Last month’s Carpentry Connect South Africa took place completely virtually, and was attended by more than 120 attendees and volunteers (i.e. trainers, instructors and helpers) from 28 countries worldwide, including 16 countries in Africa. The event included 2 Carpentries workshops, 1 Carpentries instructor training event, 2 networking events, 1 learning session and 1 opening address.
The main goal of CarpentryConnect South Africa 2021 was to build capacity for workshops through instructor training and bring together newer and more experienced community members to share knowledge, network, develop new skills, and develop strategies for building strong local communities around digital and computational literacy in Africa.
Support from the Gordon and Betty Moore Foundation‘s Event Fund allowed for, among other things, 300 GBs of mobile data bundles to be provided to 71 attendees over 19 African network providers. This enabled participation to those who would have otherwise not been able to attend such a virtual and mobile data intensive event. Often, even “free” events” cannot be attended due to the high costs of streaming video of such an event. This is particularly noticeable in contexts where Internet is pre-paid (credit is purchased in advance of service use).
This will consist of a series of events that will bring together researchers enthusiastic about bioinformatics and open science. The first virtual event is the Open Science FAIR symposium from October 11th-15th, 2021. The event aims to sensitise participants on FAIR open data science practices such as project planning and organisation, collaboration, licensing and data sharing. It exposes participants to use open science tools that facilitate these practices.
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.
Registration is now open for CarpentryConnect South Africa 2021!
The Carpentries is a non-profit organisation that teaches foundational computational, coding, and data science skills to academics, students and academic support staff worldwide. Carpentries workshops have been running at South African public universities and research institutions to hundreds of learners since 2014, and almost 100 instructors have been trained to teach digital and computational concepts to novices.
The first South African CarpentryConnect took place in Johannesburg, South Africa in September 2018. The second will be held virtually and will bring together newer and more experienced community members to share knowledge, network, develop new skills, and develop strategies for building strong local communities around digital and computational literacy at universities. Workshop fees and mobile data for African participants are funded by Code for Science and Society Event Fund.
We invite participants toregister for the following events:
Data Carpentry: 6-10 September, 9:00-13:00 SAST. This is an introduction to R, designed for participants with no programming experience. Lessons begin with some basic information about R syntax and the RStudio interface, and then move through how to import CSV files, the structuring of data frames, how to deal with factors, how to add/remove rows and columns and how to calculate summary statistics from a data frame. The lessons also touch on plotting, which is an excellent introduction to data visualisation. Space is limited to 25 learners. Register here.
Instructor training: 13-17 September, 9:00-13:00 SAST.The Carpentries workshops are taught by trained, peer, volunteer instructors. All of our Instructors complete an Instructor Training program, which teaches instructional pedagogy as well as the practicalities of teaching a Carpentries workshop. Instructors can teach workshops in their local area, travel to teach or teach or teach online. We have held workshops in over 40 countries on every continent (including Antarctica). Space is limited to 20 learners. Register here. *Please use the code “ccza43”.
Other events include:
Keynote: CarpentryConnect South Africa’s blurb in 2021 will be delivered by Dr Kari L. Jordan, Executive Director at The Carpentries on Monday 6 September at 14:00 SAST. Register here.
Networking events: The CarpentryConnect South Africa organising team will also host two networking events (Tuesday 7 and Thursday 16 September at 14:00 SAST) for our Carpentries community. These will be great opportunities to connect with like-minded people in fun, collaborative and interactive online events. Register here.
Closing: On Friday 17 September at 14:00 SAST we would like to create a space for community members to offer feedback and lessons learned on CarpentryConnect South Africa 2021 at the end of the two weeks. Register here.
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.
An online Data Carpentry workshop will take place from 12-16 April, and is aimed at students and researchers who want to start learning how to work with their data. The workshop will be hosted by UWC and sponsored by SADiLaR.
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 will be encouraged to help one another and to apply what they have learned to their own research problems.
It’s International Open Access Week (19-25 October), and UWC Library is celebrating with libraries around the world under the theme Open with a purpose: Taking action to build structural equity and inclusion.
During this week the library will host a number of webinars and presentations, and UWC has entered the international Figshare upload competition, where the individual researchers can win prizes for uploading their research data. For more information about the competition email us on firstname.lastname@example.org.
Tuesday 20th October 2020 10:00 – 11:00
Welcome by Dr Shirlene Neerputh, UWC Library Director Data Intensive Research at UWC by Prof M Vaccari, Director eResearch at UWC The Carpentries in Africa by Dr Angelique van Rensburg, The Carpentries Facilitators: Sarah Schafer & Mattia Vaccari
Wednesday 21st October 2020 10:00 – 11:00
Introduction to Figshare by Megan Hardeman, Head of Engagement at Figshare
UWC RDM Services by Mark Snyders, Manager Scholarly Communications, UWC Library Services
Thursday 22nd October 2020 10:00 – 11:30
The value of open access publishing in the times of Covid-19 pandemic infected research environment by Alfred Nqotole, Deputy Director Research Support & Scholarly Communications, UWC Library Services Open Access Publishing: UWC Editor’s Perspectives by Prof M Dinbabo and Prof R Shambare
Facilitator: Alfred Nqotole
Register in advance for this webinar: https://uwc.zoom.us/webinar/register/WN_jIWs08KGS4CiDJRKzMGgUA
About the speakers:
Angelique van Rensburg, PhD (Educational Psychology), is the Regional Consultant for Southern Africa at The Carpentries and an Extraordinary Researcher at Optentia Research Focus Area, North-West University, Vaal Triangle Campus. Angelique aims at developing strategies and workflows to adapt The Carpentries’ membership and workshop programs to function optimally in Southern Africa. In addition, her role aims to assist and advise in developing a plan to create and support a strong team of volunteer instructors across Africa.
Megan Hardeman is head of engagement at Figshare. For the last four years, she has helped researchers make the most of storing, sharing, and collaborating using Figshare and has written case studies, delivered talks and training, leads the ambassador programme, and more. Previously, she was a Product Manager at Emerald Publishing.
Mattia Vaccari is Director of eResearch and AstroInformatics Research Professor at UWC, and he coordinates UWC’s Data Intensive Research emerging niche, which brings together researchers from different fields to foster multi-disciplinary collaboration in big data science. He has worked as a Research Scientist at Imperial College London, the University of Padova and UWC, working at the junction between astronomical instrumentation, big data processing technologies and extragalactic astrophysics.
Mulugeta Dinbabo is the Chief Editor of the African Human Mobility Review (AHMR), an accredited Journal by the Department of Higher Education and Training (DHET). AHMR is an interdisciplinary journal created to encourage and facilitate the study of all aspects (i.e. socio-economic, political, legislative and developmental) of human mobility in sub-Saharan Africa.
Richardson Shambare is an Associate Professor in the School of Business and Finance (SBF) at the University of the Western Cape. Prof Shambare has a keen interest in entrepreneurship and marketing in SMMEs. He has published several peer-reviewed articles, books, and book chapters and presented research at numerous international conferences. Prof. Shambare is the co-founding editor of the Journal of Entrepreneurial Innovations. The JEI specialises in publishing research and analyses pertaining to entrepreneurship trends and particularly innovations in the small, medium, and micro enterprises (SMMEs). The JEI is an Open Access, free to publish online journal.
In addition to the webinars and sessions available, UWC has entered the international Figshare upload competition, where the individual researchers can win prizes for uploading their research data. For more information about the competition email us on email@example.com.
Please feel free to signup for any of these events or forward this email to your colleagues, students or fellow researchers. Mobile data assistance is possible for learners residing in South Africa. Further information about The Carpentries is available here.