Creating a Data Management Plan (DMP) Workshop

UWC’s Division for Postgraduate Studies (DPGS), eResearch Office and Library Research Support & Scholarly Communications hosted a workshop on creating Data Management Plans (DMPs) on 16 August 2021.

Along with UWC’s Research Data Management (RDM) Policy and the Protection of Private Information Act (POPIA), DMPs are central to the research process. The workshop provided an overview of RDM and Data Management Planning, and demonstrated some practical advice on how to craft a DMP.

Watch the recording.

Data Management Planning is ultimately most useful for the researcher, and it helps achieve the benefits that come with managing and sharing data. Increasingly, funding bodies and publishers mandate the submission of a DMP to ensure that data can be preserved and shared. UWC’s Research Data Management Policy encourages all UWC researchers to submit a data management plan in the course of their research.

eWorkshop: Command Line Interface for Genomics Beginners

Forensic DNA Lab UWC

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:

  1. Discuss practical differences between Unix and Windows;
  2. Navigate and manipulate files and folders using standard bash commands;
  3. Write basic scripts for bash including piping between commands;
  4. Access the ILIFU HPC and submit simple scripts to SLURM; and
  5. 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.

eWorkshop: Command Line Interface for Genomics Beginners

Forensic DNA Lab UWC

The Forensic DNA Lab (FDL, UWC) will be running an eWorkshop (online workshop) on using the Command Line Interface, Unix, shell and other tools for genomics. 

The course will run from 10 June to 15 July with once a week lessons.  The course is aimed at graduate students and research scientists who will work with genomic and bioinformatic datasets for the first time. We will help attendees get started in using the CLI for performing genomic workflows. Attendees require no previous experience in CLI tools.

More about the eWorkshop

Command line interface (CLI) and graphic user interface (GUI) are different ways of interacting with a computer’s operating system. The CLI allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination.

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.

After the course, participants should be able to:

  1. Discuss practical differences between Unix and Windows;
  2. Navigate and manipulate files and folders using standard bash commands;
  3. Write basic scripts for bash including piping between commands;
  4. Access the ILIFU HPC and submit simple scripts to SLURM; and
  5. Discuss folder/directory structure for genomic projects.

The course registration is now closed.

UWC’s first Data Carpentry Workshop of 2021

From 12-16 April, the eResearch Office hosted UWC’s first Data Carpentry workshop of 2021. It was an online workshop held over five mornings, and was attended by over 20 researchers. The workshop was aimed at students and researchers who want to start learning how to work with their data, and was sponsored by SADiLaR.

The eResearch Office promotes and supports the use of advanced information technologies to enable better, faster and higher-impact research, and we hope to grow the Carpentries community at UWC.

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners’ existing knowledge to enable them to quickly apply skills learned to their own research. Participants are encouraged to help one another and to apply what they have learned to their own research problems.

Lessons included data organising and cleaning in spreadsheets and with OpenRefine, and data analysis and visualisation with R and RStudio. 

Please contact eresearch-support@uwc.ac.za if you would like to be added to the UWC Carpentries mailing list.