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.
In collaboration with DPGS, a ‘Basics of R’ training module will begin on 5 July. The module will include an introductory session, after which training materials will be available through iKamva. The purpose of this training module is to equip postgraduate students with basic knowledge and skills to begin using R.
R is a programming language that is widely used by researchers in various disciplines for data manipulation, calculations and graphical display and visualisations. Anyone who would like to begin working with R as part of their research or skills development will benefit from this training module, and the lessons are aimed at people with no previous experience.
The Working with Data: Training Module, created in collaboration with DPGS, is still available on iKamva, and the Q&A session on Wednesday 8 June is an opportunity to ask questions about spreadsheets and OpenRefine.
The session is also for those who would like to begin working on the module during the vacation period.
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.
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.
Escalator has created an 8-step programme for to learn new digital technologies and skills that enhance research.
The programme is specifically targeted at womxn in humanities and social sciences in South Africa who want to learn and enhance their digital and computational research skills. Folks from any career stage are welcome to join. This includes researchers, postgraduate students, postdoctoral research fellows, librarians, IT staff, research support positions, and related areas. The programme caters for any experience level: from complete novices to those with advanced skills.
Escalator is an exciting addition to the South Africa Digital Humanities (DH) landscape. It launched last year, and has been working closely with members of the community to understand the needs for upskilling and re-skilling and learning new tools/technologies and methodologies to enhance research in an increasingly digital world. They are excited to announce the launch of this programme, based on intentional learning principles, through which they will support learning and growth.
For the full programme, see the Eventbrite page: https://bit.ly/empower-2022 To stay informed of upcoming events through the EMPOWER track, JOIN THE MAILING LIST.
After a successful introductory session on 11 May, the Working with Data: Training Module, created in collaboration with DPGS, is now live on iKamva. For those that missed the introductory session, the recording is also available on iKamva.
The purpose of the training module is to equip postgraduate students with the basic knowledge and skills needed to clean and organise their data using spreadsheets and OpenRefine. The lessons are based on Data Carpentry lessons.
The lesson materials will be available until 8 June.
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.
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.
In what has been described ‘seismic‘, the NIH’s (US National Institutes of Health) new data-sharing policy mandates that all researchers share their data. The NIH is the largest public funder of biomedical research in the world, and this shift could set a global standard for biomedical research.
In January 2023, the US National Institutes of Health (NIH) will begin requiring most of the 300,000 researchers and 2,500 institutions it funds annually to include a data-management plan in their grant applications — and to eventually make their data publicly available.
This certainly is groundbreaking news in a research landscape that has seen a steady albeit slow progression toward more openness. Mark Hahnel, founder of Figshare, agrees that this is huge news. He urges the the academic community to not lose focus on potential benefits that open data can have “for reproducibility and efficiency in research, as well as the ability to move further and faster when it comes to knowledge advancement”.
The policy, which applies to research funded by or conducted by NIH that results in the generation of scientific data, establishes the requirements of submission of Data Management Plans (DMPs), and it also emphasises the importance of good data management (RDM) practices. This includes maximizing the appropriate sharing of scientific data generated from NIH-funded or conducted research, with justified limitations or exceptions.
There is no doubt that this policy will be felt globally, by researchers and academic institutions.
In collaboration with DPGS, a ‘Working with Data’ training module will begin on 11 May. The module will include an introductory session, after which training materials will be available through iKamva. The purpose of this training module is to equip postgraduate students with the basic knowledge and skills needed to clean and organize their data in spreadsheets and OpenRefine.
