Public services

Name Description ELIXIR Node
Patents

Our contribution to innovation

Using The Lens, a patent and scholarly literature search facility, we find that ELIXIR resources are increasingly mentioned by name in patent applications. This is a clear indication of their usefulness to bioinformaticians of all sectors (academic, industry), and across the globe. We will soon expand our search to cover all ELIXIR resources, a number of which existed before ELIXIR became operational as a distributed research infrastructure. Our approach is loosely inspired from earlier ELIXIR work (Bousfield et al. 2016), but less computationally intensive, yet lightweight and repeatable so as to operationalise it as an indicator. This is considered to be a qualitative exercise as identical patent applications are known to be submitted in various jurisdictions by their authors. EP: European Patent Office. Access the full visualisations in tableau. Support from the EU-funded PathOS project. 

Impact areas to which we contribute

Using a simplified interpretation of the International Patent Classification (IPCR), patent applications mentioning ELIXIR resource names can be visualised by main fields of use. The qualitative and high-level visualisation below summarises the main impact areas to which ELIXIR resources contribute. Note that many patent applications list several IPCR classes, and that tile size is only loosely related to the number of mentions. Access the full visualisations in tableau. Support from the EU-funded PathOS project.

Supported by
Pathos logo
Pathogen Data Focus Group

Introduction

The Pathogen Data Focus group aims to establish the basis for a distributed and interoperable network of regional and national pathogen data hubs. 

Goals

Through a joint effort, the Focus group will work towards:

  • Establishing consensus and promote the use and reuse of data, metadata and analysis standards
  • Promoting FAIR data sharing and equity
  • Proposing benchmark datasets and quality assessments
  • Fostering capacity building for pandemic preparedness through training, Maturity Models and tools.
  • Liaising with global pathogen epidemiology initiatives (e.g., PHA4GE, WHO, ECDC).

The Focus group will invite experts and stakeholders to join in this concerted, expert-driven effort towards sustaining and ensuring high-quality data for global surveillance and research.

Mailing list

pathogen-data@elixir-europe.org

Subscribe to the mailing list

 

Leadership

Aitana Neves
Aitana Neves
(ELIXIR Switzerland)
Isabel Cuesta De La Plaza
Isabel Cuesta De La Plaza
(ELIXIR Spain) 
Erik Hjerde
Erik Hjerde
(ELIXIR Norway)
Physilia Chua
Physilia Chua
ELIXIR Hub Liaison
PDF test

A link

Professionalising Careers in Research Infrastructures

As a research infrastructure (RI), ELIXIR relies upon a diverse range of roles, such as trainers, data stewards, project managers, software engineers, developers, community managers. By highlighting the career options within a research infrastructure, we aim to promote interest in these roles to support the career development of researchers beyond the traditional academic paths of, for example, Principal Investigators.

As well as supporting the research community by recognising infrastructure career paths, this Focus Group will actively contribute to ELIXIR's commitment to diversity and inclusion within the research ecosystem.

Goals of the group

Initially, the Focus Group will conduct a comprehensive survey of existing job advertisements channels (including the past activity) within ELIXIR in order to classify roles (assessing function, hierarchical position, required skills, etc). The planned outcome of this mapping exercise will enhance the compatibility of job titles and clarify the relationships among different roles within ELIXIR.

The Focus Group will also collaborate with external projects with a related aim, such as ARISE, Technician Commitment, BioNT, CTLS, SciLifeLab Training or EOSC projects as well as internal ELIXIR projects and entities like ELEAD, ELITMa, RItrain(Plus), the RDM Community and RDA Focus Group , eRImote, the Impact Focus Group and the Training Platform.

Mailing list

ri-career-paths@elixir-europe.org

Subscribe to the mailing list

Group chairs

Lisanna Paladin
Lisanna Paladin
(ELIXIR Germany)
Emma Karoune
Emma Karoune
(ELIXIR UK)
Jessica Lindvall
Jessica Lindvall
(ELIXIR Sweden)
Jilly Cheshire
Jilly Cheshire
(ELIXIR Hub Liaison)
RDM Trainer Network

The ELIXIR RDM Trainer Network brings together life sciences professionals working in upskilling, training or educational activities around RDM and Data Stewardship.

We aim to be the enablers of knowledge exchange, a hub for sharing relevant training materials and discussing common challenges across the life sciences in RDM training.

Join the RDM Trainer Network

Ways to gets involved

  • Join the network’s mailing list
  • Share knowledge and expertise during meetings or via mailing lists and Slack channels
  • Attend the Network events and calls organised monthly
  • Present your work or challenges during the monthly calls

Who the Network is for

Roles working with Life Science data, irrespective of career stage, such as:

  • Researchers at all career stages, including PhD students
  • Data Stewards
  • Core support (Bio)informaticians
  • Technicians
  • Facility Operators
  • Research Software Engineers
  • IT Support Staff
  • Data Policy Officers
  • Anyone passionate about data management training in the life sciences

The Network is open to anyone interested in life science data management training, even outside ELIXIR.

Join the RDM Trainer Network

Leadership

Nils-Christian Lübke
Nils-Christian Lübke
(ELIXIR Germany)
Helena Schnitzer
Helena Schnitzer
(ELIXIR Germany)
Xenia Perez Sitja
Xenia Perez Sitja
(ELIXIR UK)

Background

The RDM Trainer Network, part of the RDM Community was conceived by the ELIXIR Training Platform during the ELIXIR-CONVERGE project (WP2).

Research Data Management Community
Join this Community

Research Data Management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have invested in RDM and launched various projects and initiatives to ensure good data management practices for scientific excellence. These projects have resulted in a rich set of tools and resources for FAIR data management.

However, these resources remain scattered across projects and ELIXIR structures, making their dissemination and application challenging. Therefore, it is important to coordinate these efforts for sustainable and harmonised RDM practices, with dedicated forums for RDM professionals to exchange knowledge and share resources.

Goals of the Community

The ELIXIR RDM Community will bring together RDM experts to develop ELIXIR’s vision and coordinate its activities in order to take advantage of the available RDM assets. It aims to coordinate RDM best practices and provide an overview of how to use the existing ELIXIR RDM services, in close collaboration with ELIXIR Platforms, Communities and Focus Groups.

The expected members of the Community are life science RDM professionals in academia and industry in ELIXIR and beyond.

The scope of the Community is:

  • The network of RDM professionals across all Nodes (and beyond);
  • The management of RDM knowledge and know-how in the form of the content of the ELIXIR RDM ecosystem;
  • The management of the RDM training resources and expertise;
  • Coordination of the interactions with external international stakeholders in the area of RDM.
RDM Community illustration, as the focal point of other resources

The initial objectives of the RDM Community focus on sustaining and consolidating the outputs of previous initiatives and projects into a unified structure. This falls into four main areas:

People network

  • Provide a forum that enables regular inter-personal knowledge exchange between life science RDM professionals.
  • Facilitate ELIXIR Node capacity building in deploying RDM services, e.g. by establishing a knowledge handbook for RDM service providers, and developing an RDM services maturity model for ELIXIR Nodes.

RDM knowledge

  • Coordinate and contribute to the RDM ecosystem content by collaborating with the editorial boards of RDMkit and FAIR Cookbook, to ensure that the content is continuously fit for purpose.
  • Collect requirements that would facilitate flow of FAIR data from researchers to repositories (such as the ELIXIR Deposition Databases) via RDM services, in order to improve the FAIRness of research data made available for life science and society at large.

RDM training

  • Provide a forum that enables knowledge, and teaching of best practices exchanges among RDM trainers.
  • Ensure that RDM training materials are being developed and FAIRified, enabling reuse and adoption by the ELIXIR Nodes.
  • Develop RDM learning paths for researchers, data stewards, tool developers and trainers.

External stakeholders

  • Create and maintain an overview of external stakeholder engagements with RDM aspects across ELIXIR Platforms, Communities, Focus Groups and projects.

Leadership

Munazah Andrabi
Munazah Andrabi
(ELIXIR UK)
Flora D'Anna
Flora D'Anna
(ELIXIR Belgium)
Niclas Jareborg
Niclas Jareborg
(ELIXIR Sweden)
Mijke Jetten
Mijke Jetten
(ELIXIR Netherlands)
Katharina Heil
Katharina Heil
katharina.heil@elixir-europe.org
(Communities Liaison, ELIXIR Hub)

Find out more

Join this Community
Review general Recommendations from Galaxy Working Group
The Galaxy Working Group has compiled a set of potential recommendations to send the Heads of Nodes (HoNs). This is a short 2 page document includes a simple table where we classify each recommendation we have collected from different sources.
 
These sources include a) the ELIXIR-Galaxy BoF in July 2015, b) a survey distributed throughout the ELIXIR constituency and the Galaxy Community Conference 2015 and c) the ELIXIR All Hands Breakout on Galaxy (March 2015) and follow up discussions by the TeCG.
 
This set of recommendations will be the basis for the final document to be submitted to HoNs (which we will share for feedback next week). To minimise bias and maximise inclusivity we would now like to request feedback from as many of you as possible. We will have this recommendations table open for discussion until Friday 25th of September.


Please add or modify any of the bullet point suggestions on the right hand column in “Suggesting” mode. Please do not delete bullet points as a whole, rather add as a comment your remarks in that case.

This is the document link:
https://docs.google.com/document/d/1S5AJpVe8kRC3zujpflJ86TGMBtrjcGkWu_DQHTiq9Wg/edit?usp=sharing

Many thanks in advance and best regards,
Frederik Coppens (ELIXIR-BE), Manuel Corpas (ELIXIR-UK)
Galaxy Working Group
Scientific Advisory Board (SAB)

The Scientific Advisory Board plays a major role in the process for reviewing and selecting ELIXIR Nodes and provides strategic scientific advice to the ELIXIR Board. The SAB is an independent body, made up of leading experts from around the world. The committee also includes two independent ethics advisors to advise on ethical, legal and social issues related to ELIXIR. The ELIXIR SAB meets twice a year. 

What the SAB does

  • Reviews applications for new Nodes and makes recommendations to the ELIXIR Board
  • Ensures scientific and technical excellence and relevance (including independent quality assurance)
  • Identifies and recommends emerging challenges and opportunities, both within and beyond ELIXIR activities (including specific periodic reviews)
  • Carries out periodic scientific reviews of ELIXIR Platforms and Communities
  • Reports directly to the ELIXIR Board and ELIXIR Director on the results of their scientific reviews of ELIXIR activities

SAB members

  • Chair: Dr Doreen Ware
  • Vice-Chair: Prof. Philip Bourne
Name Affiliation
Prof. Philip Bourne (Vice-Chair) University of Virginia, USA
Prof. Fiona Brinkman Simon Fraser University, Canada
David Glazer Verily, USA
Prof. Melissa Haendel University of North Carolina, USA
Dr Janet Kelso Max Planck Institute for Evolutionary Anthropology, Germany
Dr Danielle Kemmer Novo Nordisk Foundation, Denmark
Dr Paul Kersey Kew Gardens, UK
Prof. Bartha Maria Knoppers McGill University, Canada
Dr Eric Meslin University of Toronto, Canada
Dr BF Francis Ouellette Bioinformatics.ca, Canada
Dr Luisa Mesquita Pereira i3S Association /  University of Porto, Portugal
Dr Augusto Rendon Genomics England, UK
Dr Doreen Ware (Chair) USDA ARS, Cold Spring Harbor Laboratory, USA
Prof. Detlef Weigel Max Planck Institute for Biology, Germany

Members of the SAB at the February 2025 meeting (from left to right): Janet Kelso, Fiona Brinkman, BF Francis Ouellette, Luisa Pereira, Paul Kersey, Eric Meslin, Philip Bourne, Danielle Kemmer, Bartha Knoppers, Augusto Rendon, Doreen Ware
Service Collections Framework
Service Collection Framework diagram

The SCF is a guide to help ELIXIR Communities, Focus Groups, Platforms and Nodes to develop ELIXIR Service Collections, showcasing ELIXIR Service use in thematic areas.

  • From the ELIXIR Service portfolio, a Service list is generated according to thematic use case by ELIXIR Communities, Focus groups, Platforms and Nodes.
  • The bidirectional arrows indicate feedback avenues where gaps can be identified (i.e non-ELIXIR services) to inform the ELIXIR Service portfolio and its sustainability efforts.
  • The Service list is then encouraged to refer to the SCF to help place and present service uses according to considerations around - ‘Computational tools, data and infrastructure’, ‘Scientific workflows’, ‘Data management’, ‘Industry engagement’, ‘Anticipatory & Responsive deployment,’ and ‘Outreach & community engagement’ to generate Thematic Service Collections.
  • In this manner, Thematic Service Collections help contextualise and increase visibility of ELIXIR Services. These are then intended to benefit bioinformaticians and life scientists in easily finding, accessing, and using relevant services to meet their scientific and professional needs.
  • For ELIXIR, this helps to demonstrate to funders and stakeholders its Service utilisation and relevance in facilitating scientific discoveries and output through open science.

Log in to view the full description of the framework, with a more detailed diagram

FAQs

What is the SCF?

SCF stands for Service Collections Framework. It is an impact-informed guide that helps ELIXIR’s Service portfolio to be showcased in a manner that highlights service utility reflecting scientific use cases.

Why is the SCF needed?

To identify avenues for showcasing ELIXIR Service uses through Thematic Service Collections, with an emphasis on wider engagement of the global life sciences community - a key to sustainability.

What are Thematic Service Collections, and how are they different from the SCF?

Thematic Service Collections are produced by the SCF, and help to contextualise and highlight ELIXIR Services for scientific use cases. These are intended for the benefit of the wider life sciences community, and help life scientists to find and access requisite bioinformatic resources, as well as gain skills and adopt good practices and standards to meet their scientific and professional needs.

Who are the users of the SCF and the Thematic Service Collections?

The SCF is targeted at users across the ELIXIR structures (Communities, Focus Groups, Platforms, Nodes). ELIXIR’s Platforms enable continued Service provision, and are used when developing Thematic Service Collections.
The Thematic Service Collections are intended for use by bioinformaticians and life scientists in academia and the private sector to improve research efficiency, scientific knowledge and skills. These collections are also useful for funders and stakeholders who are able to perceive the utility and relevance of ELIXIR Services in scientific use cases and output.

Why does the SCF emphasise outreach and community engagement?

To showcase and disseminate ELIXIR Services in life sciences research.
As an organisation enabling and supporting publicly funded research, it is important for ELIXIR to demonstrate its commitment and value in enabling such large-scale collaborative research. With the post-genomics and computational era, establishing and sustaining global collaborations is key for scientific discoveries and applications. Without the active engagement of the wider community, service provision is not sustainable.

How does the SCF help with sustainability?

The SCF is designed with emphasis on ‘outcome and impact’ for service provision and their use cases. It explicitly encourages a staged development of Thematic Service Collections to aid visibility, outreach and community engagement for sustainability of ELIXIR Services its Research Infrastructure role in facilitating life sciences research

How does the SCF help funders and stakeholders?

By providing evidence of ELIXIR Service utility in various thematic areas, scientific discoveries and output. For more information on ELIXIR Impact areas, see Figure 1, Martin et al. (2021).

Can non-ELIXIR services be included in the Thematic Service Collections?   

Yes, subject to review where no existing ELIXIR Service covers the identified need for a specific collection. By principle, ELIXIR aims to reduce effort duplication, hence it will encourage the inclusion of existing and FAIR services that fill gaps in its Service portfolio.

What if I cannot fit my service use into any of the SCF categories?

The SCF is designed with due consideration to ELIXIR’s internal workings. It comprises 6 categories: ‘Computational tools, data and infrastructure’, ‘Scientific workflows’, ‘Data management’, ‘Industry engagement’, ‘Anticipatory & Responsive deployment,’ and ‘Outreach & community engagement’. If you are unsure about any aspect of the SCF and its use, please reach out for further information and advice.

Can external parties use the SCF and generate Thematic Service Collections?

Yes. In alignment with open science principles, anyone is free to use the SCF to develop collections that meet their use case. However there is limited support for non-ELIXIR members to generate Thematic Service Collections.

How do the Key Service Collections relate to the Thematic Service Collections? 

The Key Service Collections (e.g. Core Data Resources, ELIXIR Deposition Databases, Recommended Interoperability Resources) can be included as part of any Thematic Service Collections. The Key Service Collections are developed through a formal selection process led by ELIXIR.

How does the SCF and Thematic Service Collections support open science?

The Service Collections help make services more discoverable by users, hence relate to the F (findable) in FAIR. Using the SCF to develop Thematic Service Collections helps the life sciences community in their work, as well as motivates service improvements. If you use ELIXIR Services or help inform ELIXIR’s Service portfolio, then you are already supporting open science. The ELIXIR Service label is a mark of reliability, quality, open community contribution, and sustainability for life sciences and bioinformatics resources. The more these Services are used, the more useful they become.

 

 
Set up the Owl and other microphones

Meeting Owl Pro

This device contains multiple cameras, microphones and speakers in a single unit. The cameras that will cover a whole room (380 degrees) and can detect and focus on up to three individual speakers simultaneously. The microphones will cover a room with up to 12 people (more than this and the voices are a bit quiet). The speaker is loud enough for a considerably larger group. 

The Owl is controlled by an app (search "Owl Labs") which also makes it is possible to connect two together. If you are using a Mac, it can also link up with other microphones enabling a much wider coverage (see below).

To set it up

  1. Two cables connect into the base of the Owl (power and USB).
  2. The base of the Owl also has a screwthread tripod fitting.
  3. Connect the USB cable to your laptop.
  4. Join Zoom, open the camera and select the Owl. (Allow it a moment to connect.) 
  5. The camera is managed via OwlLabs app on phone or laptop.
  6. The app can control more than one Owl, select ELIXIR Owl.
    • Either allow the camera to detect the speakers (default) or use sliders to control the camera.
    • We recommend turning off the "panoramic" view.
    • Note: the Owl is able to distinguish between a voice and loud speaker. 

Samson Go Mic

The Hub has four small microphones available as part of a kit, including extension cables, 4:1 hub etc. One microphone will cover up to 10-12 people in a meeting, using more will ensure everyone is picked up clearly. 

For a single microphone, simply plug the cable in and select the device from the Zoom pop-up menu. 

Settings button (side)

  • Top: Uni-directional (aim the silver face towards the room to improve the sound and avoid background noise)
  • Middle: Bi-directional (limited value) 
  • Bottom: Omni-directional (default, picks up around the whole room, probably the most useful)

Alternatively, connect multiple devices as shown in the diagram above and follow these instructions: 

Combine devices

Macs have a tool to merge multiple microphones into one, making them visible to Zoom etc. 

  • Open Finder
  • Under Applications -> Utilities -> Audio MIDI setup (Opens a new window)
  • In the bottom left corner click the Plus sign " + " (Create Aggregate Device) 
  • This will create a new entity on the left side 
  • Rename this new entity: double-click "Aggregate device" type "Combined" or similar
  • Add devices to "Combined": middle panel, click the checkbox beside Samson Go Mic, Owl etc (as many as required) 
  • Close the window

Complete the set up

  • System Preferences -> Sound -> Select Input Device: "Combined"
  • Open Zoom (or whatever) and select "Combined" as microphone. 
  • Note: check Output Device is not also "Combined", or the sound will be going to a microphone. 

Notes

  1. The size of the room will effect any microphones performance, in a large room with a small number of people the sound will dissipate. 
  2. Zoom has a number of audio settings to suppress background noise, which can unintentionally reduce the sound level. These filters can be turned off: 
    "Settings" -> Audio -> enable "Original Sound" 
    Zoom (top left corner) "Original Sound on/off" 

Software Updates

  • Plug in Owl, connect to laptop and take control using Owl Labs app. (Laptop or mobile device) 
  • Notification "Updates available" 
  • Click to update. 
  • Two options, either
  1. Connect the Owl to wifi network to download the update
  2. Download the update through the connected mobile device
    nb. Owls do not connect to every wifi network. (Not Eduroam or those with certain security settings.)

Any questions or if these details need updating please contact david.lloyd@elixir-europe.org.
Single-Cell Omics Community
Join this Community

Single-cell and spatial omics (SCO) has revolutionised the way and the level of resolution by which life science research is conducted. It has not only impacted our understanding of fundamental cell biology, but has also provided novel solutions in cutting-edge medical research.

The rapid development of single-cell and spatial technologies has been accompanied by the active development of data analysis methods, resulting in a plethora of new analysis tools and strategies every year. Such a rapid development of SCO methods and tools poses several challenges in standardisation, benchmarking, computational resources and training.

These challenges are in line with the activities of ELIXIR. The ELIXIR Single-Cell Omics Community aims to identify the main challenges in single-cell and spatial omics research and coordinate an international effort to best serve the needs of researchers. The Community will build on top of national experiences, and pave the way towards integrated long-term solutions for SCO research.

Graphs showing increased use of SCO technologies
The SCO is rapidly expanding in terms of methods, data and tools. (a) Current count of articles using SCO technologies and cumulative number of cells sequenced and deposited in public databases. (b) Number of tools developed specifically to work with SCO. (c) Most common SCO molecular profiling technologies mentioned in publications. (d) Top 15 most targeted categories for software development in SCO. (e) Number of tools developed for SCO, split by which scripting languages are used. Data were taken from the scRNA-tools database and the single-cell studies database, and surveyed up until January 2022. Figure from Czarnewski P, Mahfouz A, Calogero RA et al. Community-driven ELIXIR activities in single-cell omics, F1000Research 2022, 11(ELIXIR):869.

Goals of the Community

The SCO Community has outlined key focus areas in their whitepaper on F1000Research. In the initial phase the Community aims to address issues in:

Training

This is the core goal of the Community. Please see the training section of our website for more info.

  • We will connect existing materials to compile a comprehensive collection of training materials, datasets and guidelines on how to teach for trainers and learners.
  • We adopt both top down and bottom up approaches via:
    1. Trainer workshops for exchanging ideas about best practices, methods and datasets, and
    2. offering advance training courses and compiling video catalogue of training material to enable self-study and asynchronous learning for researchers.
  • In the long term we aim to utilise ELIXIR TeSS to establish a well-curated ELIXIR SCO training portal, listing national and international bodies, web resources and upcoming training events.

Standardisation and interoperability

Several standards exist in the field of Single-Cell Omics (e.g. FASTQ, FAST5, BAM, CRAM), while a few processed data formats are starting to converge (e.g. tab-separated files, AnnData, HDF5, loom, SingleCellExperiment, Seurat, scverse). However, many of these have had to change in order to adapt to new technological advances that rendered previous formats inadequate.

  • We will focus on best practices for FAIRification in the SCO Community, building upon establishing and promoting data and metadata standards. This will be strongly coordinated with the Human Cell Atlas Data Coordination Platform.
  • To effectively address shortfalls in current data/metadata standard paradigms, we will work towards monitoring emerging technologies and bodies and communicate these guidelines to them. We will also help incorporate new experimental concepts into these existing guidelines. Particular focus will be on spatial gene expression, as this is already showing signs of widespread adoption.

Identifying the most appropriate and performant analysis tools

A plethora of SCO tools exist, and yet standards on how to benchmark or evaluate the accuracy of each tool are lacking. Furthermore, most benchmark efforts are focused on certain cell types or tissues. Please see the benchmarking section of our website for more info.

  • The first goal is the identification of a few scRNA-seq datasets for developing the rules to be used for defining datasets suitable to become benchmarking cases. We aim to create a central pipeline to benchmark SCO tools and define standard datasets for such benchmarks. The outcomes of benchmarking and software challenges allow data scientists to make an informed decision on the software to be used in their analytical workflows.
  • To facilitate findability and usability, we aim to contribute to tool registries and provide portable software environments of the most commonly used tools/workflows.
  • In the long term, we aim to provide cloud deployable analysis pipelines that utilise Galaxy and Chipster platforms, as well as providing curated datasets for user driven benchmark on the OpenEBench infrastructure.

Leadership

Raffaele Calogero
Raffaele Calogero
(ELIXIR Italy)
Naveed Ishaque
Naveed Ishaque
(ELIXIR Germany)
Eija Korpelainen
Eija Korpelainen
(ELIXIR Finland)
Katharina Heil
Katharina Heil
katharina.heil@elixir-europe.org
(Communities Liaison, ELIXIR Hub)

Find out more

Join this Community
The ELIXIR AAI for home organisations

The ELIXIR AAI was migrated to Life Science Login in April 2022.

The Life Science Login, a common user authentication and authorisation service for the Life Science (LS) research infrastructures (including ELIXIR) was launched on 11 April 2022, and the ELIXIR AAI was migrated to it. Home organizations now integrate with the Life Science Login.

See the LS Login page for Home Organizations for detailed information.
The ELIXIR AAI for service providers

If you are a service provider, you can integrate with the AAI using standard protocols like SAML 2.0 or OpenID Connect. When a user wants to log in to your service, you redirect them to the AAI for authentication. Once they are authenticated, you will receive information about the user (attributes), such as their name, identifier, affiliation, group memberships, and authorisations.

The ELIXIR AAI was migrated to Life Science AAI in April 2022. However, some of the ELIXIR AAI's  features are not yet available in LS AAI. To rely on those features, you need to integrate to the Legacy ELIXIR AAI, instead. Before registering your service, please check first if your service needs any of the features in this list.

  1. If your service does not require any functionality from the list you can integrate to LS AAI. Refer to the these instructions.
  2. If your service requires some of the functionality from the list, you probably need to integrate to the Legacy ELIXIR AAI. Please contact us first via email at support@aai.lifescience-ri.eu with a description of your requirement and we will confirm with you to follow instructions below. 

Useful links

Training

Instructions for services to be connected to the Legacy ELIXIR AAI

Note: for services to be connected directly to LS AAI, please refer to the LS AAI instructions.

How to integrate your service with the Legacy ELIXIR AAI

  1. First you need an LS ID for yourself. If you do not have one, get one at LS ID registration page.
  2. Once you have registered, you can register your service via this application.
  3. Log in using your LS ID, then click on the “New service” button or select it in the left-hand menu. You will be asked to choose a protocol and to fill in other information.
  4. The LS AAI administrators will review your registration. You will be notified via email about any changes in your registration.

Complete instructions

You can find a complete list of online training and webinars in TESS (ELIXIR's training portal).

Instructions for Services connected to Legacy ELIXIR AAI

Note: the ELIXIR AAI team will contact the services separately on migration to LS AAI. See the ELIXIR migration news for more information.

How to manage your service registration

You can manage your service registration via the ELIXIR SPReg application.

How to ask Legacy ELIXIR AAI to manage access to your services

In general, you can configure the Legacy ELIXIR AAI to manage access to your services by creating user groups in the Life Science AAI, adding users to those groups, and then assigning different groups to different services. The setting "Restrict access to the service based on membership in groups" in SPReg enables this functionality. When access control functionality is enabled for the service, a user accessing the service needs to have:

  • A valid membership in the ELIXIR Virtual Organisation (VO). The VO is the parent group of all other groups in the ELIXIR AAI. When a user successfully registers for an ELIXIR ID they automatically become a member of the VO.
  • A valid membership in at least one of the groups assigned to the resource.

Based on the further configuration of the service, if the user does not meet the criteria above, they can be redirected to an unauthorized page, a specific page of your choice, or offered to register into the configured groups.

See the managing access to services document for more information on the functionality.

How to set up a separate Acceptable Usage Policy in the Legacy ELIXIR AAI

An Acceptable Usage Policy can be set up by the management and service administration in your organisation. See the detailed instructions or check the slides.

Enforcing authentication via a particular Identity Provider

You can force the users to authenticate with a particular Identity Provider, and bypass the "Choose how to log in" page. See Hinting the IdP to be used in the authentication process.

How to implement Multi-Factor Authentication (MFA)

The ELIXIR Legacy AAI supports so-called "step-up" authentication. You can ask the user to perform MFA, so that the user performs MFA with their home organization (if supported), or they make use of the ELIXIR's own MFA service.

ELIXIR MFA is currently supporting several MFA methods. Users can use their smartphone application to generate a unique six digit code, use a WebAuthn capable token (i.e. FaceID device, YuiKey), or get a uniquely generated code for recovery purposes.

Register the MFA capability as a user. You will be asked to enroll a TOTP token. After that, you can enroll more TOTP tokens, WebAuthn tokens, and generate the recovery codes.

What GA4GH passports and visas are, and how to implement them

The ELIXIR AAI implements the Passport specification of the Global Alliance for Genomics and Health (GA4GH), describing the syntax and semantics for expressing a user’s access rights to registered and controlled access data.

See GA4GH passport support in the Legacy ELIXIR AAI.

Demos: Demo on transferring data access permissions from REMS to EGA
Towards Data Stewardship in ELIXIR: Training and Portal

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Toxicology Community
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Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models.

Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes.

The current main goal of the Toxicology Community is to support the integration of standards, tools and resources to support toxicology research projects and risk governance at the national and international level.

Goals of the Community

The ELIXIR Toxicology Community was created in 2020. Its goals are:

Align open solutions from toxicology research with ELIXIR services and resources

Both toxicology projects and ELIXIR Platforms and Communities have developed models, ontologies, educational material and standards.

The Toxicology Community will align efforts and maximise the benefit. For example, various toxicology projects have been using Bioschemas annotation in online training material.

Connect toxicology research with ELIXIR Platforms and Communities

More synergy can be found by more closely connecting the core ELIXIR resources and communities with the inclusive communities that have evolved over the past few years like OpenTox, eNanoMapper, diXa, OpenRiskNet, NORMAN and older communities like the Federation of European Toxicologists & European Societies of Toxicology (EUROTOX), the Society of Environmental Toxicology and Chemistry (SETAC) and European Environmental Mutagenesis and Genomics Society (EEMGS, formerly known as EEMS).

Develop open community standards

Toxicology projects like OpenTox, diXa, eNanoMapper, and others have already developed various open, domain-specific standards. Some in collaboration with ELIXIR projects like bio.tools, FAIRsharing, etc.

This goal aims to further develop open community standards to support common interest, including ontologies, APIs, data formats, deposition databases, and publication recommendations.

Leadership

Egon Willighagen
Egon Willighagen
(ELIXIR Netherlands)
Rob Stierum
Rob Stierum
(ELIXIR Netherlands)
Karine Audouze
Karine Audouze
(ELIXIR France)
Katharina Heil
Katharina Heil
katharina.heil@elixir-europe.org
(Communities Liaison, ELIXIR Hub)

Additional Community support

  • Marvin Martens (ELIXIR Netherlands)

Find out more

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Train the Trainer (TtT) website

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Training bioinformaticians in High Performance Computing

Training bioinformaticians in High Performance Computing.Esteban Pérez-Wohlfeil, Oscar Torreno, Louisa J. Bellis, Pedro L. Fernandes, Brane Leskosek, Oswaldo Trelles. Heliyon 4 (2018) e01057.
TtT and Training impact workshop report

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TtT training materials GitHub repository

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Tutorials for development of material for Galaxy

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