Category: Carpentries

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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.

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Software Carpentry Workshop to be held 24-28 July 2023

Learn basic research computing skills so you can do your work in less time and with less pain

This hands-on workshop will cover basic concepts and tools, including programme design, version control, data management and task automation. Participants will be encouraged to help one another and apply what they have learned to their own research problems.

Who should attend and Requirements

he workshop is aimed at graduate students and other researchers. You don’t need any previous knowledge of the tools that will be presented at the workshop.

You will need access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) and administrative privileges. You will need to install a few specific software packages – view these here: http://bit.ly/3puTC9K. You also need access to Zoom and Internet connectivity.

How to apply

Click HERE to complete and submit your Application Form by 19 July. Successful applicants will be notified on 20 July 2023.

For more information, please email rene.kotze@nithecs.ac.za.

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CarpentryCon 2022: Expanding Data Frontiers

CarpentryCon 2022 will take place online from 1-12 August 2022, and registration is now open. CarpentryCon is an exciting way to connect with The Carpentries community and level up data science skills. Attendance is free, and takes place over two weeks, featuring sessions that will draw participation from around the world.

The programme will include: lesson development sprints, professional and community skill building, technical skill-ups, regional subcommunity updates, updates on new curriculum development and more.

The CarpentryCon 2022 Schedule can be viewed, and all sessions will be recorded.

Read more about the event and register to attend at https://2022.carpentrycon.org/

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Opportunity: The Carpentries are Recruiting Instructors

An ongoing opportunity to build teaching skills as part of a global community is available.

The Carpentries are actively recruiting Instructors to teach Centrally-Organised workshops. These workshops (currently being held online) are a great way to connect with a global community, meet new colleagues with shared interests, and share skills with researchers around the world. The Carpentries are currently offering priority admission to our Open Instructor Training program for applicants who indicate interest in teaching centrally-organised workshops.

There is limited space and participation bursaries, valued at ~R6000, are available.
Event dates: 1 – 3 June 2022 (2.5 days)

All applicants are welcome. No specific expertise is necessary, but they do expect that trainees will have the technical knowledge necessary to teach one or more of the core lessons from Data Carpentry, Library Carpentry, or Software Carpentry. Instructor Training events are held online, so anyone with internet access and time to share can participate.

A challenge that we face in the Humanities is providing our students (and colleagues) with an opportunity to learn about computational approaches that they can apply in their current and future contexts. This instructor training opportunity will provide training to  provide the participant with foundational lessons regarding: 

  • Evidence-based teaching practices.
  • Teach you how to create a positive environment for learners at your workshops.
  • Provide opportunities for you to practice and build your teaching skills.
  • Help you become integrated into the Carpentries community.
  • Prepare you to use these teaching skills in teaching Carpentries workshops.

If you want more information, contact Juan.Steyn@nwu.ac.za or visit the workshop website: https://sadilar.github.io/2022-06-01-NITheCS-SADiLaR/.

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Data Carpentries Workshop Opportunity

CPUT’s Centre for Communication Studies is hosting a Data Carpentries workshop for participants interested in learning about research data skills in the humanities. 

See more here: https://annajiat.github.io/2022-02-07-CPUT-ONLINE. 

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

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Carpentry Connect South Africa 2021 in Review

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).

Read more about the event.

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Open Science Fair Symposium

BHKi (The bioinformatics hub of Kenya) and OpenScienceKE are proud to announce a new project, Empowering Researchers with Skills and Tools in Open Science and Bioinformatics.

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.

Register here to participate.

The organisers are also looking for presenters who have used open science practices to present their work and methods to fellow researchers. Register here to share your work. 

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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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CarpentryConnect South Africa 2021

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 to register 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.

For more information visit https://za2021.carpentryconnect.org/ 

Please note: While the event is fully funded by the organisers you will be held liable for a R500 attendance fee should you fail to attend without cancelling more than 48 hours prior.

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UWC’s first Data Carpentry Workshop of 2021

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.