Speaker
Description
Bioinformatics occupies the space between biology and computing and aims to answer
questions in biology using analytical and computing methodology. At the South African
National Bioinformatics Institute (SANBI), our research focus is on methods to store, retrieve
and analyze genetic information that spans both communicable and non-communicable
diseases. In the context of Public Health, that is a need to interrogate genetic information
(DNA) from both hosts (human) and pathogens (bacterial or viruses) to understand
susceptibility to diseases and ultimately to track infection trends in real time.
The ever-increasing volume of data being generated in the public domain places a strain on
in-house computing resources. While the computing facility at SANBI-UWC is adequate for
initial R&D, these resources are inadequate to complete projects timeously. The nature of
the bioinformatics workflows that require CHPC resources can be grouped into (1) high
throughput computing resources that are needed to describe the 1000s of genetic messages
in a genome, versus (2) high performance computing resources that is needed to model a
drug-protein interaction environment - these simulations require days/weeks of dedicated
compute time.
We have leveraged the CHPC facility in the context of infectious disease research with a
view to analyze genetic variation in bacterial genomes, and to identify drug targets in
pathogen genomes. These analyzes requires an environment that is able to support
reproducible workflows and virtualization of the software environment. Examples of these
use cases will be described.
Presenter Biography
Alan Christoffels is the Director of the South African National Bioinformatics Institute and the DST/NRF
Research in Bioinformatics and Public Health Genomics. After completing his studies in 2001, he moved
to Singapore for a postdoc in the Sydney Brenner lab with a focus on genome evolution. During this
time he contributed to the annotation and genome analysis of the Pufferfish genome and developed
method for detecting genome duplication events. This methodology was later used in other international
genome projects while he established his group in Singapore in 2004. In 2007 he returned to South
Africa and established his group at the South African National Bioinformatics Institute based on the
University of the Western Cape campus. He has driven a number genomics projects on the African
continent. During the past 4 years his team has focused on infectious disease models including
M.tuberculosis. The Christoffels laboratory (christoffels.sanbi.ac.za) has been building tools
(combattb.sanbi.ac.za) and analyzing data that leads to a better understanding of host-pathogen
interactions. Central to these methods is a computational platform that relies on reproducible workflows
and a graph database. The ultimate goal is to ensure that these methods are readily accessible by
biomedical researchers with a view of improved disease surveillance.
