The first in a series of three Data Science for Biology workshops was held at UKZN’s Nelson R. Mandela School of Medicine, attended by delegates from various African centres of research excellence, creating fertile ground for multi-disciplinary and multinational collaboration.
Focusing on reproducible data analysis using R – a programming language for statistical computing and graphics – the inaugural three-day workshop attracted clinical and biological researchers keen to learn about R and data analysts wanting exposure to clinical datasets.
Workshop instructor, Assistant Professor Laura Symul of the Université catholique de Louvain in Belgium, said there were several other coding languages, however, R was free, open-sourced, designed for statistical analysis – especially in biology and medicine – and allowed full reproducibility of the analysis.
Dr Joseph Elsherbini, a Data Scientist at Ragon Institute of Mass General, the Massachusetts Institute of Technology (MIT), and Harvard, said the workshop honed in on reproducibility because in science it was crucial that researchers were able to reproduce the results of any given study. ‘By doing so using code and R, fellow researchers can trace the exact steps (analysis) taken by the initial researcher in a study. Reproducibility is about making progress from data already obtained.’
The workshop was a platform for novice researchers to familiarise themselves with the benefits of R, introducing participants to R and biostatics basics, exploring data analysis and visualisation, and offering practical considerations for clinical research.
The second workshop will focus on high dimensional data with the final workshop focusing on bioinformatics, which is important because the human body changes its gene expression in response to a number of factors including disease and diet. Observing those changes closely could help researchers identify which genes are more important for developing medical interventions, Elsherbini explained.
The workshop series is the result of a partnership between the Ragon Institute; the University of Maryland School of Medicine in Baltimore and Washington University School of Medicine in St. Louis in the United States, and UKZN collaborators: College of Health Sciences’ Centre for the AIDS Programme of Research in South Africa (CAPRISA), the Africa Health Research Institute (AHRI), and the Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE).
Physiology Academic Development Officer in the School of Laboratory Medicine and Medical Sciences at UKZN Ms Asiphaphola Ludidi, whose doctoral research focuses on metabolic disorder – especially pre-diabetes in females, said the workshop was most helpful in creating better ways to represent and analyse the results of her research. Ludidi felt she could apply what she learned not only to her PhD but also on how to analyse data on student support – an important work deliverable for her. She thanked UKZN for offering the workshop and for encouraging transdisciplinary research.
Ms Leslie Kendou, a master’s degree candidate at the Centre International De Référence Chantal Biya in Cameroon, said she would return home having gained new skills she could now teach her peers using R.
Similar sentiments were shared by Mr Derrick Semugenze, a PhD candidate at Uganda’s Makerere University and the University of Amsterdam whose doctoral research is titled: Association of Viral Exposure with TB Disease.
Semugenze said he had enjoyed learning hands-on data analysis and how to draw graphs at the workshop. Another win for him was getting to engage delegates from other institutions for potential research collaboration.
It is envisaged that by the end of the workshop series, participants will have acquired fundamental computational skills, bioinformatics best practices, exploratory data analysis, and modelling techniques. The subsequent workshops will be held every six months.
Words and photograph: Lunga Memela