Training services
| Name | Description | ELIXIR Node |
|---|---|---|
| EMBL-EBI, ELIXIR UK | ||
| ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Netherlands | ||
| ELIXIR Czech Republic | ||
The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts. The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH. |
EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Belgium, ELIXIR France, ELIXIR Denmark, ELIXIR Italy | |
How to reach the Life Sciences community beyond Academia, in Industry and in the Job Seeking Market, through training? Inspired by this question, ELIXIR, its German Node and BioNT, put together a bioinformatics training needs survey. Besides providing valuable input for the survey collaborators, the results of the survey directly impacted BioNT’s training. This project builds on the experience of the survey and proposes what could be the next step. BioNT develops and delivers free and openly accessible training workshops that, while still accessible to the academic community, target trainees that are seeking a job in the biotech/biomed sector, as well as employees of the diverse ecosystem of Small and Medium Enterprises (SMEs) in the Life Sciences. The project gathers the expertise of both academia and SME partners, putting together a 12-events program divided into two curricula (4 courses in the basic curriculum delivered twice, 4 courses in the advanced curriculum, for a total of 8 different courses), with offers ranging from introduction to programming and bioinformatics, to system administration and machine learning. The first of BioNT’s workshops, “A practical introduction to bioinformatics and RNA-seq using Galaxy'' will be delivered in early September, providing further insights into the challenges and practical aspects of providing training to SMEs and job seekers. This project will foster the interaction and exchange between ELIXIR, especially the German, Spanish and Norwegian nodes connected to the BioNT project, and the academic and SME partners at BioNT. This would be achieved through a face-to-face meeting hosted by one of BioNT’s SME partners, HPCNow!, in Barcelona. During this meeting, we aim to work on two main goals:
Both documents will be shared within the different communities attending the meeting, potentially reaching the training community worldwide. The event will be open to anyone from the involved ELIXIR nodes. |
ELIXIR Germany, ELIXIR Spain, ELIXIR Norway | |
Building on the existing ELIXIR Train-the-Trainer programme, this ELIXIR Staff Exchange project allowed trainers in ELIXIR Nodes to travel to another Node and receive training as part of the ELIXIR Train-the-Trainer programme. Successful participants of the ELIXIR Train-the-Trainer courses were also eligible to apply for travel grants to deliver training in another ELIXIR Node. The project also introduced the term Certified ELIXIR Trainer for an individual who has completed the full ELIXIR Train-the-Trainer course and delivered at least two bioinformatics courses in the twelve months following the completion of the Train-the-Trainer course. |
ELIXIR Belgium, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, ELIXIR France | |
| ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Germany, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR UK | ||
There is a lot of material to teach software development, data manipulation, etc., but much of it is scattered, disorganized, contradictory, or inaccessible because it assumes too much prior knowledge. Contrarily there is a lack of training material in biocuration and for the development of content standards (terminologies, minimum information checklists, exchange formats) and their use in e.g. annotation tools. Nevertheless, funders and researchers increasingly call for enhanced, standards driven experimental annotation at the source and data sharing to maximise data reproducibility and reuse, in order to drive science and scientific discoveries. To tackle this evident gap, this ELIXIR project led by ELIXIR-UK with support from other ELIXIR Nodes aims to leverage the work of the existing Software Carpentry initiative and launch the Data Carpentry initiative for ELIXIR, closely working with the existing international Data Carpentery network. The outcomes of the project are published: Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action. |
ELIXIR UK, ELIXIR Norway, ELIXIR Finland, ELIXIR Italy, ELIXIR Belgium, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Slovenia, ELIXIR Estonia, ELIXIR Czech Republic, ELIXIR France, ELIXIR Israel, ELIXIR Portugal | |
The Task 3 has four main objectives:
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ELIXIR Italy, ELIXIR Sweden, ELIXIR UK, ELIXIR Belgium, ELIXIR France, ELIXIR Slovenia, ELIXIR Estonia, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR Portugal, ELIXIR Spain, ELIXIR Denmark, ELIXIR Norway | |
| ELIXIR Belgium | ||
The aim of this Implementation Study is to guide ELIXIR users to identify those competencies they require and the suitable courses to acquire such competencies to be able to carry out their daily work more effectively. The Study will establish three Work Packages (WP) bridging efforts across ELIXR Platforms, key bioinformatics and data-science initiatives, and Industry partners, to meet Industry needs.
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ELIXIR UK, EMBL-EBI, ELIXIR Netherlands, ELIXIR France, ELIXIR Luxembourg, ELIXIR Estonia, ELIXIR Switzerland, ELIXIR Italy, ELIXIR Finland, ELIXIR Belgium | |
| ELIXIR Germany, ELIXIR Norway, ELIXIR Spain | ||
| ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Greece, ELIXIR Netherlands, ELIXIR Spain | ||
| ELIXIR UK | ||
| ELIXIR UK | ||
| ELIXIR UK | ||
| ELIXIR UK | ||
ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate. |
ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium, ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France | |
| ELIXIR Italy | ||
| EMBL-EBI, ELIXIR UK | ||
Part of the EOSC-Hub project proposal it to establish an ELIXIR Competency Centre (ECC). The EOSC-Hub proposal is currently under review by the EC and a funding decision is expected around late summer 2017 with a tentative project start date of January 2018. The focus of the ECC is to look at the distribution of reference data sets within the EOSC environment and it is proposed by the Compute Platform ExCo to kick-start the work within the ECC through a proof of concept study (funded by the ELIXIR-Hub) on making big data sets available on remote compute infrastructures. Therefore the overall purpose of this Proof of Concept Study is to bring together funded work already taking place within ELIXIR-Excelerate, EUDAT2020 and the ELIXIR nodes into an integrated activity:
This study is now completed, the work is described in the end report. The outcome of this study is summarised in a webinar: This study is associated with: The use of Cloud & VM for training. |
ELIXIR Sweden, ELIXIR Germany, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Finland | |
Part of the EOSC-Hub project proposal it to establish an ELIXIR Competency Centre (ECC). The EOSC-Hub proposal is currently under review by the EC and a funding decision is expected around late summer 2017 with a tentative project start date of January 2018. The focus of the ECC is to look at the distribution of reference data sets within the EOSC environment and it is proposed by the Compute Platform ExCo to kick-start the work within the ECC through a proof of concept study (funded by the ELIXIR-Hub) on making big data sets available on remote compute infrastructures. Therefore the overall purpose of this Proof of Concept Study is to bring together funded work already taking place within ELIXIR-Excelerate, EUDAT2020 and the ELIXIR nodes into an integrated activity:
This study is now completed, the work is described in the end report. The outcome of this study is summarised in a webinar: This study is associated with: The use of Cloud & VM for training. |
ELIXIR Sweden, ELIXIR Germany, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Finland | |
| ELIXIR Germany, ELIXIR Italy, ELIXIR Sweden | ||
| ELIXIR Belgium, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Norway | ||
The ELIXIR Training Platform (TrP) is building a network of training resources and services that aim to promote collaboration, visibility, and standardisation. SPLASH, a digital hub, showcases core services like TeSS and enhances the training life cycle. Work Packages focus on infrastructure, guidelines, and Train-the-Trainer resources. Collaboration across ELIXIR entities is essential, as are standardised guidelines and a supportive community for knowledge sharing. The project's success will transform training delivery within the community. Lead partners: BSC (Spain), INAB/CERTH (Greece), NBIS (Sweden) The ExCo's role in governing the Training Platform involves overseeing and following up on the tasks in the Work Programme. This includes providing regular oversight through chairing monthly TrCG calls and supporting the organisation of the annual meeting for platform members. Effective communication and alignment with other platforms are emphasised, along with providing feedback and recommendations based on wider community consultation and long-term goals. Additionally, strategic planning is necessary to ensure the platform's sustainability and explore avenues for additional support, including industry engagement and competitive funding calls. Activity 1: Project management and coordinationExCo’s will govern the platform and the work conducted by its members. This includes overseeing and follow-up on the tasks undertaken in the Work Programme. To effectively oversee the Training Platform activities, the responsibility includes chairing the monthly TrCG calls. Additionally, it involves assisting in the coordination of the annual meeting for the Training Platform members. In order to maintain alignment, it is crucial to establish regular channels of communication with the other Platforms. As part of the Hub's outreach activities, providing feedback on the Training Platform's initiatives is essential. This feedback should be based on recommendations derived from consulting the wider ELIXIR TrP community and ensuring alignment with ELIXIR's defined long-term goals (Priorities and Ambitions). Moving forward in the 2024-2026 CoS Project, continuous strategy work needs to be taken as to prepare for the future and consolidate the work ongoing. This is an important aspect with regards to the platform's sustainability and life cycle. Particular focus will be given in pursuing additional venues of support that will complement the existing and planned activities of the Training Platform. Examples of such venues include traditional competitive funding calls, private-public partnership efforts as well as industry engagement. Lead partners: VIB (Belgium), SIB (Switzerland), Athena Research Center (Greece) This work package focuses on consolidating the Training Platform Infrastructure, including both its services and resources. This is specifically important to keep increasing collaboration with the community and make the Platform and its activities visible to all stakeholders. To do so, a technical infrastructure to support related activities is essential. This WP comprises the existing Training Metrics Database and aims to expand it to better support communities and standards as well as SPLASH (the acronym SPLASH is short for Skills, Professional development, Learning Assessment, Support and Help along the training life cycle), a digital environment representing a “one-stop-shop” for ELIXIR Training Platform services. Content of SPLASH will be produced in WP3, and the SPLASH website will be constructed in WP2. Activity 1: Expanding the TMD to support communities and standardsA key component in measuring the impact of the ELIXIR Training Platform is the Training Metrics Database (TMD). The main goal of this Task is to enhance and improve the overall functionality of the service, while also updating and further refining the feedback survey questions to better reflect the changes in the overall regulatory frameworks (GDPR, etc). As an example, the survey questions could be complemented by “impact stories” / narratives tied to the respective training efforts. In order to better facilitate this, a direct connection to existing initiatives (such as the ELIXIR Impact Focus Group and the RIPath) will be assessed. Looking beyond ELIXIR, the additional functionality will also aim to support topic-specific and/or Node-specific survey questions, as well as use by communities not directly tied to ELIXIR (such as the Bioconductor community). The expectation is that TMD will be ultimately supported as a multi-node service delivery plan, with distinct Nodes picking up the various responsibilities, which include software maintenance, service hosting, user support, etc). Activity 2: Establishing the technical infrastructure and operations of the Training Platform’s Training Life CycleThe main effort of this WP will be to establish the technical infrastructure components that are currently missing, ultimately providing a coherent space for the content and outcomes of the Training Platform. One key aspect is the requirement for these resources and documentation to be open, easily maintained for sustainable purposes, and tailored for a non-technical audience which will allow better adoption amongst the training coordinators and providers across the Nodes. This activity will work to achieve this by adding the technical functionality in these resources and creating documentation for standard operating procedures that will assist existing and new technical maintainers to be onboarded and provide clear instructions on how to use these technical resources. Lead partners: NKUA (Greece), The Arctic University of Norway (Norway), University of Cambridge (UK) The main objective of this work package is to establish comprehensive guidelines for the complete training life cycle, which will be featured on the SPLASH website. These guidelines will be demonstrated through a few pilot cases that address currently missing topics. The aim is to create a framework that encompasses various aspects, such as designing and implementing training resources, maintaining FAIR principles, establishing pathways, and delivering effective training, while also maintaining links and alignment to relevant efforts within ELIXIR (such as the Open Science activity in Node CoS). Additionally, the work package focuses on defining the roles and expectations of a Training Coordinator and Training Platform members from both the ELIXIR TrP and Node perspectives. This includes formalising expectations, creating Node-specific requirements, and developing an onboarding process for new Training Coordinators. The ultimate goal is to establish a clear identity for ELIXIR Training Platform members and facilitate a more formal recognition process. Activity 1: Unleashing the ELIXIR Training LifecycleThe main goal of this WP is to build upon the BioHackathon23 Training SPLASH project and provide a framework (as a set of guidance documents/webpages) of the training services that can be used in combination towards a complete ELIXIR training life cycle, i.e., starting planning a training event, to the design and implementation of the individual training resources, to the connection across a pathway while maintaining the FAIR principles, to the skills required to effectively deliver it, to gathering and reporting course assessment. This is meant to reuse/expand/build on the TrP handbook homogenising across the structure provided in the training lifecycle, and serve as content for the technical infrastructure developed in WP2. Activity 2: Defining a Training Platform Standard Operating ProcedureThe Training Platform interacts with diverse communities throughout the ELIXIR ecosystem and aims to consolidate access to services and resources across the training lifecycle. Many standardised processes already exist within the platform, but the majority are based on TrP tradition and culture rather than clearly defined and documented procedures. The growing scale of operations necessitates a shift toward more formalised practices as the Training Platform expands its contributions and the TrP community changes and grows. Establishing a clear framework now will help immerse new members in the ELIXIR training community, provide structure and clarity to new Training Coordinators, and promote quick engagement with TrP activities. Mapping ELIXIR Training Platform activities and formalising member roles also paves the way to introduce a more formal recognition process for member roles and their contributions. The goals in WP3 will be complementary linked to ELIXIR-STEERS WP4 ‘Strengthening and equipping ELIXIR Nodes and Node staff with key skills and resources in organisation, management and training ́. Lead Partners: SIB (Switzerland), EMBL Heidelberg (Germany), Sapienza Università di Roma (Italy), University of Bradford (UK) The objectives of this task are to consolidate all Train the Trainer (TtT) resources within the Training Platform's technical infrastructure, expand the TtT efforts to include impact assessment and onboarding, and foster the growth of the TtT community (considered for co-development with TtT content creation and training delivery under the People/Node Tiers in addition to the links to ELIXIR-STEERS WP4, Task 4.1 and 4.3). The activities for the TrP WP4 will involve populating dedicated web pages/portals for TtT within the Training SPLASH, ensuring easy access and maintenance of TtT materials. It will also include FAIRification of content through a GitHub repository, developing additional resources for specific needs, implementing an impact assessment strategy, and creating a supportive environment for TtT instructors to share experiences and knowledge. Activity 1: Consolidating the TtT programme, materials and contentThis Task will be focused on consolidating the TtT resources, in alignment with the 5 steps of the TrP Life Cycle , to facilitate reuse by ELIXIR Nodes and beyond, and onboarding of TtT instructors. The task has clear links with ELIXIR-STEERS WP4 activities. Activity 2: Nurturing of theTtT instructors’ communityThis activity will be funded and covered as part of the ELIXIR 2024-2028 Programme People Tier. |
ELIXIR Belgium, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Ireland, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Sweden, ELIXIR UK | |
| EMBL-EBI | ||
| ELIXIR UK | ||
| ELIXIR Slovenia | ||
| ELIXIR UK, EMBL-EBI | ||
| ELIXIR Netherlands | ||
| ELIXIR Germany, ELIXIR Spain | ||
| ELIXIR Portugal, ELIXIR Slovenia | ||
| ELIXIR Italy | ||
| ELIXIR Finland | ||
| ELIXIR France | ||
The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline. In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for preexisting tools or extend the functionality of the current workflows. This Implementation Study aims to:
To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers. This study is closely linked with the work of the Bioschemas Community. |
ELIXIR France, ELIXIR UK, EMBL-EBI, ELIXIR Finland | |
| ELIXIR Belgium, ELIXIR Germany, ELIXIR Norway | ||
The FAIR (Findable, Accessible, Interoperable and Reusable) principles aim to maximize the discovery and reusability of digital resources. While the principles have enjoyed rapid uptake across communities (ELIXIR, G20, EOSC, H2020, NIH), the implementation details remain unclear. Recently, we developed a prototype software infrastructure and a set of metrics to assess the FAIRness of digital resources (http://fairmetrics.org/). In this ELIXIR Implementation Study we will put these into practice for the ELIXIR community by starting to FAIRify ELIXIR Core Data Resources ArrayExpress, ENA, PDBe, PRIDE, CatH, CHEMBL, ChEBI, UNIPROT, HPA, INTERPRO, MINT, and STRING-db. Our study will first establish effective guidelines for implementation, then involve hands-on FAIRification workshops, in which FAIRness will be assessed before and after the work done. Our work will raise awareness around what it takes to be FAIR, and to help drive interoperability between core ELIXIR resources and with efforts outside of ELIXIR. |
ELIXIR Netherlands, ELIXIR UK, EMBL-EBI, ELIXIR Italy, ELIXIR Sweden | |
| ELIXIR Switzerland, ELIXIR UK | ||
| ELIXIR Germany | ||
| ELIXIR Germany | ||
The objectives of this task are to:
Task 2 will continue to implement the concept of “co-production” between TrP and the collaborating Platforms, Communities or Nodes in the WPs where such interactions are called for. It is important to note for WP2 in particular, that the organization of dedicated hackathons towards preparing new training materials is no longer considered a priority to be funded from TrP Core Funding. However, as it is evident that these training material generation hackathons are still needed, it is expected that they will be funded through other sources such as the co-production model , e.g. by Communities, Platforms, Nodes or other projects that are in need of those hackathons, as well as utilizing the already existing funding schemes by the Hub (Staff Exchange, Travel Grant, etc). |
ELIXIR Greece, ELIXIR Finland, ELIXIR Sweden, ELIXIR Portugal, ELIXIR Italy, ELIXIR UK, ELIXIR Spain, ELIXIR Belgium, ELIXIR Slovenia, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Germany, EMBL-EBI, ELIXIR Ireland | |
Gap analysis, training materials development and training deliveryThe objectives of this task are to:
This study will develop a 'Co-production' model whereby the Training Platform works with a Platform, Community or Node to plan training events, requiring commitment (expertise and/or funding) from the appropriate body. Under current funding, the Training Platform wil be able to support, each year:
WP1 - Gap analysis in ELIXIR Platforms, Communities, Nodes and Industry Work Package 1 will produce a biannual report on the training needs and gaps for all ELIXIR Platforms and Communities with a prioritization of training courses, through dedicated surveys and in a limited number of dedicated meetings between the TrP and representatives of the Platforms, Communities, Nodes, resource providers and Industry WP2 - Development of Training materials for identified gaps and for ELIXIR Services, Resources, and Communities The Training Platform will organize hackathons to gather the experts in the identified topics and together produce training materials, to be made available in TeSS, adhering to the concepts of FAIR (also in relationship with the respective group of the TrP), and tracking of their reuse available. The use of such materials will be promoted in
WP3 - Scaling up ELIXIR Training The Training Platform will launch a competitive RFP to select topics for a limited number of training courses, and will also support running of new or mature courses which are organized and funded by other Platforms, Communities or Nodes. |
ELIXIR Greece, ELIXIR Slovenia, ELIXIR Sweden, ELIXIR Netherlands, ELIXIR Italy, ELIXIR Hungary, ELIXIR Portugal, ELIXIR Norway, ELIXIR Luxembourg, ELIXIR France | |
| ELIXIR Germany | ||
| EMBL-EBI | ||
This staff exchange program aims at enhancing the collaboration of the Portuguese and Swiss Nodes to initiate collaborative training in data management and bioinformatics with Brazilian R&I organisations. The participants intend to collectively plan and deliver a course in biological data management, during which ELIXIR resources and guidelines related to data management will feature heavily. Parallel to this, initial discussions will start to assess the possibility of sharing experiences about Train-the-Trainer initiatives in ELIXIR and in the Brazilian organisations involved, thereby fostering future collective initiatives. Altogether, it is anticipated that the project will usefully raise ELIXIR’s visibility with, and appreciation by, Brazilian bioinformaticians, notably with regards to ELIXIR’s resources and know-how. Data management skills of approx 15 life scientists will be improved. Ongoing activities to establish national leagues of bioinformatics students in Portugal and Brazil will have a milestone in March 2023, at the Bioinformatics Open Days (BOD), foreseen at University of Minho (Portugal), where representatives of Brazil are also expected. The Portuguese league (https://lpb.dei.uc.pt/) has been started this year, fostered by the Brazilian experience (https://lbb.ime.usp.br/home), and will run from December 2022 to March 2023, with a scientific committee of experts from Europe and Brazil, and featuring the participation of teams from the EU and South America. This will be mimicked in the Brazilian league to start early 2023 and finish in June 2023, in the X-Meeting 2023, the international conference of the Brazilian Association for Bioinformatics and Computational Biology, which will be held on Curitiba, Paraná, Brazil, from the 13th to the 16th of June 2023 (https://www.x-meeting.com/events/), co-located with the proposed course. These initiatives are student-driven competitions aimed to foster interest in the Bioinformatics field. Impact statementThis programme will contribute to the internationalization of all organisations involved. For ELIXIR, this project contributes directly to implementing its International Strategy, with a key country in Latin America. The discovery of participants' landscape regarding data management will benefit the state of the art of this topic and seed further collaborations in the future, based on the relationship capital developed during the project. The initiation of discussions towards Train-the-Trainer initiatives is likely to trigger future collaborative courses. |
ELIXIR Portugal, ELIXIR Switzerland | |
This implementation study is designed to
The outcomes of this study have been published in F1000Research and were presented in a webinar. Part of this work has been presented in the ISB Biocuration 2019 meeting (Cambridge, UK, April 2019):
and also in the ELIXIR All-Hands Meeting 2019 (Lisbon, Portugal, June 2019):
This work is carried out in collaboration with |
ELIXIR UK, ELIXIR Switzerland, EMBL-EBI, ELIXIR Luxembourg, ELIXIR Slovenia | |
This implementation study is designed to
The outcomes of this study have been published in F1000Research and were presented in a webinar. Part of this work has been presented in the ISB Biocuration 2019 meeting (Cambridge, UK, April 2019):
and also in the ELIXIR All-Hands Meeting 2019 (Lisbon, Portugal, June 2019):
This work is carried out in collaboration with |
ELIXIR UK, ELIXIR Switzerland, EMBL-EBI, ELIXIR Luxembourg, ELIXIR Slovenia | |
| ELIXIR Belgium, ELIXIR Norway, ELIXIR Portugal | ||
| EMBL-EBI | ||
| ELIXIR Finland | ||
TeSS is the ELIXIR Training Portal, and has been developed in the Training Platform programme The TeSS Infrastructure Service sets out to develop the TeSS as a full fledged infrastructure |
ELIXIR UK, ELIXIR Estonia, ELIXIR Sweden, ELIXIR Italy | |
Scientists have been managing data ever since they collected specimens and shared results of their study with their peers. The advent of the digital computer has allowed for data acquisition in unprecedented amounts to the extent that the organisational task of data management (DM) has become a core activity. Also, external pressure is rising on researchers in general to make sure their experiments are reproducible and that the resulting data is accessible and reusable for others for a longer time (“data stewardship”, DS). This pressure puts even higher demands on the data management practice. Data management and stewardship plans will be a prerequisite for most (public) funding soon. However, data management and data stewardship are not everyday practice for researchers and they are considered more of an administrative task rather than a contribution to proper research. The goal of this implementation study is to kick-start coherent DM/DS activities in ELIXIR and formulate and implement first solutions for good DM/DS in ELIXIR. Currently, there are two main activities in this project, namely to develop and deliver training in DM/DS, as well as to build an infrastructure component (portal or wizard) to support good DM/DS. These two parts will use each other’s results but be executed as separate and complementary projects. More investments are needed after this period to reach a broader audience and feedback experience. DM/DS methods particularly for larger research projects for instance require more structural planning and are not in the scope of this Implementation Study. The two main target audiences for both of these activities are life science researchers who have to make DS plans on the one hand, and data stewards, curators, data managers and other experts in data handling on the other hand. In addition, members of these audiences who are involved in ELIXIR will be asked to actively contribute and help assemble and review the information for the training events, as well as the content of the portal. |
ELIXIR Netherlands, ELIXIR Czech Republic, ELIXIR Luxembourg, ELIXIR Switzerland, ELIXIR Slovenia, ELIXIR UK, ELIXIR Estonia, ELIXIR Portugal, ELIXIR France, ELIXIR Norway, EMBL-EBI, ELIXIR Sweden, ELIXIR Belgium | |
| ELIXIR Portugal | ||
This study aims to empower the expanding ELIXIR network, supporting members in growing their capacities is necessary in order to maintain the quality of ELIXIR training, services and resources. The Training Platform will continue to expand the Train-the-Trainer (TtT) framework (developed under EXCELERATE) to increase the skills of ELIXIR trainers as well as their number across Nodes. WP1 - Train the trainer
WP2 - Management and operationsA gap analysis will be undertaken in 2019 to assess the needs in training of management and operations across Nodes. A working group will be formed to design and implement this analysis, with suitable training resources on management and operations being made available through TeSS. |
ELIXIR Italy, ELIXIR Switzerland, ELIXIR Portugal, ELIXIR UK, EMBL-EBI, ELIXIR Netherlands, ELIXIR Spain, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Luxembourg, ELIXIR Norway | |
Capitalizing on the outcomes of the Work Programme 2019-2021, we continue to support the ELIXIR members to grow their skills and capacities in order to maintain the quality of ELIXIR training, services and resources. The TP continues to expand the Train-the-Trainer (TtT) framework, to increase the skills of ELIXIR trainers as well as their number across Nodes. The Node’s capacity in management and operations will be developed through specific actions aligned with the results of the gap analysis previously performed in the 2019-2021 Work Plan. |
ELIXIR Italy, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR UK, ELIXIR Slovenia, ELIXIR Sweden, ELIXIR Portugal, ELIXIR Germany, EMBL-EBI, ELIXIR Greece | |
The focus of this task is TeSS, the ELIXIR Training Platform’s flagship resource and key reference training portal for the ELIXIR community. This is the principal channel of communication and aggregator of information about ELIXIR training events. TeSS began as an ELIXIR-UK pilot project prior to EXCELERATE, and has matured during EXCELERATE. As of July 2018, TeSS had displayed more than 8,000 training events, with a monthly average of at least 200 upcoming events; in addition, TeSS currently holds more than 1,000 training materials, aggregated from 51 training providers, of which 13 are ELIXIR Nodes. In the last three years, TeSS has been visited by around 13,000 unique users across Europe and beyond. This task has four main objectives:
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ELIXIR UK, ELIXIR Belgium, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Denmark, ELIXIR Slovenia, ELIXIR France, EMBL-EBI, ELIXIR Israel, ELIXIR Netherlands | |
This study will build on the EXCELERATE (WP11) training grant. WP1: Publication and adoption of the ELIXIR Training toolkitThis Work Package will draft a Training Handbook detailing all of the materials developed so far, aiming to provide a comprehensive reference resource for developing training capacity.
WP2: Toolkit expansion – Impact assessmentThis Work Package will tailor the strategy and core metrics developed through EXCELERATE to also measure the impact that training is having on ELIXIR Services, Platforms and Communities through
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ELIXIR UK, ELIXIR Spain, EMBL-EBI | |
The ELIXIR Training Platform has developed a series of training best practices and guidelines, covering several aspects of training development and delivery. These practices are the building blocks of the ‘ELIXIR Training Toolkit’, a collection of resources available in the ELIXIR website. The toolkit will be maintained and updated during this task as well as disseminated to the ELIXIR community for its adoption. |
ELIXIR Spain, ELIXIR UK, ELIXIR Italy, ELIXIR Norway, ELIXIR Sweden, EMBL-EBI | |
Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course. Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting. Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner. As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider. This study is now complete, the final report and other documents will be added as they are available. |
ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium, ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany | |
Bioinformatics analysis typically involves a large number of software and reference data, making the installation process a time-consuming task. This problem is aggravated in a course setting, where every participant needs to have an identical installation, sufficient hardware to run it, and, ideally, access to an identical set-up after the course. Ready-to-run virtual machine (VM) images containing an operating system and pre-installed analysis software, as well as containers, are gaining momentum in bioinformatics. These images and containers can be run on cloud platforms, which allows easy scaling for running tens or hundreds of simultaneous jobs in a course setting. Several ELIXIR Nodes already provide cloud resources for national use. In order to enable also other Nodes to use cloud for training, it is necessary to investigate which of these cloud providers would be willing to provide cloud resources for international use in a sustainable manner. As cloud, VMs and containers are new topics to many bioinformatics trainers, it is important that technical help is available. ELIXIR needs to have a streamlined process for requesting cloud resources and technical help, so that a suitable cloud is found promptly for a course and there is a clear mechanism for reimbursing the technical personnel and computing resource costs for the provider. This study is now complete, the final report and other documents will be added as they are available. |
ELIXIR Finland, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR France, ELIXIR UK, ELIXIR Belgium, ELIXIR Spain, ELIXIR Slovenia, ELIXIR Germany | |
| ELIXIR Finland |