[version 1; peer review: 2 approved, 2 approved with reservations]
No competing interests were disclosed.
The rapid evolution of bioinformatics and data-driven life sciences necessitates widespread, effective training solutions capable of transcending geographical and institutional boundaries. ELIXIR, as a pan-European bioinformatics research infrastructure, has strategically embraced e-learning methodologies to meet this challenge. This white paper systematically reviews the current landscape of e-learning initiatives across various ELIXIR Nodes and Communities, detailing both historical developments and contemporary practices. It identifies core attributes and desirable features of effective e-learning, presenting an analysis of diverse educational platforms and the deployment of Learning Management Systems (LMS) within ELIXIR’s framework. Emphasis is placed on the interactive, open-access, and sustainable nature of these resources, exemplified by platforms such as the Training e-Support System (TeSS) and the ELIXIR-SI eLearning Platform (EeLP). The paper highlights critical advancements toward standardization and interoperability through initiatives such as the adoption of SCORM protocols, facilitating resource reuse across Nodes. Additionally, the integration of e-learning into broader educational strategies—such as hybrid learning environments and structured learning paths—is examined. Finally, future directions are discussed, including strategies for integrating e-learning with traditional training methods, enhancing trainer expertise, and further expanding the availability and FAIRification of bioinformatics training resources.
The
The term “e-learning” has been subject to varied interpretations across different contexts, prompting ELIXIR and GOBLET trainers to engage in a collaborative workshop to establish a precise definition. The outcomes of this discussion were formalized in a report (
Eight essential attributes of e-learning were defined by the trainers: (1) online, (2) open access, (3) interactive, (4) easy-to-use, (5) prerequisites, (6) measurable learning outcomes, (7) maintainable, and (8) sustainable. An additional seven attributes were judged to be desirable: (1) available on demand, (2) self-paced, (3) contextual, (4) quality control, (5) scalable, (6) interoperable, and (7) support. While many of these attributes also apply to traditional classroom teaching, it is the interactivity of the e-learning material which replaces the interactions with the trainer and other course participants. It is the inherent interactivity of e-learning which makes for an active learning process. In a recent survey, 63.2% of industry respondents and 84.1% of those in academia indicated that their preferred training format was “E-learning materials to consult anytime” (
Several of the attributes make e-learning likely to reach a large audience: (1) open access, (2) contextual, (3) easy-to-use, (4) interactive, and (5) measurable learning outcomes. By eliminating the need for trainer availability and leveraging digital delivery, e-learning is particularly well-suited for capacity building. Once the technical aspects of creating e-learning courses have been mastered, trainers can efficiently make use of their time by adopting this approach, particularly when the course has already been taught many times. E-learning courses have the advantage that they can be followed by an infinite number of students anytime and anywhere. This gain in efficiency has led to widespread adoption of e-learning by institutions worldwide, including numerous ELIXIR Nodes.
The implementation of e-learning across ELIXIR Nodes has largely occurred through independent efforts, with several Nodes actively participating in the
It summarises which Nodes provide e-learning (as defined above), the year the first e-learning was made available, the website(s) where the e-learning courses are listed, as well as the conditions to access the e-learning courses. There are currently 9 ELIXIR nodes which offer e-learning. EMBL-EBI was the first to do so in 2011, followed closely by the Swiss node and, over the years by the remaining nodes. The majority of Nodes have a single website from which trainees can choose to follow free e-learning courses (except for ELIXIR France). Login is not required to access the e-learning courses except for those of ELIXIR Belgium, Finland, Romania and Slovenia. Note that some Node institutes adopted e-learning prior to being part of the Node, or even prior to the creation of ELIXIR.
| ELIXIR Node | First E-learning Course | Website(s) with E-learning Courses | Accessibility |
|---|---|---|---|
| ELIXIR-BE | 2020 |
|
Login required; mostly free |
| ELIXIR-CH | 2012 |
|
Open and free |
| ELIXIR-DE | 2016 |
|
Open and free |
| ELIXIR-FI | 2019 |
|
Login required; mostly free |
| ELIXIR-FR | 2024 |
|
Open and free |
| ELIXIR-RO | 2024 |
|
Open and free, login required |
| ELIXIR-SI | 2015 |
|
Login required; mostly free |
| ELIXIR-UK | 2015 |
|
Multiple accessibility options |
| EMBL-EBI | 2011 |
|
Open and free |
The VIB (Flemish Institute of Biotechnology) coordinates the activities of the ELIXIR Belgium Node’s endeavours. Embracing the digital age, VIB has pioneered an e-learning platform that complements the traditional classroom short-format courses. This platform primarily caters to novices, offering an array of beginner-level courses that serve as a foundation for future scientific research. The journey began with biosafety, where the first e-learning modules, crafted by external experts, laid the groundwork for what would become a robust educational framework. Since 2020, the VIB Training team has been diligently expanding this platform, introducing 2-3 new courses annually. The curriculum spans a diverse spectrum, delving into the basics of bioinformatics, guiding learners through the essentials of data management, and equipping them with vital programming and computing skills in Linux, Python using
The SIB Swiss Institute of Bioinformatics is the institute that oversees the work in the Node. Learner-centred education (e-learning, course material, videos) complement teacher-centred education – practically all e-learning courses offered are at the beginner level. The first e-learning courses developed at SIB were
The German Network for Bioinformatics Infrastructure (de.NBI), which represents the German ELIXIR Node (
The content spans basic bioinformatics topics such as Research Data Management (RDM) (
The ELIXIR-Finland Node CSC organises a wide range of training in bioinformatics, AI and data analytics, High Performance Computing, programming and data management. Our
Our bioinformatics e-learning courses include
Our Research Data Management (RDM) Competence Center offers a wide range of webinars and tutorial videos on RDM, providing practical guidance to support researchers at every stage of the data lifecycle. The self-study
The Institut Français de Bioinformatique (IFB) is a federation of regional platforms plus a coordination platform called IFB-core. The IFB Training team only started to work on
Romania became an ELIXIR Observer in 2023 and is working toward full membership, with the Romanian Bioinformatics Cluster (CRB) as its official node. Since 2018, the Romanian Society of Bioinformatics (RSBI), a CRB founding member, has led national bioinformatics training efforts, organising a large number of bioinformatics workshops (
To address this, CRB launched an initiative in 2024 to improve the FAIRification of bioinformatics training resources. The initial step was to directly adopt an existing solution developed by ELIXIR Nodes, the ELIXIR-SI eLearning Platform (see next section).
Community option is crucial for such a platform to effectively achieve its objectives. Therefore, CRB launched a community consultation to assess: existing e-learning approaches with the Romanian research community, perspectives of training FAIRification, preferences for training material management systems and the level of interest in a national e-learning platform. Conducted in collaboration with the Open Science Knowledge Hub at the Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI), the consultation gathered 222 responses, including 54 from life sciences.
While multiple institutional e-learning platforms exist in Romania, most are restricted to university-affiliated users, and 83% of respondents expressed a need for a national e-learning platform. Although this high positive rate may be influenced by survey biases, it indicates a strong need to provide community wide solutions. Additionally, the consultation assessed awareness and usage of ELIXIR-affiliated training resources. Galaxy Training was relatively well known and used (13 out of 54 respondents) whereas awareness of TeSS was extremely low (only 2 out of 54 respondents), suggesting that systematic engagement actions are needed to enhance awareness and visibility of training registries within the community.
The ELIXIR-SI Node is based at University of Ljubljana, Faculty of Medicine. Within the Slovenian Node, the Centre ELIXIR-SI and its e-learning team is responsible for e-learning activities. This team initiated the establishment of the ELIXIR e-learning group within the project ELIXIR-EXCELERATE and which is now part of TrP. The Centre ELIXIR-SI team developed the
ELIXIR-UK is a distributed network of 28 (and growing) research-performing organisations, representing national expertise in data-driven life sciences and providing a platform for UK bioinformatics resources to engage with ELIXIR. As part of its e-learning initiatives, ELIXIR-UK members have developed a wide range of courses and training materials tailored for the higher education and research community, with a strong focus on Research Data Management (RDM), data science, and bioinformatics.
A key achievement in this space is the ELIXIR-UK flagship Data Stewardship Training Fellowship, which has facilitated the creation of diverse e-learning resources, including materials within the Galaxy Training Network and concise video-based courses such as RDMbites. Additionally, the
Beyond content development, ELIXIR-UK actively contributes to community building and capacity development. It co-leads the
EMBL-EBI provides a range of training across the field of data-driven life sciences to guide researchers in both accessing open data using EMBL-EBI data services and analysing their own data. The
Tutorials are designed for self-paced learning and cover a broad spectrum of topics in data science. They range from beginner-level tutorials like
Curated collections of on-demand training materials, including recorded webinars and course materials, bring together a variety of training on a specific topic, such as
This section provides an overview of the diverse array of educational resources available across various ELIXIR Communities – groups of experts across
Fostering knowledge transfer in biodiversity data management and analysis is one of the five main goals guiding the work of the ELIXIR Biodiversity Community. The aims are to: (1) support community-driven skills sharing focused on understanding how to benefit from the use of available standards and best practices; (2) connect developers of tools/workflows/databases with user communities through training that responds to changing technologies and associated services; and (3) expose collections of biodiversity-related training materials, for example through TeSS, the Galaxy Training Network, and RDMkit.
Actions to develop and share training resources that embrace at least some of the essential or desirable attributes that define e-learning are to date largely driven by initiatives with which the ELIXIR Biodiversity Community interacts. A key example from the biodiversity genomics domain is the
A goal of the ELIXIR Biodiversity Community is to continuously improve offerings of the ERGA Knowledge Hub and other platforms by supporting and encouraging the development of more training content that delivers rich e-learning experiences.
The ELIXIR Galaxy Community has integrated e-learning as a key aspect of its training strategy, aligning with ELIXIR’s mission to build bioinformatics skills and data management capacity across Europe. The Galaxy Project offers an accessible platform for large-scale life sciences data analysis, complemented by interactive, on-demand training materials (
The Galaxy Training Network (GTN) (
Galaxy’s e-learning adheres to ELIXIR’s essential attributes of interactivity, open access, and sustainability. Materials include SMART learning objectives, self-assessment tools, and automated quality checks. Metadata compliance ensures interoperability and discoverability through platforms like ELIXIR TeSS. By offering flexible, high-quality resources, the Galaxy Community supports a global audience in advancing their bioinformatics expertise.
The Plant Sciences Community is an interdisciplinary group of researchers who aim to develop and leverage tools, databases, standards and best practices for plant research (
To ensure broad and effective adoption of the Plant Community Service Bundles, interactive e-learning materials have been established, accessible through both TeSS (
To anchor learning in real-world applications, an engaging and interactive CorkOak tutorial (
By weaving together interactive modules, detailed documentation, and practical exercises, the Plant Community Service Bundles e-learning suite offers an engaging, adaptable, and effective learning environment—equipping plant scientists across ELIXIR and beyond to confidently use new tools and approaches in their research.
The goals of the ELIXIR Single-Cell Omics (SCO) Community are to identify the critical challenges in the rapidly evolving field of single-cell and spatial omics data, as well as to bring together international efforts so as to address the needs of the research community. As described in their white paper (
The development and inclusion of e-learning reflects the dynamic progression of educational technology, with numerous life science data hubs enhancing the quality, accessibility, and relevance of these learning resources. E-learning is defined as education supported by digital technologies, accessible online or via intranets, characterized by its self-paced, open-access and interactive nature. While e-learning and open-access, online training materials are both suitable to increase training capacity compared to traditional trainer-lead courses, e-learning distinguishes itself by its interactive approach, for instance through the inclusion of quizzes which test the learners’ knowledge and provide feedback on wrong answers.
Organizations and institutions, including ELIXIR Nodes and Communities, have independently developed a wide range of e-learning resources, from beginner-level courses to advanced modules covering bioinformatics, data management, and programming. EMBL-EBI and ELIXIR Switzerland pioneered an e-learning offering more than 13 years ago. Now, EMBL-EBI provides FAIR training in data-driven life sciences, including self-paced tutorials and curated collections. ELIXIR Switzerland’s offering has recently expanded by 2-3 new courses every year, providing a comprehensive offering in bioinformatics, programming and computing topics, data management and SIB resources. In 2015, ELIXIR Slovenia set up the
The ELIXIR communities are actively engaged in enhancing bioinformatics skills through diverse online learning resources. The Biodiversity Community supports community-driven skills sharing and connects developers with user communities through targeted training, maintaining the ERGA Knowledge Hub for sharing educational resources on biodiversity genomics. The Galaxy Community offers over 400 tutorials on bioinformatics tools, visualization, and FAIR data management through the Galaxy Training Network, promoting accessibility and scalability. The Plant Sciences Community conducts the FONDUE Datathon to train participants in submitting plant genomic data to EBI repositories and introduces Service Bundles for comparative genomics, multi-omics data analysis, and phenotyping data publication. The Single-Cell Omics Community focuses on upskilling scientists in single-cell and spatial omics data analysis and standards, providing a range of training materials, including slides, exercises, and recorded lectures, available online to support the research community in addressing critical challenges in this rapidly evolving field.
Efforts to make e-learning resources FAIR—Findable, Accessible, Interoperable, and Reusable—align with the broader mission of making life-science data more accessible and collaborative. The adoption of best practices, such as adhering to standardization through ontologies and developing certification frameworks, ensures that materials harmonize with the efforts of the global scientific community. Looking ahead, strategic documents like white papers could consolidate current achievements in e-learning while addressing challenges related to standardization and technological integration. These initiatives collectively strengthen the e-learning strategy, positioning it as a leader in delivering premier, forward-thinking educational resources to the life-science community.
While e-learning is being developed and offered in a number of ELIXIR Nodes, there are many Nodes which have yet to do so. These nodes may wish to use the ELIXIR-SI eLearning Platform (EeLP) to create and host their e-learning courses, rather than invest in developing their own solution. To give these Nodes a jump start, an e-learning course ‘
The ELIXIR Nodes and Communities have developed their e-learning content independently, using different Learning Management Systems (LMS). However, reusable e-learning materials require these to be interoperable, i.e. in a standard format supported by the Learning Management Systems (LMSs) being used. Sharable Content Object Reference Model (
A new development in the training field is to combine e-learning and trainer-led courses. E-learning has significantly enhanced ELIXIR’s training offerings as these have been integrated in institutional onboarding trajectories in ELIXIR UK, and soon in Belgium. The implementation of e-learning as a pre-learning trajectory for, e.g. the ‘Statistics using R’ course in ELIXIR-BE, led to new course offerings integrating several modalities after the pandemic and encouraged trainers to professionalize their skills in creating e-learning compatible activities. These activities can be reused in in-person training, ensuring consistency and quality. Additionally, the future development of learning paths with e-learning components in ELIXIR Switzerland promises to provide structured and comprehensive training experiences. These approaches not only maximize resource efficiency but also offer flexible, accessible learning opportunities for participants across different regions.
Looking ahead, several initiatives are poised to shape the future of e-learning. A key initiative involves the development of Train-the-Trainer programs aimed at equipping educators with the skills necessary for effective online teaching. These programs emphasize the importance of interactive, engaging content that is pedagogically sound and technically robust, catering to diverse learner needs, criteria which also apply to e-learning.
No data is associated with this article.
We thank Patricia Palagi for insightful comments on the manuscript.
This article provides a comprehensive overview of the e-learning initiatives developed across ELIXIR Nodes and Communities.
The topic is highly relevant, given the rapid evolution of bioinformatics and the growing need for FAIR training solutions. The manuscript brings together a list of practical resources and initiatives from across Europe that offers a valuable snapshot of the current e-learning landscape within ELIXIR.
One of the main strengths of the article is its broad and inclusive scope. The authors successfully document e-learning activities across multiple ELIXIR Nodes and examples of thematic Communities. Such a way, they offer concrete examples of platforms, pedagogical approaches, and technical solutions. The structured presentation of Node-specific initiatives in Europe are listed in the Table 1. While each Node is presented, a broader summary table is missing. It is not possible to compare the Nodes as they do not all provide the same type of resources for the same group of people. Summarising the diversity of the Nodes will help readers to find the information they need.
The manuscript also provides a clear and well-referenced definition of e-learning in the ELIXIR context, grounded in prior community discussions (Attwood et al., 2016). The distinction between essential and desirable attributes of e-learning resources is particularly useful and offers a practical framework that can guide future course development. The emphasis on FAIR principles, interoperability (e.g. SCORM adoption), and reuse of training materials is well aligned with ELIXIR’s broader strategic goals.
Finally, the discussion of future directions, including hybrid learning models, learning paths, and Train-the-Trainer initiatives, adds value by situating current efforts within a longer-term vision for sustainable training infrastructure.
While the article is rich in descriptive detail, it would benefit from a more explicit synthesis across Nodes and Communities. For example, a short comparative analysis highlighting common challenges (e.g. sustainability, learner engagement, maintenance costs, assessment of learning outcomes) and successful mitigation strategies would strengthen the manuscript and help readers extract transferable lessons.
In addition, although many platforms and courses are described, there is limited discussion of evaluation metrics or evidence of impact. Where available, even qualitative indicators such as learner numbers, completion rates, or user feedback could help substantiate claims about effectiveness and scalability.
The manuscript could also clarify more explicitly how the proposed essential and desirable attributes are currently met across the described initiatives. A concise mapping or summary indicating which attributes are systematically addressed and which remain aspirational would improve coherence between the conceptual framework and the descriptive sections.
Finally, given the rapid pace of technological change, a brief discussion of potential risks (e.g. platform dependency, long-term maintenance of interactive content, or trainer workload) would provide a more balanced perspective.
Overall, this article represents a valuable and well-documented contribution to the bioinformatics training literature and will be of interest to training coordinators, infrastructure developers, and policy makers within and beyond ELIXIR. With minor revisions to strengthen synthesis and discussion of impact, the manuscript is suitable for indexing and provides a solid reference point for future developments in e-learning within large research infrastructures.
Maybe it has been already discuss but a table summary will be appreciated to highlight the different services and type of resources provided by each Node.
How to assess the « quality »? enhancing the quality, accessibility, and relevance of these learning resources.
Is the topic of the opinion article discussed accurately in the context of the current literature?
Yes
Are arguments sufficiently supported by evidence from the published literature?
Yes
Are all factual statements correct and adequately supported by citations?
Yes
Are the conclusions drawn balanced and justified on the basis of the presented arguments?
Yes
Reviewer Expertise:
Bioinformatics, teaching innovation
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
The manuscript by Zahn-Zabala summarized the development of ELIXIR Nodes and Communities for bioinformatics e-learning. It discussed platforms such as TeSS and Eelp for interactivity, accessibility, and sustainability of the developed resources. The authors also provided overview of integration of these eLearning resources to broader educational schemes. I have the following points for the authors to consider.
1. While it is understandable ELIXIR from Europe is the focus of the manuscript, the introduction will be benefit by highlighting similar bioinformatics e-learning portals in other places such as the NCBI Learn Portal, DNA Subway from CyVerse, Genomics workshop from Carpentry to name a few. How e-learning portals from ELIXIR nodes are complementary to these resources?
2. The manuscript has described offering by each Node in detail. However, it remains unclear how effectiveness is evaluated. Table 1 could add additional columns to include main features of each node and ways of evaluation.
3. ELIXIR Nodes and Communities are complementary. A diagram showing the relationship between ELIXIR Nodes and Communities will help reader to better appreciate the e-learning landscape of ELIXIR.
4. The recent AI development, in particular LLM, has the potential to transform bioinformatics education. One of the ELIXIR (FI) does have an AI component. How ELIXIR account for this LLM possibility, which could be a worthy point to discuss as future directions.
Is the topic of the opinion article discussed accurately in the context of the current literature?
Yes
Are arguments sufficiently supported by evidence from the published literature?
Yes
Are all factual statements correct and adequately supported by citations?
Yes
Are the conclusions drawn balanced and justified on the basis of the presented arguments?
Yes
Reviewer Expertise:
bioinformatics, sequencing data analysis, LLMs in bioinformatics and medical informatics
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.
This opinion article systematically reviews e-learning initiatives for bioinformatics education across 9 ELIXIR Nodes and 4 Communities. It defines the core and desirable attributes of effective e-learning (e.g., open access, interactivity, interoperability), highlights key platforms (e.g., TeSS, EeLP) and best practices (e.g., adoption of SCORM standards for resource reuse), maps regional implementation efforts, identifies gaps in cross-node coordination and global outreach, and outlines future directions for standardization and capacity building.
The work fills a critical need for centralized documentation of European bioinformatics e-learning resources. therefore, I would like to recommend its indexing in F1000 Research. However, bioinformatics e-learning is a cross-country trend, the article fails to engage with global literature on the topic and lacks non-European perspectives and comparative global evidence—particularly insights from emerging economies (e.g., China, India) that offer complementary models. a notable example is China's education reform "101 Plan", which features robust cross-regional collaboration mechanisms and AI-enhanced teaching tools; personally I am the lead expert in bioinformatics education for this program).
Additionally, the article requires supplementary citations for statistical claims and unvalidated factual statements.
Is the topic of the opinion article discussed accurately in the context of the current literature?
Yes
Are arguments sufficiently supported by evidence from the published literature?
Yes
Are all factual statements correct and adequately supported by citations?
Partly
Are the conclusions drawn balanced and justified on the basis of the presented arguments?
Yes
Reviewer Expertise:
Bioinformatics
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
This paper provides an overview and history of e-learning activities across ELIXIR nodes. The paper is informative, but could be much more informative if it provided guidance on lessons learned over the course of establishing e-learning resources. For example, how do ELIXIR nodes avoid redundant e-learning content? Its seems all nodes developed RDM materials - why? It could also be much more informative if it expanded on future directions.
Other comments that need corrections include:
- Table 1 website column - Not every link is to an LMS, so text below table should not refer to "LMS of choice"
- Many abbreviations are repeated throughout document. The entire paper needs to be read and updated by a single author as it currently reads like all authors wrote a section and the sections do not connect to each other. Each node talks about different aspects of e-learning for example.
- Aren't all ELIXIR e-learning materials in TeSS? Correct statement " All SIB e-learning courses are found in TeSS" or remove.
- German paragraph has repeated text that should be removed
- German paragraph has a hanging sentence "This library not only facilitates..."
- Finland paragraph - please define CSC abbreviation
Some aspects of the paper are so ELIXIR focused that external non-European reviewers cannot follow. This reviewer does not understand "The videos and coding examples from the perturbation modeling AHM workshop will be part of an e-learning module".
Is the topic of the opinion article discussed accurately in the context of the current literature?
Yes
Are arguments sufficiently supported by evidence from the published literature?
Yes
Are all factual statements correct and adequately supported by citations?
Yes
Are the conclusions drawn balanced and justified on the basis of the presented arguments?
Partly
Reviewer Expertise:
bioinformatics training
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.