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.
Registration has opened for the Coding Summer School (CSS) 2024.
This is a joint effort between the Centre for High Performance Computing (CHPC) of the Council of Scientific and Industrial Research (CSIR) and the National Institute for Theoretical Computational Science (NITheCS) aimed at training researchers across South Africa and Southern Africa in the fundamentals of programming, data science, HPC, and computational sciences.
The CSS will take the format of a hybrid event where participants will be required to attend specific universities and research locations. The University of the Western Cape will be one of these locations for the CSS, taking place from Monday 29 January 2024 until Friday 9 February 2024.
Eligible Applicants:
The CSS is aimed at postgraduate students and researchers in STEM fields focusing on the fields of astronomy, biology, computer science, chemistry, engineering, mathematics, medical, and physics.
Format:
- Lectures/tutorials occur Monday to Friday - Lecture/tutorial times: 10:00 - 16:00 with breaks each day - Notes, quizzes, and assignments provided - Certificates awarded to qualifying students
Week 1:
Participants will learn the fundamentals of Python and data science which will allow them to analyze and manipulate various datasets. They will also be introduced to Linux and Bash in order to learn HPC skills.
Week 2:
In week two, participants are exposed to Python applications, covering machine learning, probability & statistics, and various domain specific topics.
How To Apply:
For more information and if you wish to attend the CSS, kindly follow the link below to register:
https://events.chpc.ac.za/event/120/
Space is limited at the various locations so make sure to register soon to book your place.
There are representatives from each university and some research institutes, known as champions. For any further queries and logistics @UWC, contact fisingizwe@uwc.ac.za
For general inquiries please contact: training.chpc@csir.co.za
Research data management (RDM) is an integral component of the research process. A data management plan (DMP) provides detail of how your research data will be managed. A workshop held on 2 Augusts aimed to provide an overview of what DMPs are, why a postgraduate student would need one, and a practical guide on putting one together.
Workshop contents:
What is a data management plan (DMP)?
Why postgraduate students need DMPs
How to put together a DMP plan
Workshop outcomes:
Basic understanding of the UWC RDM policy and the POPI Act
Understanding of the implications of these policies for postgraduate research
Practical skills for putting together a RDM plan for thesis research
Young astronomy researchers have the opportunity to learn skills that will allow them to bridge the gap between academia and launching their careers in the workforce. SKIES (SKilled, Innovative and Entrepreneurial Scientists) is an ambitious project that offers training for astronomy researchers (PhD candidates and young postdoctoral researchers) in developing new skills, integrating Open Science, innovation and entrepreneurship. The training workshop will take place in Cape Town from 4-8 April 2022, hosted at the UCT GSB Conference Centre.
Only a fraction of astronomy doctoral graduates (about 10%) remain in academia, which means that the skills acquired in the course of their research need to be effectively transferable in order to achieve a smooth transition from academia to the private sector. Advanced degrees in STEM (Science Technology Engineering and Mathematics) subjects are widely accepted to be an excellent basis for careers in, among others, the tech industry, but most graduates find that they need to learn additional skills. An ability to confidently navigate the Open Science landscape combined with a capacity for innovative thinking can set astronomy graduates apart and allow them to fulfill their potential and develop into well-rounded scientists and professionals.
Madagascar Astronomy Python Workshop 2017. Credit: IAU Office of Astronomy for Development archive
The field of astronomy research is collaborative and international, and students are trained in diverse skills, ranging from theoretical approaches and big-data science to observations and laboratory work. Thus, there is a unique opportunity to integrate a modern skills course with the existing programme.
SKIES will reach about 500 astronomy graduate students and young researchers in Europe (Germany, the Netherlands, Poland and Portugal) and South Africa as it is implemented across various astronomy research organisations. Researchers from the University of Cape Town (UCT) will be leading the project in South Africa, which includes PhD candidates from other organisations across the country. Dr Lucia Marchetti, from UCT’s Department of Astronomy, is the principal investigator for SKIES in South Africa. “I am thrilled to be able to offer this opportunity to our PhD candidates”, says Dr Marchetti. “Their astronomy training already provides them with many theoretical skills that they can apply to jobs outside academia. With this training, we will show them how they can best exploit and translate their knowledge into a job beyond astronomy, and ensure that all our astronomy students are fully equipped for whichever path they decide to take after their PhD.”
The SKIES training workshop in South Africa consists of three modules co-created by academics and career development consultants: design thinking, open science and responsible research; innovation and entrepreneurship; and a career-oriented masterclass that includes mentoring. The week-long program includes speakers and guests from universities and industries and young researchers will have the opportunity to learn from and be inspired by experts and leaders, as well as learn best practices and techniques.
From CV-writing and communication to business models and organisational theory, to design thinking and creativity, they will be introduced to a range of techniques that they can take with them going forward professionally. Participants will be given insight into what enterprise support is available, the role of a technology transfer office, how funding models operate, as well as how social entrepreneurship works and how to pitch an idea for commercial and academic purposes. Guests will give presentations that speak to individual experiences. These speakers include Simon Travers and Imogen Wright, founders of Hyrax Biosciences, Dries Cronje, CEO & founder of Deep Learning Café, and Tshegofatso Masenya, the 2021 winner of the EDHE (Entrepreneurial Development in Higher Education) Entrepreneurship Intervarsity National Winner.
The SKIES project will also deliver a mini online open course (MOOC), which will support partner organisations in running similar courses. This will remain available after the project has ended to ensure its impact and legacy.
Head of eResearch Office and Astroinformatics Research Professor at the University of the Western Cape (UWC), Prof Mattia Vaccari echoes Dr Marchetti’s optimism, adding that “the bridging of this gap is particularly important for South Africa in the increasingly global talent search in the era of the Fourth Industrial Revolution”. UWC’s Technology Transfer Commercialization Specialist, Luan Africa, is also enthusiastic about the initiative, and how it will allow young researchers “to see the broader value, applicability, and transferability of their rigorous scientific training. We are hopeful that participants will exit with a more entrepreneurial mindset, underpinned by a constant need to upskill, learn from mistakes and take continuous action on ideas. We are thrilled to contribute to this wonderful programme.”
Dr Bonita de Swardt, head of Strategic Partnerships for Human Capacity Development at the South African Radio Astronomy Observatory (SARAO), expects that this exciting collaboration “will lead to increased employability of doctoral candidates, in industry or through entrepreneurship, who will be effectively working on high-impact areas to benefit broader society on the African continent”.
For more information:
Prof Mattia Vaccari Director, eResearch Office University of the Western Cape mvaccari@uwc.ac.za
Mr Luan Africa Technology Transfer Specialist: Commercialization Technology Transfer Office University of the Western Cape lafrica@uwc.ac.za
Dr Lucia Marchetti Senior Lecturer in Astronomy University of Cape Town H2020 SKIES SA Lead lucia.marchetti@uct.ac.za
The SKIES (SKilled, Innovative and Entrepreneurial Scientists) training workshop (4-8 April, 2022) is now open for registration. SKIES is a training and mentorship program, and this workshop is aimed at South African based astronomy PhD candidates and young researchers**, and focuses on career development, open science and entrepreneurship.
The event will take place on April 4-8, 2022 at the UCT Graduate School of Business Conference Center in Cape Town (but it will also be possible to attend online). The programme features hands-on exercises, external speakers to showcase career opportunities, and the possibility to interact with astronomy alumni.
Participants will learn about the basics of innovation and entrepreneurship, as well as how to improve creativity and develop a business model. All materials have been developed by astronomers, for astronomers.
The workshop registration is free and all lunches will be covered (note: dinners, accommodation and travel are NOT covered). Each participant will get a certificate of attendance at the end of the programme.
There are a maximum of 40 places to this training workshop (we can accommodate a maximum of 30 in-person attendees and the rest should be online). We recommend in-person attendance if possible.
You will receive a confirmation of acceptance for participation in the event by latest 29 March. For any questions please contact Dr Lucia Marchetti: lucia.marchetti@uct.ac.za
**This program will prioritise PhD and early career post-doc/researchers, but if you are a Masters student and you would be interested in joining this training workshop, please send an email to lucia.marchetti@uct.ac.za and we will keep you posted if there will be any available space closer to the date.
CPUT’s Centre for Communication Studies is hosting a Data Carpentries workshop for participants interested in learning about research data skills in the humanities.
The workshop is free and delivered by the Carpentries, co-ordinated locally and affiliated with the South African Centre for Digital Language Resources (SaDiLAR) based at NWU. It will be held online between 9am and 1 pm on Mondays in February, and there are some spaces available. Anyone interested should register on the google form before end of day Thursday this week: https://forms.gle/SvSCVaqVW9BuS3Me9
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.
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.
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:
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.
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.
