service Access Control

Protected Access to Sensitive Data for Analysis

Growing the FAIR-enabling portfolio of products

Establishing and shaping the landscape of Core and Community Biological Databases

Connecting and brokering Node contributions to ELIXIR Data resources

Consolidating the Training Platform Infrastructure (services and resources)

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All the Platforms have a role in developing ELIXIR’s network of distributed, interoperable Services

This includes development and the shaping of policies and practices

Recommended Interoperability Resources

The ELIXIR Research Software Ecosystem

Advanced Service Access Control

Protected Access to Sensitive Data for Analysis

Growing the FAIR-enabling portfolio of products

Establishing and shaping the landscape of Core and Community Biological Databases

Connecting and brokering Node contributions to ELIXIR Data resources

Consolidating the Training Platform Infrastructure (services and resources)

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In 2024-2028 we will oversee a suite of core ELIXIR Infrastructure Services and promote the other Services managed by our Nodes

This network and our services will underpin other pan-European projects in EOSC and EHDS

Technology is also all about people. In 2024 we are:

Compute Platform: Steven Manos, Frederik Coppens, Dilza Campos, Paul De Geest, Rafael Andrade Buono, Alexander Kanitz, Pavel Vyskočil, Klára Moravcová, Milan Daneček, Ludek Matyska, Dominik F. Bucik, Jan Pavlíček, Pavlína Špringerová, Peter Bolha, Slávek Licehammer, Jana Broncova, Adam Skrášek, Viktória Spišaková, Lukáš Hejtmánek, Radek Polášek, Adrián Rošinec, Matej Antol, Martin Kuba, Alexander Sczyrba, Harald Wagener, Sven Twardziok, Ulrike Taron, Valentin Schneider-Lunitz, Luiz Gadelha, Nils Hoffmann, Michael R. Crusoe, Sebastian Beyvers, Kaur Alasoo, Jonathan Tedds, Gavin Farrell, Corinne Martin, Justin Clark-Casey, Santiago Insua, Rob Finn, Juha Törnroos, Aino-Riikka Corell, Janne Lauros, Stefan Negru, Tristan Perard, Alvaro Gonzalez, Jemal Tahir, Christophe Blanchet, Franck Giacomoni, Thanasis Vergoulis, Eleni Adamidi, Giacinto Donvito, Marco Tangaro, Christophe Trefois, Sascha Herzinger, Venkata Satagopam, Soumyabrata Ghosh, Helena Rasche, Anne van der Kant, Ivar Janmaat, Stian Soiland Reyes

Data Platform: Tom Lenaerts, Flora D'Anna, Christophe Dessimoz, Julien Gobeill, Lucy Poveda, Monique Zahn, Patrick Ruch, Paul van Rijen, Séverine Duvaud, Sebastian Beier, Ulrike Wittig, Daniel Arend, Fabio Liberante, Gavin Farrell, Aravind Venkatesan, Claire O’Donovan, Guy Cochrane, Matt Jeffryes, Melissa Harrison, Ugis Sarkans, Zahra Waheed, Teresa D’Altri, Alban Gaignard, Valerie Wood, Allyson Lister, Philippe Rocca-Serra, Thanasis Vergoulis, Christos Ouzounis, Fotis Psomopoulous, Emidio Capriotti, Paola Turina, Adel Bouhraoua, Alexander Monzon, Damiano Piovesan, Silvio Tosatto, Luana Licata, Federico Bianchini, Sveinung Gundersen, Mihail Anton, Niclas Jareborg, Wolmar Nyberg Åkerström, Brane Leskošek

Interoperability Platform: Bert Droesbeke, Flora D’Anna, Tarcisio Mendes de Farias, Vassilios Ioannidis, Marek Suchánek, Nils Hoffmann, Tony Burdett, Wei Kheng Teh, Clare Garrard, Fabio Liberante, Antonio Hermoso Pulido, Julia Ponomarenko, Ibrahim Emam, Falk Hildebrand, Munazah Andrabi, Nick Juty, Allyson Lister, Philippe Rocca-Serra, Susanna-Assunta Sansone, Flavio Licciulli, Ivan Mičetić, Danielle Welter, Marek Ostaszewski, Chris Evelo, Denise Slenter, Elena Domínguez-Romero, Tooba Abbassi-Daloii, Federico Bianchini, Korbinian Michael Bösl, Nazeefa Fatima, Sveinung Gundersen, Wolmar Nyberg Åkerström, Brane Leskošek, Polonca Ferk

Tools Platform: Björn Grüning, Salvador Capella Gutierrez, Herve Menager, Rafael Buono, Ana Claudia Sima, Adrián Rošinec, Michael R. Crusoe, Veit Schwämmle, Piotr Jaroslaw Chmura, Hedi Peterson, Jonathan Tedds, Mihail Anton, Renato Alves, Alban Gaignard, Mateo Boudet, Hrishikesh Dhondge, Fotis Psomopoulos, Pier Luigi Martelli, Allegra Via, Magnus Palmblad, Matus Kalas, Dimitris Bampalikis, Stian Soiland-Reyes, Nicola Soranzo, Johan Gustafsson, Leyla Jael Garcia-Castro, Bhavesh Patel

Training Platform: Eva Alloza, Fotis Psomopoulos, Jessica Lindvall, Alex Botzki, Bruna Piereck, Geert van Geest, Patricia Palagi, Vojtech Spiwok, Daniel Wibberg, Helena Schnitzer, Priit Adler, Katharina Heil, Mihail Anton, Paulyna Magaña, Kim Gurwitz, Piv Gopalasingam, Patricia Carvajal, Lisanna Paladin, Renato Alves, Eija Korpelainen, Olivier Sand, Hélène Chiapello, Eleni Adamidi, Thanasis Vergoulis, Vassiliki Iconomidou, Zoi Litou, Maria Doyle, Loredana Le Pera, Allegra Via, Roland Krause, Celia Van Gelder, Mijke Jetten, David Dolan, Erin Calhoun, Daniel Faria, Gil Poiares-Oliveira, Brane Leskošek, Nadja Žlender, Krzys Poterlowicz, Katarzyna Kamieniecka, Khaled Jumah, Alexia Cardona

Research data management and knowledge sharing

2 x 5 minutes talks

5 minutes questions

RDM Community

Mijke Jetten, ELIXIR Netherlands

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ELIXIR Interoperability Platform

Tony Burdett, EMBL-EBI

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#ELIXIR24

RDM Community

Mijke Jetten, ELIXIR Netherlands

What is the RDM Community

Research Data Management is a key strength of ELIXIR and a focus in several Platforms�Technology is also all about people

[Network] Knowledge exchange & capacity building

[Ecosystem] Content & editorial for e.g. RDMkit, FAIR Cookbook, DSW

[Training] Trainers, learning paths & resources, e.g. TeSS

External stakeholders beyond ELIXIR

White Paper

#ELIXIR24

Links to other parts of ELIXIR

Hands-On RDM with ELIXIR Groups: Crafting Short and Long-Term Strategies [June 11 AHM workshop]��The existing ELIXIR Communities and Focus Groups are key interaction partners that deal with real-world RDM problems and challenges for their respective domains. They offer a possibility for knowledge exchange and capacity building that goes both ways �

Initiate the first steps in this conversation & help us shape our strategy

#ELIXIR24

What has been achieved so far�Future work �

Community webpage�Community framework

Onboarding document�Monthly meetings

Standardised processes

[Interoperability Platform, FAIR Service Framework]

DATAREX Implementation Study [2024-26]

Portfolio of products

Best practices

4

DS “people” handbook

Maturity model RDM services providers

Requirements for data brokering system

#ELIXIR24

Join the RDM Community [currently 223 members!]

Co-leads RDM Community + Network [WP1]: Munazah Andrabi (ELIXIR-UK), Flora D’Anna (ELIXIR-BE), Niclas Jareborg (ELIXIR-SE) & Mijke Jetten (ELIXIR-NL) [+ Hub support: Katharina Heil]

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Ecosystem & Training [WP2]: WP2: Danielle Welter (ELIXIR-LU), Korbinian Bösl (ELIXIR-NO), Alexia Cardona & Xènia Pérez Sitjà (ELIXIR-UK)

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WP3 Capacity Building [WP3]: Flora D'Anna, Ivan Mičetić (ELIXIR-IT) & Mijke Jetten

https://elixir-europe.org/communities/research-data-managementMeeting frequency: 2nd Tuesday of the month 14-15 CE(S)T

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#ELIXIR24

ELIXIR Interoperability

Platform

Tony Burdett, EMBL-EBI

The ELIXIR Interoperability Platform

Mission

• Help people and machines to discover, access, integrate and analyse biological data
• Encourage international life science community to adopt standardised file formats, metadata, vocabularies and identifiers

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Commissioned Services 2024-2028

• Continue building the FAIR Service Framework
• Products, Processes and Practices

#ELIXIR24

What has been achieved so far and why it’s important

#ELIXIR24

What is the ELIXIR Interoperability Platform

Portfolio of products

2

Best practices

4

Standardised processes

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Continue building the FAIR Service Framework

#ELIXIR24

What is the ELIXIR Interoperability Platform

Portfolio of products

2

Best practices

4

Standardised processes

3

Assemble products into reusable processes that drive good practice

#ELIXIR24

What is the ELIXIR Interoperability Platform

Portfolio of products

2

Best practices

4

Standardised processes

3

Understand community practices, to improve processes and create new products

#ELIXIR24

Next steps and getting involved

Practices

• Three use cases (modelling, disease maps, metabolomics/lipidomics)
• Short Survey �to Communities

Products

• Redesigning the RIRs
• Help us shape

the future of the RIRs

by filling in our

user survey!

• Coordinating content generation for RDMkit & FAIR Cookbook

#ELIXIR24

How to get involved - Interoperability Stories

• Intrinsically Disordered Protein Community Exploiting Bioschemas
• Alasdair Grey [link]
• Plant Sciences Community Showcase
• Cyril Pommier [link]
• Rare Disease Community: examples from EJP RD
• Friederike Ehrhart [link]
• Mapping DCAT-based EJP RD Metadata Model to Bioschemas
• César Bernabé [link]
• Galaxy: much more than workflow management
• Björn Grüning [link]
• FAIRtracks and Omnipy
• Sveinung Gundersen [link]

#ELIXIR24

Reproducible analytics and infrastructure

2 x 5 minutes talks

5 minutes questions

Galaxy Community

Frederik Coppens, ELIXIR Belgium

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ELIXIR Research Software Ecosystem

Bjoern Gruening, ELIXIR Germany

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#ELIXIR24

Galaxy Community

Frederik Coppens , ELIXIR Belgium

What is the Galaxy Community

• Open, web-based research environment for data-intensive computational research
• Started in life sciences but now far beyond in other domains
• Foster the use and development of Galaxy

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https://galaxyproject.org/

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What has been achieved so far and why it’s important

#ELIXIR24

What has been achieved so far and why it’s important

• Bring-Your-Own-Storage
• Bring-Your-Own-Compute

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Next steps and their impact

Reducing environmental impact

Federated sensitive data analysis

Community sustainability

Expand the portfolio of tools & workflows

#ELIXIR24

Links to other parts of ELIXIR

#ELIXIR24

How to get involved

https://elixir-europe.org/communities/galaxy

https://galaxyproject.org/community/contributing/

#ELIXIR24

ELIXIR Research Software Ecosystem

Björn Grüning, ELIXIR Germany

What is the ELIXIR Research Software Ecosystem

FIND

bio.tools registry

WorkflowHub registry

OpenEBench

EVALUATE

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Biocontainers

DEPLOY

Galaxy

RUN

#ELIXIR24

What has been achieved so far and why it’s important

• Open software (meta)data
• Standards-based
• Improves navigation
• Enables data exchange
• Facilitates curation
• Improves the sustainability of metadata-based resources

#ELIXIR24

Next steps and their impact

• More than "Tools": all software (including Workflows)
• More than "Bioinformatics": all research

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• Bring software description to the developers

#ELIXIR24

Links to other parts of ELIXIR

Platforms:

• Compute: TRS API
• Interoperability: BioSchemas
• Training: TeSS, GTN links
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Communities:

#ELIXIR24

Learn more, reuse, get involved, join us!

https://research-software-ecosystem.github.io

Gitter room

https://app.gitter.im/#/room/!uTwilrwbvjYdQaMDXe:gitter.im

Slack channel

https://app.slack.com/client/T01E2PXFUE8/C01J3HH76F4

GitHub

https://github.com/research-software-ecosystem/

#ELIXIR24

Federated service delivery

2 x 5 minutes talks

5 minutes questions

TeSS (Training eSupport System)

Carole Goble, ELIXIR UK

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Access and identity management

Jana Broncova, ELIXIR Czech Republic

#ELIXIR24

TeSS (Training eSupport System)

Carole Goble, ELIXIR UK

TeSS - ELIXIR Training Portal https://tess.elixir-europe.org/

Aggregate training events, materials, videos, e-learning, portal to sources.

Register, organise and curate training assets: FAIR training*, collections, workflows, learning paths.

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One-stop for trainers & trainees at national & international level.

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Showcase for ELIXIR training, gathering point for training-related information.

* Rule 4, Ten simple rules for making training materials FAIR, PLoS Comp Bio 2020

#ELIXIR24

Achievements

2694 materials

218 upcoming events

144K+ past events

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open source

open data

#ELIXIR24

Digital Research Skills Australasia

Photon and Neutron (PaN) training

Open Science training in the Netherlands

Digital Research Alliance of Canada

SciLifeLab

#ELIXIR24

Strong collaboration with Training Platform Programme

#ELIXIR24

Next steps & Impact CoS (Training Programme, Infra funding, Node (UK,EE)

Activity

Impact

Shared DevOps across Nodes and RIs

Sustained service

#ELIXIR24

Links with ELIXIR – Training Aggregator & Info Service

Nodes

Communities

Scientific & Technical

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Products, including data resources

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Projects

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content & curation

integration

content & curation

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community perspective

content & curation

integration

project perspective

content & curation

integration

national perspective

#ELIXIR24

Getting involved

Acknowledgements

Club

https://tess.elixir-europe.org/about

EE: Hedi Peterson, Ivan Kuzmin

UK: Finn Bacall, Munazah Andrabi, Xènia Pérez Sitjà, Alexia Cardona, Carole Goble, Phil Reed

FR: Olivier Sand BE: Alexander Botzki ES: Eva Alloza

Australia: Melissa Burke SE: Mihail Anton, Jessica Lindvall PAN: Oliver Knodel

NL: Celia van Gelder GR: Zoi Litou FI: Tommi Nyronen

#ELIXIR24

Access and identity management

Jana Broncova, ELIXIR Czech Republic

Have you heard of AAI?

Unified gateway for users to access services

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#ELIXIR24

What is ELIXIR AAI?

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Key functions::

• Authentication (identity)
• Authorization (privileges)
• It supports federated approach

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#ELIXIR24

What has been achieved so far and why it’s important

• ELIXIR AAI from 2017
• EOSC-Life project: expands AAI solution to more Life Science communities - > LS AAI (2022)
• LS AAI statistics (not only ELIXIR):
• Currently 220 production service integration
• More than 17 000 users

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• Stable infrastructure with ongoing development
• Well established brand also in EOSC

#ELIXIR24

Next steps and their impact

• Why to continue evolving LS AAI?
• to cover needs of the research communities in a changing environment
• to influence the future
• How?
• Via ELIXIR work program 2024-2026 (Strategy)
• Via projects: GDI, ENTRUST,... (Blueprints, pilots, implementation)
• Via cooperation with other science clusters (eg. Enviro), other Elixir platforms and community engagements (Experience and Requirement mapping)
• What we can get? (examples)
• Improved functionality, compatibility with other environments, knowledge sharing cross discipline research support

#ELIXIR24

Links to other parts of ELIXIR

Platforms:

• Compute (our base)
• Training (engagement calls, workshops)
• Tools (services)
• Data (access control to data/storages)
• Interoperability (technology and processes)

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Interconnecting Nodes (node services, infrastructures)

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People: users, service providers

#ELIXIR24

How to get involved

• Do you have a service ? Integrate it with LS AAI :)
• Are you a user? Register a LS ID.
• Do you have an idea/question? Contact us: support@aai.lifescience-ri.eu

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Engagement calls ELIXIR web LS AAI web

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#ELIXIR24

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