eResearch Report 2017 - 2018 - Page 34



Supporting the research endeavour
Systems biology and big data are key to
unravelling the complex interplay between
Mtb and the human host.
This ensured that the data was
secure and that SATVI researchers
could access the data from their
computers over the network or
from anywhere in the world.
“The data sets generated on
the CyTOF are massive, and I
soon realised that the network
was a bottleneck,” says Rustin.
“I arranged for the network link
between the controller computer
and the building switch to be
upgraded. This significantly
improved the speed of the backup
of the data sets to the research
data repository located in the
Upper Campus data centre.”
Curating the data for
open publishing
As the funder of this project, the
Bill & Melinda Gates Foundation
requires that the data sets be
published in a reliable openaccess repository. Thus far
the team has identified UCT’s
institutional repository ZivaHub
as a good option for sections of
the data, while the NIH-supported
ImmPort repository will house
the remainder. The curation
32
of the data is not completely
straightforward, though, says
Dr Mbandi Kimbung, a SATVI
researcher who is working on
preparing this data set so that it
can eventually be published and
shared with the public. Using
one raw data set, the SATVI
researchers are undertaking a
number of different research
projects. The outcome is a range
of processed data sets, each
looking at different aspects of the
same blood samples.
“The question of who would
control the data was important
to the ethics committee,” says
Kimbung. ZivaHub was an
attractive option for hosting
the clinical database, as it
assigns a UCT digital object
identifier (DOI) to the data that
establishes its ownership. “Also,
with ZivaHub, we can edit the
data during the lifecycle of
the project and have complete
control over when the data is
made public.”
“This has resulted in very rich
sets of data, with a range
of layers that can now be
integrated,” explains Kimbung.
“It is an attempt to model the
immune system, to see whether
that can help us to understand
the development of TB.”
Large gaps remain in our
understanding of the complex
interactions between the TB
bacterium and the human immune
system. Improving this is critical
to developing better interventions
that will halt TB transmission.
In addition to curating the data,
Kimbung and the team also had
to factor in the requirements
of ethics committees around
the use of samples from human
participants in research. The
data needed to be completely
de-identified before it could be
published, for instance.
“Systems biology and big data
are key to unravelling the complex
interplay between Mtb and the
human host,” says Scriba. “The
recent advances in technology and
data science are already bearing
fruit and I am very excited about
the new biological insights and
innovative medical interventions
that are emerging.”





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