DIR – UWC eResearch Office

18 November 202418 November 2024

Postdoctoral position in Data Science for Food Systems

The eResearch Office at UWC is a division under the Deputy Vice-Chanellor Research and Innovation that promotes the use of information technology to enable fast and high impact research. Part of its mission is to drive and coordinate advanced uses of data-driven approaches to multi-, inter- and trans-disciplinary research in a dynamic environment for skills development and academic growth. A postdoctoral fellowship position is available for an outstanding candidate to undertake cutting-edge research in the development of data technology for sustainable food systems. The fellow will be awarded a tax-free fellowship for up to 2 years with opportunities for academic and personal development.

Prerequisites:

The prospective candidate should be a holder of a doctoral degree obtained within the past five years in the field related to Natural, Computer, Mathematical or Agricultural Sciences. The applicant should have interest and/or experience in modelling data of biological systems, be familiar with the concepts of sustainability within food systems and able to work without supervision, as well as in a team.

The successful candidate will be involved in the following roles:

– Conducting research in the area of data science applied to food systems
– Develop original research and publication
– Involvement in sourcing research grants
– Science engagement
– May be requested to assist with various activities that support the eResearch agenda for the University.
– Mentor and support postgraduate students.

Interested candidates can send their CV and motivation letter to Dr Frederic Isingizwe at fisingizwe@uwc.ac.za or to Prof Clement Nyirenda at cnyirenda@uwc.ac.za.

The position remains open until filled.

6 August 20247 August 2024

Software Carpentry: Shell, Git, Programing with R

Learn basic computing skills to conduct research
Software Carpentry aims to help researchers get their work done in less time and with less pain. This hands-on online workshop covers basic concepts and tools, including programme design, version control, data management and task automation. Participants will be encouraged to help one another and apply their learning to their own research problems.

Who should attend?
Graduate students and other researchers. You don’t need any previous
knowledge of the tools that will be presented at the workshop.

Venue
Training takes place online. The instructors will send you the information
you need to connect to this workshop.

Requirements
You will need access to a computer with a Mac, Linux, or Windows operating
system (not a tablet, Chromebook, etc.) on which you have administrative
rights. You will also need an up-to-date browser and a few specific software
packages installed – see here: https://bit.ly/3LLL0Dp.

Questions?
If you have a query, please email thuthukile.khumalo@nithecs.ac.za or
visit https://bit.ly/3LLL0Dp.

2 December 20222 December 2022

CHPC-NITheCS Coding Summer School 2023

30 January 2023 – 10 February 2023

The Centre for High Performance Computing (CHPC) and the National Institute for Theoretical and Computational Sciences (NITheCS) are organizing a coding summer school that offers introductions to Foundations of Theoretical and Computational Sciences on topics such as Data Visualization, Data Analysis, Modelling and Simulation, Stochastic Methods, Machine Learning and Software Management.

A basic programming course that introduces participants to Linux (Ubuntu) command line and bash scripting, and the Python programming language will be given as a foundational tool for the school.

Students registered for Honours, Masters and PhD studies as well as postdoc fellows, in South Africa are eligible to apply and the attendance is free of charge. The school will take on a physical form at various university locations around the country, therefore participants will be required to attend one of the university locations.

The University of the Western Cape will provide one of these locations on its campus, and all interested candidates are encouraged to apply.

Course content

Daily lectures and interactive tutorials
Moodle used as the learning management environment
PDF notes, exercises, and YouTube videos provided
Zoom used for live streaming
Slack used as official communication medium
Prizes awarded to select students

Requirements and Registration

Participants are encouraged to bring their own laptops but where it is not possible, the organizers might assist to access an on-site computer. No programming skills and basic Linux knowledge are required, although that would be an advantage. Applications can be done at this registration link and more information on the can be obtained here.

Important dates

Closing date for registration: Saturday, 31 December 2022
Notification of successful candidates: by 16 January 2023
School start and orientation: Monday, 30 January 2023
School end: Friday, 10 February 2023

13 July 2022

Africa Open Science Hardware Summit

AfricaOSH is an organisation that aims to inspire African makers, and is focused on open source scientific tools and hardware. They seeks to promote and provide a platform for innovation and creation in Africa, and hold annual events.

The 2022 annual summit theme is Growing the Do-It-Yourself & Do-It-Together (DIY/DIT) Culture for Community Transformation : a focus on Open Health, and promises to be insightful, educative, innovative and fun. The event will be hosted by MboaLab and take place from 29 September-1 October in Yaounde, Cameroon. Read more about it here.

Applications to attend the 2022 AfricaOSH annual summit are now open: https://docs.google.com/forms/d/e/1FAIpQLSdOwXEONbacMeYX5p1BEpWT20uyQZuByTiRBkLfgGPDXKjUhA/viewform

26 May 2022

ilifu-supported Africa CDC course at SANBI

SANBI are currently teaching a course on SARS-CoV-2 (COVID-19) bioinformatics to visitors from public health labs across Africa. The course is taking place at the University of the Western Cape from the 23 to 27 May 2022, and is using ilifu, South Africa’s big data infrastructure for data-intensive research.

Africa CDC aims to strengthen capacities and capabilities at public health institutions in Africa in order to detect and respond quickly and effectively to disease threats and outbreaks. They have data-driven interventions and programmes, and SANBI has been working with Africa CDC since 2018.

In 2020, the Africa CDC launched its Institute of Pathogen Genomics (IPG), which has been at the forefront of supporting SARS-CoV-2 sequencing on the African continent. SANBI is one of the specialist centres assisting Africa CDC in its work developing pathogen genomics and bioinformatics. As part of this role, they are running a week-long course on SARS-CoV-2 sequence analysis for people from public health labs in 9 African countries – Morocco (Institut Pasteur du Maroc), Egypt (Central Public Health Laboratory), Ethiopia (Ethiopian Public Health Institute), Uganda (Center Public Health Institute), Kenya (National Public Health Laboratory), Senegal (Institut Pasteur de Dakar), Zambia (Zambian National Public Health Institute), Ghana (Noguchi Memorial Institute for Medical Research) and South Africa (National Institute for Communicable Diseases). Nigeria (Nigeria CDC) and DRC (Institut National de Recherche Biomédicale) could not attend in-person, but are participating online.

**Back row** (L-R): Ziphozakhe Mashologu, Wael Saif, Harris Onywera, Peter van Heusden, Alan Christoffels, Leonard Kingwara, Ayitewala Alisen, Abebe Negeri, Abdelmajid Eloualid, Amadou Diallo. **Front row** (L-R) Susan Alicia Fernol, Michelle Lowe, Annie Chan, Tracey Calvert-Joshua, Quaneeta Mohktar, Francis Ahiakpah, Moussa Diagne. Not present: Mpanga Kasonde, Akil Prince, Emmanuel Lokilo .

SANBI have been ilifu partners since its inception, and Peter van Heusden, Senior Bioinformatician at SANBI, is one of the organisers of the workshop. He says that participants have found it to be “an excellent resource to support public health bioinformatics”. ilifu is a node in the South African national data infrastructure which enables South African researchers to be leaders in the strategic science domains of astronomy and bioinformatics.

Course participants working on data analysis in SANBI’s Aaron Klug seminar room, 23 May 2022.

The training relies on cloud infrastructure provided by Ilifu – each lab gets their own installation of SANBI’s SARS-CoV-2 Workbench to work on, and gets hands-on experience with uploading data, doing data analysis and visualising their results. While the current training has focused on SARS-CoV-2, the discussions have ranged across a number of other infectious diseases that these public health labs are responding to: HIV, TB, hepatitis, malaria, influenza and other pathogens. SANBI sees this training as feeding into Africa CDC’s efforts to build a Community of Practice in public health bioinformatics and genomic surveillance.

23 May 202223 May 2022

Training Opportunity : Data Science and Machine Learning

A training opportunity for data science and machine learning is available and registration closes on 25 May.

Makerere University School of Public Health (MakSPH) in Kampala, Uganda, is working in partnership with four other African universities to research the COVID-19 response in Africa. Through the collaboration, a community of practice (COP) has been establised. It is aimed at developing the capacity of African institutions to prepare, analyse and respond to disease epidemics successfully.

As part of the COP, and in partnership with IBM Research Africa (IBMRA) scientists, who have expertise in artificial intelligence (AI), data science, and machine learning, the project has organised a capacity-building opportunity on data science and machine learning.

Participants interested in or with a background in data science, artificial intelligence, machine learning and cloud computing are encouraged to register. There is no minimum skill requirement aside from computer literacy.

Topics that will be covered include analysing the impact of COVID-19 on essential health services using time series analysis; learning from COVID-19 models to support what-if scenario analysis; and intervention planning and descriptive statistics to analyse NPIs implemented in African countries.

The training will be conducted online through Webex, with an expected engagement of about 2 hours every week. Facilitation will be in both English and French, and the programme will run until October 2022.

Interested participants can register here : https://shorturl.ae/Gd3EC
by 25 May 2022.

14 January 202214 January 2022

Africa Women in Data Science: Online Event

DARA Big Data (Development in Africa through Radio Astronomy), in partnership with the Office of Astronomy for Development (OAD), IDIA (Inter-University Institute for Data Intensive Astronomy) and SARAO (South African Radio Astronomy Observatory) is hosting a free 3-day Africa Women in Data Science online event. The event will coincide with International Women’s Day 2022 and will also mark the one year anniversary of the publication of the SARAO Women in Data Science report.

The event organisers hope to help build a thriving African community of female data scientists and promote skills development for women who are interested data science careers. Registration for the event closes January 31 2022.

The event will take place from 8-10 March 2022, which coincides with International Women’s Day. It aims to increase African women’s participation in the 4th Industrial Revolution (4IR) to build a prosperous, resilient Africa of the future. The integral role of African women for the 4IR will be discussed and various opportunities will be showcased for young women hoping to get into the field of data science.

Africa Women in Data Science is free to attend and will be split into a conference on Day 1 (March 8) and a hackathon on Days 2 and 3 (March 9-10). The conference will feature inspiring female panel discussions, presentations from leading industry experts and question and answer sessions. Day 1 is open to anyone across Africa with a keen interest in data science. To register for the conference, only complete the first section of the registration form.

Enquiries can be emailed to linzi.stirrup@manchester.ac.uk

29 July 20213 August 2021

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.

eWorkshop: Command Line Interface for Genomics Beginners

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 10^thJune to 15^thJuly 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.