First Genomic Data Carpentry Workshop in Africa

UKZN hosted the first Genomics Data Carpentry workshop in Africa from 2-3 December 2019.

The institution’s Big Data and Informatics Research Flagship as well as the SARCHI Chair in Quantum Information Processing and Communication (Quantum Research Group) supported the event, which saw a great turnout of predominately postgraduate research students.

The Carpentries is an open-source group that aims to capacitate academics and students that lack the data and software science skills required in the information age of the fourth industrial revolution. The UKZN Big Data and Informatics research flagship shares this objective, and UKZN has hosted numerous data science workshops using the carpentries curriculum.

The Genomic data workshop curriculum covers:

•    Project management using open source spreadsheet

•    Introduction to Shell

•    Introduction to cloud and data wrangling using Shell scripts to access and manipulate genomics data over the Amazon AWS cloud server.

The lessons are novice-friendly and engage participants in hands-on practical sessions.

The event was opened by lead instructor, Dr Moses Okpeku of the Discipline of Genetics, School of Life Sciences at UKZN. The UKZN team consisted of Dr Matthew Adeleke, lecturer in the Discipline of Genetics, School of Life Sciences; Dr Solomon Uriri, postdoctoral Research Fellow, School of Chemistry and Physics; Mr Tadiwanshe Gutsa, MSc student in Civil Engineering, School of Engineering; Ms Oluwafisayo Kaka, MSc Student in Information Systems and Technology, School of Management, IT and Governance; Mr Ayodeji Ogunde, PhD student in Civil Engineering, School of Engineering; and Ms Thembelihle Luthuli, PhD student in Population Studies in the School of Built Environment and Development Studies.

The project management lesson used Excel, a common tool employed by academics. This was followed by shell lessons on the Amazon AWS cloud server which most delegates had not used previously. The session utilised about 21 Shell commands, reused consistently to encourage familiarity. Each lesson started off with a discussion to familiarise delegates with the tools and build their confidence.

In his closing address, Big Data and Informatics Pro Vice-Chancellor and Head of the UKZN Quantum Research Group, Professor Francesco Petruccione, encouraged delegates to actively improve their data science skills as Africa suffers a shortage of skilled people to fulfil the requirements of the Information Age. Further workshops are planned for 2020.

Words: Oluwafisayo Kaka

Photograph: Supplied