ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR

Larcombe, Lee; Hendricusdottir, Rita; Attwood, Teresa K.; Bacall, Finn; Beard, Niall; Bellis, Louisa J.; Dunn, Warwick B.; Hancock, John M.; Nenadić, Aleksandra; Orengo, Christine A.; Overduin, Bert; Sansone, Susanna Assunta; Thurston, Milo; Viant, Mark R.; Winder, Catherine; Goble, Carole; Ponting, Christopher; Rustici, Gabriella

doi:10.12688/f1000research.11837.1

Cited by 16 publications

(12 citation statements)

References 14 publications

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“…Every country has a specific teaching focus and different amounts of training courses. In general, ELIXIR UK and ELIXIR Switzerland offer a broad portfolio of training courses similar to de.NBI / ELIXIR-DE 60 , 61 , whereas smaller ELIXIR nodes, like Estonia, are only able to offer a few courses including the main research aspects in their countries.…”

Section: Future Plans and Conclusionmentioning

confidence: 99%

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

et al. 2020

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The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR infrastructure. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training & Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 300 training courses were carried out with about 6,000 participants and these courses received recommendation rates of almost 90% (status as of July 2020). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.

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Section: Future Plans and Conclusionmentioning

confidence: 99%

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

et al. 2020

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“…Such paucity of training also negatively impacts the ability of biological investigators to collaborate with their statistics and math counterparts, because of the inability to speak each other’s language. In addition, an estimated one-third of biomedical researchers do not have access to proper data analysis support [1]. The only way to address these deficiencies is with training.…”

Section: Introductionmentioning

confidence: 99%

“…The only way to address these deficiencies is with training. The need for such training cannot be overstated: while the majority (>95%) of researchers work or plan to work with large datasets, most (>65%) possess only minimal bioinformatics skills and are not comfortable with statistical analyses [1,2]. This overwhelming need drives the demand, which, at present, greatly exceeds supply [3].…”

Section: Introductionmentioning

confidence: 99%

Community-Driven Data Analysis Training for Biology

et al. 2018

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The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.

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“…Similarly, REST [Fielding2000] and REST-like webservices are starting to get documented and annotated with OpenAPI (https://www.openapis.org/), previously called Swagger. OpenAPI has the same goal as bio.tools, as well as other annotation solutions, such as BioSchemas [Larcombe2017]: FAIR annotation [Wilkinson2016, Mons2017] of webservices. There is increasing notion that this is needed to move the field forward [Exner2017, Hanwell2017].…”

Section: Introductionmentioning

confidence: 99%