Tackling the bioinformatics skills gap worldwide

ELIXIR joined CODATA and RDA to organise an international summer school in research data science.

There is a vast array of technologies and techniques that help scientists process and analyse the ever growing volumes of research data. Along with the rapid development of these techniques, there is a growing demand for comprehensive training in Research Data Science, an emerging interdisciplinary field covering data management, large scale analysis, statistics, visualisation, software development and others.

photo from the trainingTo meet the training needs of life science researchers, ELIXIR teamed up with H3ABioNet and GOBLET and organised an Advanced Bioinformatics Workshop, as an extension of the annual Research Data Science Summer School in Trieste, ltaly, held by Research Data Alliance (RDA) and the Committee on Data of the International Council of Science (CODATA).

The Summer School took place on 6-17 August 2018, ELIXIR Training contributed by providing two instructors from ELIXIR Belgium and ELIXIR Slovenia. The  Bioinformatics Workshop (20-24 August) followed immediately after the Summer school, and was one of the four advanced workshops, that focused on a particular scientific domain. Led by Fotis Psomopoulos (ELIXIR Greece) with Gabriele Schweikert and Amel Ghouila, the workshop programme covered advanced hands-on tutorials on computational methods for genomic and sequencing data, Machine Learning application in bioinformatics, and experimental design.

"We were happy to join CODATA and Research Data Alliance in organising this school. Global collaboration in research data training in essential as there is clearly a big demand all across the world, which no single organisation can meet. We had participants from African, Asian and European countries, ranging from graduate students and postdocs, to senior researchers and principal investigators", says Celia van Gelder, co-leader of the ELIXIR Training Platform.

Daniel Ouso, a graduate student from the Jomo Kenyatta University of Agriculture and Technology in Kenya knows from his own experience how much this kind of course is needed:

"I work on detection of viruses transmitted by mosquitoes and other infectious microbes, to understand transmission dynamics. For a long time I’ve been interested in learning more about working with data and big data analytics, but the training opportunities in  Kenya are still very limited. The Summer School was spot on! The Machine Learning session in the ELIXIR Bioinformatics Workshop was entirely new to me and quite demystified the subject. It also opened up new exciting research routes for my future PhD project. I plan to further build upon my knowledge and share what I learned with my colleagues in Kenya. I definitely look forward to similar opportunities by CODATA, ELIXIR and others.”

photo from the trainingChadia Ed-Driouch, a PhD student from the University Abdelmalek Essa├ódi in Morocco adds: “In my PhD thesis, I use machine learning to infer functional gene networks from information in the Gene Ontology and the gene expression profile. The CODATA-RDA Summer School and the Bioinformatics workshop were a great opportunity to understand and improve my knowledge at the level of data processing and visualization.”

All the course materials for the Bioinformatics workshop are freely available via the course website (doi: 10.5281/zenodo.1440890 ) and will be reused in future training events. Materials for the foundational schools can be found online as well.

A global perspective on ELIXIR Training

Bioinformatics training is one of ELIXIR's priorities, also in terms of international collaboration. Bioinformatics Training was one of the first areas where ELIXIR engaged international partners such as GOBLET (the Global Organisation for Bioinformatics Learning, Education and Training), BD2K Training Coordination Center, and the Software and Data Carpentries. The ELIXIR Bioinformatics Workshop in Trieste was the result of an ongoing dialogue among CODATA, RDA and ELIXIR that started over two years ago.

The Research Data Alliance and CODATA have been organising international data science training since 2016 and has been gradually building an international network of schools organised across the globe. Apart from the Summer School in Trieste, there have been similar events in Sao Paulo, Brisbane and Kigali and will expand in the future.

The overall goal is to train young researchers in the basic principles of research data science, with a particular focus on young researchers in low- and middle-income countries. Hugh Shanahan from Royal Holloway University of London and one of the organisers of the Summer School explains:

“There is an urgent need to equip researchers in all fields of science in the necessary skills to work effectively with data. This is all the more critical for young researchers in low- and middle-Income countries. It is absolutely essential that the ability to exploit and benefit from the big data revolution in science does not become another dividing line between the global North and South.”

The bioinformatics advanced workshop is an extension of the basic curriculum to allow participants to get a hands-on experience in working with life science data. ELIXIR joined the Summer School in 2018 and there are already plans to organise similar workshops alongside the 2019 edition of the Summer School.

“We are very happy to have ELIXIR on board. Having the advanced workshops alongside our training really gives our students an opportunity to go deeper in their particular domains and get a better understanding of data analysis techniques in bioinformatics. By combining our foundational course with the ELIXIR advanced workshops we can reach out to a broader audience and cater for diverse training needs. We look forward to continuing our collaboration with ELIXIR in the coming years.”

Mon 8 October 2018