2021eResearchReport - Flipbook - Page 18
Capacitating our
next generation for
a data-intensive
future
To maintain UCT’s competitive edge our
young researchers need to build the
expertise to reap the benefits of the data
they gather. Mandy Mason of the IDM is
working with UCT eResearch to connect
her students to that training.
“Research runs on a foundation of work
performed by postgraduate students and
postdoctoral researchers,” says Mandy
Mason, an emerging researcher based
at UCT’s Institute of Infectious Disease
and Molecular Medicine (IDM). “So, it is
imperative to invest in and build research
capacity at this level.”
Mason, currently a Research Officer in
the Molecular Mycobacteriology Research
Unit (MMRU), led by Prof. Valerie Mizrahi
and Prof. Digby Warner, was selected
as one of 18 young African fellows for
the Crick African Network (CAN) first
African Career Accelerator Awards. She
initiated contact with UCT eResearch to
get the necessary training for the MMRU’s
students to not only process, but also
manage the valuable data gathered in the
research process.
The CAN African Career Accelerator
Awards are designed to help earlycareer researchers make the transition
to leading their own investigations and
building their research groups in Africa.
The two-year fellowship saw Mason build
on her research skills and expertise in
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eResearch Report | 2019-2020
mycobacterial physiology in relation to
Tuberculosis (TB).
Her current research focus is on
improving understanding of the biology
of Mycobacterium tuberculosis (Mtb),
the bacterium that causes TB. By
investigating a wide range of bacteria
with engineered genetic vulnerabilities,
she hopes to find some that are more
susceptible to being killed by both new
and existing drugs.
As part of the research, they are
using Next Generation Sequencing
(NGS) which has revolutionised genomic
research because of the rate at which
the human genome can be sequenced
with this technique, but with it comes a
considerable volume of data.
“Research technology has moved so
fast and formal training is not keeping
pace,” says Mason. “Our students, who are
trained in biology and laboratory work,
are now generating high-throughput
data (such as large NGS or digital image
datasets) that need skills in computing to
manage, manipulate and analyse.”
Here the facilitation and potential for
the support of UCT eResearch looks to be
invaluable to these efforts.
Discovering UCT eResearch
During her CAN fellowship, Mason
intended to split her time equally between
UCT and the Francis Crick Institute in
London – a state-of-the-art biomedical
research institute. The COVID-19
pandemic prohibited this long-term
research visit, but during an earlier
short visit, she was encouraged to also
engage with and make use of local digital
research support at UCT. She did so by
tapping into the eResearch network to
provide local and sustainable support and
training that could facilitate not only her
research, but would also extend to the
research of her colleagues in the MMRU.
“This system of being able to connect
with one central resource that coordinates and so can direct you to the
services you need, is a good one,” says
Mason. “It is challenging for researchers,
never mind postgraduate students, to
know what training and resources are
available to them and how to access this.”
UCT High Performance Computing online
training
The High Performance Computing (HPC)
team, Andrew Lewis and Timothy Carr,
offered an introductory presentation
about the HPC and provided online
training for postgraduate students in
the MMRU. This engagement was a real
highlight, says Mason, as it directly
assisted students to understand what
resources the HPC offers for their projects
and opened the door for them to engage
directly with these services.
“It has been a struggle to support
our biological and medical scientists
in acquiring the appropriate computer
skills and the level that they need,” she
says. “It is intimidating for a beginner,
but our students need to be supported to
overcome any hesitancies and learn these
skills otherwise we will lose touch with
what is happening with our data.”
their project data-management needs.
This was facilitated by direct support
from Niklas Zimmer, manager at DLS, who
assisted the MMRU in creating a group on
the Open Data ZivaHub platform which
will serve as a resource to publish their
data accompanying future publications.
Students were able to engage directly
with Digital Library Specialists, such as
Sanjin Muftic, who gave personalised
advice regarding their data management
needs and plans.
“Data hygiene is so important,” says
Mason. “It is often seen as an additional
administrative burden separate from
research, but actually good data
management is a matter of good research
practice.”
Mason says she sees great potential
in this facilitated and networked local
support that is available across all levels
of research at UCT. While this is only the
beginning of their working relationship
with eResearch, she feels that this is one
that she is very keen to invest more time
in building.
She is supportive of the investment
that UCT is putting into the management
and resourcing of these services and feels
a part of the vision of eResearch
“As researchers we are in the business
of generating, curating, interpreting
and sharing data. The ability for African
researchers to control, access and get
attribution for data that is generated
locally, serves as a key component in
driving our research and developing our
researchers in what is becoming a highly
competitive research space,” says Mason.
“But if we cannot process, analyse and
preserve that data properly here, we
lose our edge, and data rather serves as
a commodity export from Africa. This is
why the work UCT eResearch is doing to
is so important to the future of research
at UCT and on this continent.”
Below: Mandy Mason, based at UCT’s Institute of
Infectious Disease and Molecular Medicine (IDM) is
one of 18 young African fellows for the Crick African
Network (CAN) first African Career Accelerator Awards.
Image credit: Robyn Walker
Building a firm foundation for data
management
Mason also worked with the Digital
Library Services (DLS) to connect MMRU
students with services and support for
Supporting research
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