The eResearch Office (ERO) in collaboration with the Research Development and Postgraduate Support (RDPS) are organizing a seminar on the use of REDCap, a web application for collecting and managing research data.
The purpose of this session is to comprehensively cover the many stages involved in a REDCap project, from a general overview, the initial setup, progressing through data entry and data export processes as well as using advanced features and specialized modules.
Zindi, a Data Science platform and social enterprise with a focus on building a “data science ecosystem” in Africa, is looking for volunteer Ambassadors. The role will involve creating awareness in your own communities about data science and Zindi activities. Zindi’s mission is to build the data science ecosystem in Africa. They are a Cape Town-based company with a vision for a vibrant community of data scientists across Africa, mobilised towards solving the region’s most pressing problems.
Find out more and register to become an ambassador: https://bit.ly/3IViXPw
UWC’s Forensic DNA Lab (FDL) hosted an eWorkshop (online workshop) on using the Command Line Interface, Unix, shell and other tools for genomics.
The course was aimed at graduate students and research scientists who will work with genomic and bioinformatic datasets for the first time and ran from 10thJune to 15thJuly in two hours weekly sessions.
Seventeen (17) participants were registered, including staff, Honours, Masters and PhD students from different institutions including the South African Biodiversity Institute; University of the Western Cape; Stellenbosch University; University of Johannesburg; University of Pavia (Italy) and ICGEB/UCT.
More about the eWorkshop
Command line interface (CLI) and graphic user interface (GUI) are different ways of interacting with a computer. The CLI ‘is a text-based interface used to interact with software and operating system by typing commands into the interface and receive a response in the same way’. The GUI on the other hand, is a visual-based interface featuring the use of graphic images such as windows, icons and menus, and is navigated mostly using a mouse and the keyboard sometimes.
The CLI is important for proficiency in genomics as most bioinformatics tools use the shell and have no graphical interface. Importantly, CLI is essential for using remote high performance computing centers e.g. ILIFU, CHPC.
The course was designed to impart the following knowledge and skills to the participants:
Discuss practical differences between Unix and Windows;
Navigate and manipulate files and folders using standard bash commands;
Write basic scripts for bash including piping between commands;
Access the ILIFU HPC and submit simple scripts to SLURM; and
Discuss folder/directory structure for genomic projects.
The ilifu cluster computing infrastructure was used for training tasks, which included lessons on basic Unix bash commands and practical activities which required specialised Singularity containerized software.