Training bioinformaticians in High Performance Computing

Training Bioinformaticians in High Performance Computing, 6-7 April, Malaga
ELIXIR-EXCELERATE HPC course, April 6th-7th, 2017, Malaga, Spain


Researchers from the BitLab Group at the University of Malaga led by Oswaldo Trelles (INB/ELIXIR-ES) along with Louisa Bellis (ELIXIR-UK), Pedro Fernandes (ELIXIR-PT) and Brane Leskosek (ELIXIR-SI) have published the article "Training bioinformaticians in High Performance Computing" in the Heliyon journal featuring a Train the Researcher workshop that took place on April 6th-7th, 2017, in Malaga. The article discusses the training approaches that can be used to teach High Performance Computing (HPC) to life sciences researchers and also describes the outcomes of that particular course.

Bioinformatics has undoubtedly become a Big Data science, requiring increasingly larger computational platforms to extract knowledge from raw data. However, it is estimated that only 1% of computer scientists have expertise in HPC, and this percentage lowers drastically in the case of bioinformaticians. Therefore, in this article, the authors describe a training methodology to teach HPC to bioinformaticians, from the allocation of resources to the deployment, e-learning and feedback mechanisms, and the teaching approach. Furthermore, they discuss how the teaching methodology affects the quality of the training from a pedagogical perspective, and describe common pitfalls that should be avoided when teaching HPC.


? Esteban Pérez-Wohlfeil, Oscar Torreno, Louisa J. Bellis, Pedro L. Fernandes, Brane Leskosek, Oswaldo Trelles. Training bioinformaticians in High Performance Computing. Heliyon 4 (2018) e01057. doi: 10.1016/j.heliyon.2018.e01057