Facilities - University of the Witwatersrand

  • Bioinformatics Facility at Wits

    4th May 2012

    Wits Bioinformatics, lead by Acting Director, Dr. Scott Hazelhurst, is situated on the 12th Floor of University Corner. Wits Bioinformatics has a core of academics, postdoctoral fellows and postgrads. The team works with researchers across Wits, who are part of their  community.

    They teach the following formal courses as part of various curricula:

    • Introduction to bioinformatics: this is a two-week intensive module taught in various honours programmes: Molecular and Cell Biology; Human Genetics; Molecular Medicine and Haematology.
    • Computational Molecular Biology: honours module in computer science
    • From 2013 there will also be an undergraduate course.

    They also coordinate and teach a number of short courses throughout the year. For ore information on the events hosted by the Bioinformatics Facility at Wits click here.

    Research in bioinformatics is done in a number of schools across Wits and the facility plays a coordinating role in this. There are also a number of research projects carried out from Wits Bioinformatics, including EST clustering, protein targets, copy number variation, and gene discovery.The following projects are currently being carried out by people in Wits Bioinformatics, most of them in collaboration with other researchers or elsewhere.

    •Bioinformatics of viral diversity
    •Evolutionary biology
    •Experimental algorithms and high-performance computing
    •Assembly of second generation sequence data
    •Functional annotation of novel data
    •Genome-wide Association Studies
    •Human Diversity Studies.

    Wits Bioinformatics provides a number of services for the Wits and broader bioinformatics community.

    Consulting – We have capacity to provide some consulting for projects which require bioinformatics, including tool and technique advice and some training. For significant help, we would expect to become research collaborators or make some other arrangement. Projects which require significant bioinformatics expertise should be discussed with us at proposal stage.

    Tools -We have a number of on-line tools available for bioinformatics. Our wEMBOSS server is used for training as well as by researchers who need to use bionformatics tools.

    High-Performance Computing – We run a research computer cluster which is available to members of the bioinformatics community. The cluster contains 100 cores and roughly 40TB of data storage. Two of our machines have 96GB of RAM and one has 72TB. This is also a node on the SA National Compute Grid.

    Databases  – We mirror some of the key databases including Genbank and PDB and we can mirror or host other data bases.

    Structural Targets Databases – The brain-child of a former staff member, Dr Abdelkrim Rachedi,  these databases and tools are available for use.

    Contact information

    Email: or visit the Wits Bioinformatics contact page

  • Affymetrix Microarray Laboratory

    4th May 2012

    The Department of Molecular Medicine and Haematology has been involved in Leukaemia and Lymphoma diagnosis and research for more than twenty years. Current services include immunophenotyping, molecular cytogenetics (FISH, M-FISH) and PCR (including QT-PCR) for the surrounding academic hospitals. The Department recently established the Affymetrix GS3000 platform for gene expression profiling (GEP) and genotyping. The Research Diagnostics Group (headed by Dr Lesley Scott) and the Cytogenetics Group (headed by Dr Pascale Willem) currently make use of the Affymetrix Platform for research purposes: (1) to investigate the pathology of leukaemias and lymphomas and to develop a single-platform diagnostic assay for leukaemia classification which is intended to complement existing diagnostic profiles and address skills shortage for current services; (2) to assess copy-number alterations in a number of cancers with high prevalence in South Africa, including oesophageal and colorectal cancers. The Cytogenetics group is also soon to begin complementing existing routine cytogenetic diagnostics with Affymetrix genotyping arrays.

    This Department has engaged with members from the Wits School of Information and Electrical Engineering in an effort to apply engineering principles and artificial intelligence algorithms towards the development of a GEP classifier. Clinical information is combined with GEP to determine the accuracy of classification while also exploring microarray data to determine the functionality and mechanisms of disease pathogenesis. This group holds fortnightly focus meetings which discuss technicalities of microarray technology and also recently hosted a workshop on genome-wide association studies. The workshop brought together experts in human genetics to discuss the prospect of performing genome-wide association studies in a Southern African setting.

    The Facility

    The dual Laser capacity Affymetrix Research Microarray Platform is a complete work-station for Affymetrix GeneChips. It is suitable for gene expression profiling, exon array analysis, SNP discovery, tiling arrays etc. Also part of the microarray facility is an Agilent Bioanalyzer used for nucleic acid analysis.

    Contact information

    Lesley Scott, Tel: +27 11 489 8565