ELIXIR as a global actor in bioinformatics training

ELIXIR trainers and training materials help to build bioinformatics capacity worldwide

bioinformatics workshop - photo from the classThe rapid growth in the volume and diversity of biological data promise a better understanding of the basic biological processes. But to analyse these data and transform this information into new insights, life science researches need new skills in data manipulation, computer science and statistics. There is a growing demand all around the world for training in data management, large scale analysis, machine learning or data visualisation.

The mission of the ELIXIR Training Platform is to meet this demand both within Europe and globally. Besides managing bioinformatics training programmes for researchers in ELIXIR Nodes, the Platform is working with global partners in building bioinformatics capacity on a global scale. 

Celia van Gelder (ELIXIR Netherlands), the ELIXIR Training Platform co-Lead said: “We know from first-hand experience how urgent the bioinformatics training is among life science researchers.  Whereas it's relatively straightforward to find a bioinformatics training in Europe - thanks to ELIXIR and the ELIXIR TeSS portal - training opportunities in other regions tend to be more be limited. That's why it's so important to work with our global partners and create a global pool of training materials and trainers." 

ELIXIR partners with H3ABioNet and GOBLET to organise the Advanced Bioinformatics Workshop, which extends the annual Research Data Science Summer School in Trieste, Italy, held by Research Data Alliance (RDA) and the Committee on Data of the International Council of Science (CODATA). The first such event took place in 2018, followed by the second edition this year in August.

bioinformatics workshop - photo from the classThe 2019 edition of the workshop covered topics such as Machine Learning in bioinformatics, metagenomics pipelines or experimental design and attracted 19 participants from four continents. Thanks to travel grants offered by CODATA to researchers from low- and middle-income countries, many of the participants came from African or Asian countries. 

Fotis Psomopoulos, the workshop coordinator and instructor from ELIXIR Greece said: "The feedback from participants was overwhelmingly positive. As our workshop extends the CODATA-RDA Summer School curriculum, we know the participants will have the basic skills in data wrangling and programming. We can therefore focus on advanced techniques for analysing life science data. "

From participants' feedback:

  • The course was well structured, the content was very good and the delivery was just excellent. I have learnt new concepts, and understood better concepts that I already knew. All the instructors were just too good, and very approachable and easy to work with.
  • I enjoyed the introduction since it introduced me to the very basic terms and definitions of a research experiment and I enjoyed machine learning and deep learning as well. Nextflow, new and useful. (...) I believe I learned something important for my future projects.

It's equally important to keep the training materials open to everyone, so the participants can consult them any time after the event and share them with their colleagues. Open access training materials also help to build the training capacity right where it's needed.

The materials developed by Psomopoulos and his colleagues  have been already re-used at a Machine Learning workshop organised in collaboration with ELIXIR Switzerland during the BC2 conference in Basel in September. They will be reused again at another training workshop, held as part of the ISCB Africa ASBCB 2019 Conference in Kumasi, Ghana, in November 2019. Although ELIXIR will not be involved in the delivery of the training, its links with H3ABioNet and GOBLET make it easier to exchange and re-use different training materials and build bioinformatics training capacity around the world.

The training materials for the Bioinformatics workshop are available online via the course website

  • Amel Ghouila, Maria Tsagiopoulou, Phelelani Thokozani Mpangase, Scott Hazelhurst, & Fotis E. Psomopoulos. (2019, September 1). ELIXIR / CODATA-RDA Research Data Science Advanced Workshop on Bioinformatics (Version v1.0.0). Zenodo. http://doi.org/10.5281/zenodo.3381146 
Tue 8 October 2019