More Data Openness in NIH Policy

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.

Nature, 16 February 2022

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.

Read the full NIH Policy here.

Find out more about Research Data Management (RDM), Data Management Plans (DMPs) and see our useful DMP Resources and Tools.

Working with Data: a Training Module

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.

UWC Team wins Cluster Challenge

A UWC student team, the “Parallelizers”, were winners at the CHPC (Centre for High Performance Computing) 2021 Student Cluster Competition, and will go on to compete at the prestigious ISC 2022 Student Cluster Competition later this year. The CHPC Student Cluster Competition gives undergraduate students at South African universities exposure to the High Performance Computing (HPC) world. 

Team members Ruchelle Coetzee, Rofhiwa Matumba, Randall Buckton and Jaco Ferreira are all undergraduate Computer Science students at UWC. The team will be joined by Vanessa Dimtcheva and Edward Ramashia (from the University of the Witwatersrand) to make up the Centre for High Performance Computing (CHPC)’s team competing at the ISC 2022 Student Cluster Competition in Hamburg, Germany in May/June 2022. 

Team mentor from SANBI, Peter van Heusden, provided access to training resources and assistance along the way. “SANBI has been committed to supporting the Student Cluster Competition since 2013, providing technical advice, space on our computing environment and mentorship. We are of course overjoyed at the success of Team Parallelizers!”

Jaco started forming the team in early 2021, and they started training together as soon as they had a full team. The first round of the competition started in June, and the Parallelizers qualified for the next round, which took place in November. Ruchelle, currently a third year BSc Computer Science student, says she was shocked when she found out they had won. Teams were unaware of each other’s progress, so “it was difficult to know if we were on the right track”. “I had known one thing about Linux going into this competition and that was the existence of it”, she jokes. She was aware that some of the other teams already had Linux experience, and had previously dominated the competition, so “there was a factor of intimidation added”. Jaco, a first year at the time of the competition, now in his second year of his BSc, also acknowledges how intimidated he was by the more experienced other teams. He says that this actually “helped us with a sense of competitiveness and allowed us to push that extra little bit”. 

Rofhiwa was motivated by the opportunity to run software and solve problems using very powerful hardware. “As a computer science student, the competition would also provide me with a  channel to exercise my computational skills outside of my course content in a very relevant and fast-growing field”. The competition was impressive, with more than forty teams from universities across South Africa and other African countries competing in the first round. The final round was between four teams.

However, they don’t believe that it was just being the lucky underdogs that made them winners – “what ultimately gave us the victory was our team communication”, says Jaco. By speaking openly with each other, “we were able to overcome the difficulties presented by the online environment that we had to work on and were able to understand each other’s strengths and weaknesses.” Randall (currently in his fourth and final year of the extended curriculum BSc Computer Science programme), agrees. “I believe our good team chemistry along with our commitment to this competition led to us winning the competition”. 

The CHPC SCC required teams to build small high performance computing clusters. They were given a selection of applications to optimise and run on their cluster to demonstrate their design’s performance. Each team was assigned a budget and a parts list (the hardware was provided) from which they designed their cluster, and the teams were judged on a combination of their benchmark results and their cluster design. Rofhiwa describes the process: “we were required to benchmark (test the running efficiency) of software that would put good use to the systems made available to us and to develop an understanding of the networking systems that enabled us to do so”. 

“We worked long, hard and smart to ensure we gave it our everything, especially in the final round, and came out on top” says Randall. What does this win mean for these students going forward? “Winning this competition has boosted my confidence in myself”, says Randall. “The fact that I started with little to no knowledge on how to navigate Linux’s terminal, how to compile things and run benchmarks, and then 7 months later using all of this to win the competition is a testament to myself of what I am capable of doing”. Ruchelle also feels excited about her future. Her knowledge of Linux and cluster computing has “grown exponentially” in the last year, and her interest in the world of high performance computing has been piqued. “This competition allowed me to learn about this new world and gain heaps of exposure by learning through experience”. 

“Winning has given me the confidence to pursue high performance computing as a career choice in the future”, says Rofhiwa. “I am very proud of what we have  been able to achieve as a team and as a group of friends”. 

The ISC 2022 Student Cluster Competition, co-organized by the HPC-AI Advisory Council and ISC Group, will take place during the ISC High Performance Conference in June. The competition will follow a hybrid model, with some teams participating on-site and others, like the CHPC team, virtually. Final submissions are expected mid-May, after which the team will be interviewed and present their findings. 

The ICS HPC (previously known as the International Supercomputing Conference) Student Cluster Competition will include “applications that address education and applied learning towards accelerating bioscience research and discovery”. The student teams will be tasked to test several applications that are used by scientists and researchers. The CHPC team will be competing amongst international peers, all showcasing their expertise in “a friendly yet spirited competition that fosters critical skills, professional relationships, competitive spirit and lifelong friendships”. South Africa has historically performed well in the competition, and although they are also juggling university work, the team has started preparing for the competition. “We are making progress by division of tasks and responsibilities”, says Ruchelle. 

The call for participation for the CHPC 2022 Student Cluster Competition will be distributed in the next few weeks and will be communicated here. 

For more information, interested students can contact
Peter van Heusden pvh@sanbi.ac.za 
Eugene de Beste eugene@debeste.co.za

Closing the skills gap for young researchers

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
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 

Ms Michelle Willebrands 
H2020 SKIES Project Manager
Leiden University 
willebrands@strw.leidenuniv.nl

Training Opportunity: SKIES Registration is Open

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.

Register now to secure a place : https://www.groundstation.space/skies-training-and-mentorship-programme-south-africa/

Registration closes on March 25th, 2022.

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.

CODATA-RDA School of Research Data Science – South Africa

The volume and variety of data that researchers and students are required to work with continues to grow. In order to work effectively with large datasets, data skills are becoming increasingly important, and can be enormously empowering.   

The Department of Information Science of the University of Pretoria, in collaboration with DIRISA, SADiLaR and NeDICC, presents the CODATA-RDA School of Research Data Science. This school is aimed at postgraduate students and early career researchers, and teaches foundational data science skills. The material covered by the programme is fundamental to all areas of research, and thus open to researchers and professionals from all disciplines that deal with significant amounts of research data. The goal is to provide a practical introduction to these topics with some theory and extensive hands-on training.

Topics covered include:
– Open Science
– Introduction to Unix Shell
– Introduction to Git
– Open and Collaborative Research
– Research Data Management
– Data Cleaning – using Open Refine
– Data Analysis and Visualisation – using R
– Data Intensive Social Science
– Author Carpentry
– Information Security
– Machine Learning and Neural Networks
– Research Computational Infrastructure

Please refer to the document below or the website (http://datascienceschools.co.za/) for more information. The deadline for applications is 31 March 2022

Quantum Computing Research Funding Opportunity

The Research Office at Wits University and SA QuTI (the South African Quantum Technology Initiative) have successfully raised funds to support the Quantum Initiative, and have extended an invitation to final year students to apply for funding. Students (from any faculty), engaged in a quantum project may apply, and mentorship and/or collaboration with existing quantum hubs is encouraged but is not essential.

For more information, contact Taariq Surtee: Taariq.Surtee@wits.ac.za

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 herehttps://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

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.

Register here: https://www.astro4dev.org/2022/01/11/registration-open-for-africa-women-in-data-science-event-iwd2022/

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

Webinar: RDM and Kikapu

A webinar on Monday 30 August discussed RDM (research data management) at UWC and Kikapu, our institutional research data repository. Practicing RDM has become an integral part of doing research, and good data management needs to be practiced throughout the research lifecycle. Mark Snyders (UWC Library) and Sarah Schafer (UWC eResearch Office) presented on various aspects of RDM and Kikapu.

https://youtu.be/BzwxJ4TKVmQ
Watch the recording

Relevant documents:

UWC’s RDM Policy

Kikapu Data Deposit Guidelines