Page 15 - UCT2012 Health Sciences

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Health Sciences
Department Of Clinical
Laboratory Sciences
Computational Biology Group
Head of Group: Associate Professor
Nicola Mulder
Group Profile
The University of Cape Town Computational Biology
(CBIO) Group is the centre of Bioinformatics activities at
the university. It was originally set up as a Node of the
National Bioinformatics Network, which aimed to develop
capacity in bioinformatics in South Africa, and to perform
world-class bioinformatics research. The CBIO Group is
located within the Institute of Infectious Disease and
Molecular Medicine (IIDMM) in the Health Science Faculty,
and integrates researchers interested in bioinformatics at
the university. The group performs bioinformatics research
and provides training and services in the discipline.
The mission of the UCT Computational Biology Group
is to become an exceptional, internationally recognized
research and training center, addressing the challenges of
bioinformatics capacity development in South Africa.
CBIO has a large network of connections with other
bioinformatics groups in Africa through the African Society for
Bioinformatics and Computational Biology, and a pan African
bioinformatics network for H3Africa (H3ABioNet). The group
also has close ties with the African Institute for Mathematical
Sciences (AIMS) by supervising student essays.
Training Activities in the Group
Undergraduate and Postgraduate teaching
The group teaches a module for Molecular medicine
students and several modules for the Health Science
Honours programme. It also coordinates the Health
Science Honours Programme in Bioinformatics. However,
the main focus of the group is on postgraduate education,
and the group supervises a number of students (listed
later). The CBIO staff also organize and teach on a national
course program for postgraduate bioinformatics students.
Renaud Gajoux –PhD
Holifidy Arisoa Rapanoel –Master’s with distinctions
Boitumelo Mofolo –awarded Master’s degree, will graduate
in 2013
Arjun Khoosal –Honours degree
Catherine Van Zyl –Honours degree
Rebone Meraba – Honours degree
Sasha Moola – Honours degree with distinctions
Other Training Activities
The CBIO groups runs short specialized workshops for
researchers. In 2012 this included:
High-throughput Biology and Human Genetics Course
(Mauritius) Jan 2012
Workshop on Population Genetics and Genomics (June
UniProt and TubercuList Workshop (November 2012)
Microbiome Workshop (November 2012)
Chipster Workshop (December 2012)
Bioinformatics Service-Related Outputs
Human Genetics Division: Ayton Meintjes and Gerrit Botha
work as part of the group’s services team by providing
support to other researchers. These include the following
activities: Human Genetics Research Unit: Gerrit processed
human exome data from 6 patients. He made use of the
ICTS HPC ( to do quality
control, alignment, post-processing and SNP calling.
Visualisation was done with the Galaxy genome viewer
together with IGV (Integrated Genome Viewer). He also
processed full human genome data from 5 patients using
the same hard-ware and tools, including SVA (Sequence
Variant Analyzer). Ayton is working with Professor Ramesar
from the Human Genetics Division on an AfriVariants
database for local population genetics data.
Immunology Division: Gerrit worked with Heather Jaspan
on analyzing her microbiome data on infants with HIV-
infected mothers, and Ayton worked with Associate
Professor Jo-Anne Passmore on array data her group
generated on cervical samples.
Medical Biochemistry Division (Blackburn lab): assistance
was provided with running large peptide blasts on the ICTS
HPC cluster. Pre- and post-processing of data was done
using customized tools in Galaxy on our local server.
Molecular and Cell Biology Department: EST data from the
resurrection plant Xerophyta Humilis was assembled and
genes were predicted. Assembled genes were annotated
using a combination of tools such as InterProScan, Blast
and Blast2GO. All modules from basecalling to annotation
were integrated in our local Galaxy installation, so we can
easily rerun the complete workflow. Gerrit also processed
and assembled EST data from human, bats and mice.
Some modules specific to this pipeline were developed
and integrated in our Galaxy installation. Ayton pro-
vided support for analysis of array data for Maize and we
performed function and path-way analysis on the results.