A webinar on Monday 30 August discussed RDM (research data management) at UWC and Kikapu, our institutional research data repository. Practicing RDM has become an integral part of doing research, and good data management needs to be practiced throughout the research lifecycle. Mark Snyders (UWC Library) and Sarah Schafer (UWC eResearch Office) presented on various aspects of RDM and Kikapu.
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.
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.
On 6 July, the eResearch Office held a webinar on REDCap, a powerful tool for electronic data capture and management. The session was facilitated by Director of the eResearch Office Prof Vaccari, and included presentations from members of the eResearch Office, as well as two informative and inspiring presentations from UWC researchers who make regular use of REDCap for their research – Faheema Kimmie-Dhansay and Tamryn Frank.
REDCap (Research Electronic Data Capture) is a browser-based, metadata-driven Electronic Data Capture (EDC) software and workflow methodology for designing clinical and translational research databases. It is widely used in the academic research community: the REDCap Consortium is a collaborative, international network of more than 2400 institutional partners in over 115 countries, with more than 590,000 total end-users employing the software for more than 450,000 ongoing research studies. REDCap users can benefit from a broad range of data collection functionality, and take control of their data collection work. It is a powerful tool for secure methods of flexible and robust data collection, and although it was originally developed for the Health Sciences, it can be used in any discipline.
About our Guest Presenters
Faheema, a Biostatistician with qualifications in Dentistry and Clinical Epidemiology, is currently working at UWC’s dental faculty and is pursuing her PhD in the risk factors associated with the incidence of caries in children under 6. She has a special interest in the detection of caries in adults and children, alike, and is interested in statistical models analysing time-varying covariates.
Tamryn is a researcher at the UWC’s School of Public Health (SoPH). She works in the food environment policy space, in the field of obesity- and NCD prevention. This informs her current PhD research, which is in the area of obesity prevention policies in low income settings. She is currently serving on the research working group advising the South African National Department of Health on Front-of-Package labelling. Prior to joining the SoPH, Tamryn worked as a primary health care dietitian for eight years for the Department of Health. Her masters research focused on human rights and food security.
Every year, Figshare, in partnership with Digital Science and Springer Nature, conducts the largest survey of its kind to discover global attitudes towards open data.
Researchers from around the world are invited to participate in The State of Open Data Survey 2021.
The aim of the survey is to find out about global experiences and attitudes towards sharing data, how researchers handle research data, the challenges that researchers and institutions face in regard to data, and its impact on workload and resources.
The eResearch Office invites researchers and students to participate in a webinar on REDCap on Tuesday 6 July at 11am.
REDCap (Research Electronic Data Capture) is a browser-based, metadata-driven Electronic Data Capture (EDC) software and workflow methodology for designing clinical and translational research databases. It is widely used in the academic research community: the REDCap Consortium is a collaborative, international network of more than 2400 institutional partners in over 115 countries, with more than 590,000 total end-users employing the software for more than 450,000 ongoing research studies.
REDCap users can benefit from a broad range of data collection functionality, and take control of their data collection work. It is a powerful tool for secure methods of flexible and robust data collection, and although it was originally developed for the Health Sciences, it can be used in any discipline.
The webinar will include an introduction to the REDCap platform and its main features, a demonstration on how REDCap data can be used for analysis and visualisation, as well as brief presentations of use cases by colleagues at UWC. We will conclude with questions directed at the panel.
We will also be addressing any UWC-specific related REDCap queries, and if there are any pressing questions that you would like to raise, please feel free to email us prior to the webinar at firstname.lastname@example.org
Five years since the formal publication of the FAIR data principles, a newly published white paper, Springer Nature’s The Future of FAIR, looks at the real-world impact of FAIR. An international cohort of research data professionals share their opinions and offer commentary on the impact of the FAIR data principles to date, as well as what the next steps in research data management are.
Varsha Khodiyar on the Springboard blog writes that the “burgeoning open science (or open research) movement aims to make public and charity funded research as transparent and accessible as possible, and available for use to all to use, extend and build on. Research data is central to this vision, and to many policies and initiatives launched in recent years encouraging the adoption of open science practices. The impact of the FAIR data concept on open science advocates, position statements, policies and funding opportunities is unmistakable”.
UWC Library Services and the eResearch Office have created a short survey to gather information about Research Data Management (RDM) practices and needs at UWC. The aim of this survey is to identify current RDM practices with a view towards establishing data management services and guidance for researcher communities at UWC. All UWC faculty, staff, researchers and students are invited and encouraged to participate.
RDM is the process of organising and documenting data processes (collection, description, curation, archiving and publication) within a research project throughout the research life-cycle. Well-managed data leads to coherent, shareable and reusable research, and practicing good RDM means that researchers can achieve far more efficiency with their data.
The aim of this survey is to establish what kinds of research data you collect, where such data is held, and how it is being managed. The purpose is to identify current RDM practices with a view towards establishing data management services and guidance for researchers at UWC.
Participation is voluntary and no personal information will be requested that might identify individuals. The survey is strictly anonymous, and participants are free to withdraw from the research at any time.
The data will be stored on an internal server in the Kikapu data repository with controlled access. This information will be used to formulate improved institutional procedures for managing and curating research data.
H3ABioNet (Pan African Bioinformatics Network for the Human Heredity and Health in Africa) is offering a short course in Research Data Management (RDM) in June 2021. The course is aimed at graduate students and biomedical scientists who are currently working on clinical genomics and bioinformatics projects in Africa, and registration closes on 24 May. It will take place over four days from 22-25 June from 10:00 to 14:00.
About the Course
The Research Data Management (RDM) short course will introduce the principles and practices of RDM and provide practical advice for implementing these practices in an African research context. Nicky Mulder is Principal investigator of H3ABioNet, and leads UCT’s Computational Biology (CBIO) group which is an ilifu partner.
Topics covered will include data discovery and re-use, data documentation and organization, data standards and Ontology, data storage and security, repositories and policies, FAIR & reproducibility and best practices in developing an effective Data Management Plan.
After the course, participants should be able to:
Understand what research data management is;
Recognize why research data management is necessary;
Understand best practices and aspects for research data management; and
Have knowledge of the RDM tools available at your institution and online.
The course will only provide a foundation for continued learning in research data management and will not teach any advanced RDM aspects.