Author: UWC eResearch Office

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Using machine learning for food quality and safety assurance

The latest research published by eResearch Office’s Dr Frederic Isingizwe on detecting defects in fresh agri-food products dealt with detecting soft damage to apple fruit while they are still invisible to the naked eye.

Damage to fresh agri-food products due to brute impact or compression force can occur during handling and transport, can be invisible at an early stage but becomes more pronounced with time, either in the consumer’s hands or on a retailer’s shelf. Such damage to fresh produce accelerates the deterioration of fruit and vegetables and can facilitate infections by micro-organisms, which makes products unsafe to consume.

The research was conducted to aid with sorting and grading fresh products, either at an industrial or smaller scale. We demonstrated that these invisible defects can be detected using shortwave hyperspectral imaging techniques and by using machine learning algorithms, we established the degree to which the differentiation of defective from sound apple fruits is feasible.

Read more about this work here.

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IBM Research Africa to host a Virtual Seminar Series on ‘What’s Next in AI (Artificial Intelligence)’

As AI continues to mature, nations around the globe are adopting it more and more to drive large-scale transformation and competitiveness; Africa is no stranger to this. From agriculture and health services to translating languages, AI can play an important role in helping Africa tackle economic problems.

Creating an AI ecosystem and forging local and global relationships is vital. During the past decade, local groups of industry practitioners and researchers have been actively hosting events, including Data Science Africa and Deep Learning Indaba, towards this goal. The African machine learning community has been steadily growing.

This August, on 18th and 25th, IBM Research Africa is inviting academics, students, developers, researchers and AI practitioners to a dialogue on the future of AI through this series of seminars delivered by some of IBM Research’s leading Scientists in Africa and other global labs. With a focus on advances in trustworthy AI, neural and symbolic learning, reasoning and language understanding, this series will launch a continent-wide conversation on the future of AI and the role of the African computing community in inventing what’s next for AI in Africa.

To learn more on the event, follow the link here and to register, click here.

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Upcoming Kikapu Webinar

The Library and the eResearch Office will be hosting a webinar that focuses on our Institutional Data Repository, Kikapu.

The webinar will take place on 30 August at 11am.
Register here.

Kikapu is UWC’s online institutional research data repository. It is a versatile platform for publishing and accessing research data and scholarly outputs, and accepts a wide variety of non-traditional research outputs and file formats. Research data and any associated documents can be stored and shared in either primary or refined versions.

Read more about Kikapu.

Introduction to Research Data Management and Kikapu

The webinar will cover the following:

Introduction to Research Data Management (RDM) and Kikapu:
– What is research data 
– Why publish research data
– Open Access
– FAIR Data principles


Introduction to Kipaku – UWC’s Institutional Research Data Repository
– Creating an account
– Uploading content (datasets)
– Publishing uploaded content (datasets)
– Citing published content
– Tracking record statistics

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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.

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DIRISA Student Datathon Competition

DIRISA (the Data Intensive Research Initiative of South Africa) has organised a student datathon to showcase how open research data can be used to come up with creative and innovative solutions to some of South Africa’s problems. It is open to undergraduate and graduate students above the age of 18, and is free to enter.

DIRISA is one of the three pillars of South Africa’s National Integrated Cyber Infrastructure System (NICIS), and will be hosting the virtual four day tournament from 26 to 29 July 2021.

In this annual event, student teams from South African universities compete in the development of software applications based on data science, artificial intelligence and other leading edge technologies, to solve relevant South African challenges. Last year’s theme was To provide a South African solution related to the COVID-19 pandemic, and in 2021, participants will be expected to source open datasets to find solutions.

Here is the link for the event page https://sdc.dirisa.ac.za/.

Registration is open, and the competition begins on 26 July.

Find out more and sign up to enter.

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Watch the NITheCS Roadshow at UWC

On 15 July, the eResearch Office hosted a NITheCS Roadshow at UWC titled ‘Transition from NITheP to NITheCS and how it can benefit your University‘. The session was moderated by eResearch Director Prof Mattia Vaccari, and Prof Francesco Petruccione (NITheCS Interim Director) gave a presentation and answered questions. Watch the video recording:

Prof Mattia Vaccari moderated the NITheCS Roadshow session last week.
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UWC eResearch Office partnering with FSNet-Africa project in interdisciplinary research on African food systems

Food Systems Research Network for Africa (FSNet-Africa) is a collaborative project between the University of Pretoria’s (UP) African Research Universities Alliance (ARUA) Centre of Excellence in Sustainable Food Systems, the University of Leeds (UoL) (United Kingdom), and the Food, Agriculture, and Natural Resources Policy Analysis Network (FANRPAN).

FSNet-Africa is an ARUA – UK Research and Innovation (UKRI) Research Excellence Project funded by the Global Challenges Research Fund (GCRF); its major contribution to addressing the SDG challenges will be the focus on developing a new understanding of the African food system. It will aim to develop the FSNet-Africa Food Systems Framework and utilising systems-based methodologies to conduct research that enhances understanding of the framework’s components, their interactions, and ultimately the leverage points for food system transformation.

The Fellowship

Dr Frederic Isingizwe from the eResearch Office is one of UWC’s two recipients of the FSNet-Africa fellowship, a two-year research fellowship (July 2021 to June 2023) for early career researchers who are supported in their research to identify and evaluate climate-smart, nutrition-sensitive, poverty-reducing interventions in African food systems.

In addition to research project funding, fellows are supported through participation in a series of structured activities in science, mentorship and leadership development, and by establishing long term research networks, which currently involve ten African Universities and the University of Leeds. This will ensure that the fellows are positioned in the necessary enabling environment and provided with the opportunity to develop the necessary skills to implement impact focused interdisciplinary research related to African food systems and significantly advance their academic careers.

During the fellowship, each fellow will be assigned at least two mentors, from both African and UK universities. These carefully matched research-triads will be interdisciplinary teams that enable the fellows to receive the support they need to develop and implement quality interdisciplinary research projects. This will also create opportunities for fellows and mentors to build meaningful relationships with researchers outside of their own organisations, which can lead to longer term collaborations.

The Research

Understanding African food systems and developing evidence-based interventions to address gaps and systems failures is fundamental to achieving four critical food systems outcomes – nutritious food (safe and high-quality); equitable inclusive systems (social aspects e.g. gender); sustainable environmental approaches and efficient systems (economic considerations e.g. poverty reduction).

The fellows’ research will focus on a systems approach (rather than a discipline-specific approach) to understanding African food systems, whereby the conceptualisation recognises:
– that gender and poverty are cross-cutting issues, influencing not only labour, inputs and types of farming systems (supply), but also diets and food cultures (demand);
– formal and informal supply chains through which food moves from farm to consumer and the different actors and regulations that govern those chains (and the interactions between them);
– key emerging actors within the food systems, such as “agripreneurs” setting up businesses in the agri-sector, and critical drivers of change (e.g. urbanisation and the growing African middle class).

Frederic’s research in the fellowship will focus on developing data-driven solutions for the food supply chain. Aspects such as quality monitoring of agri-food products along the food chain and optimisation of supply chain processes will be the main focus. The project will aim to develop solutions that help improve quality, safety and reduce loss of food along the food chain.

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Introducing ESCALATOR

An exciting addition to the South Africa Digital Humanities (DH) landscape, ESCALATOR has recently launched, and aims to establish a local community of practice within DH. SADiLaR (the South African Centre for Digital Language Resources) is behind the project which will focus on the adoption of digital research methodologies and practices to the Social Sciences and Humanities.

“Humanities and Social Sciences research and education are in dire need of strong coordinated interventions to enable the pervasive adoption of digital research methodologies and practices. Over the past few years several capacity development initiatives were implemented within various institutions and communities, but South Africa still lacks a national, integrated active community of practice in this space”.

SADiLaR

Working groups like Python study group and the R study group provide valuable long-term learning opportunities and supportive communities. Additionally, the ESCALATOR Digital Champions Initiative is a multi-track mentorship and networking programme that complements other activities, and is open to researchers, professional staff, and students from the 26 public universities and research councils in South Africa.

Find out more about the project.

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NITheCS Roadshow at UWC

The eResearch Office will be hosting a NITheCS Roadshow at UWC titled ‘Transition from NITheP to NITheCS and how it can benefit your University‘. NITheCS, or the National Institute for Theoretical and Computational Sciences, was formerly known as NITheP, or the National Institute for Theoretical Physics. Its new name emphasizes its much-widened scope to supporting research, training and engagement across a wide range of fields. The session will be moderated by eResearch Director Prof Mattia Vaccari, and Prof Francesco Petruccione (NITheCS Interim Director) will give a presentation and answer questions.

Register here to attend the roadshow and see more details below.

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REDCap Webinar Recording

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.

Watch a recording of our REDCap webinar.

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.