Wits Computational Molecular Biology Programme

About us...

Based in the School of Computer Science at Wits, the Computational Molecular Biology Research Programme has a strong algorithm and data structure design focus. At the moment our main work is exploring problems which are very expensive, particularly taking into account large data sets. Our key projects are:

• EST clustering: here we are looking at the design of a key algorithm in genome or DNA sequence assembly. The work has strong theoretical and engineering components.
• Phylogenetics of HIV (working with the National Institute for Communicable Diseases Aids Vaccine Research Programme)
• Parallelisation of algorithms using Linux clusters.

We also have an interest in applications of machine learning and intelligent agents, Grid computing, and open source software development.

We gratefully acknowledge our funding through the SA National Research Foundation, the SA National Bioinformatics Network, and the Carnegie Foundation (though the Wits Interdisciplinary Aids Research Grant).

Members

Academic Staff

• Scott Hazelhurst
• Anton Bergheim

Postgraduate Students

• Anna Badimo, PhD Student
  Project title: Phylogentics of HIV

• Gloria Aikhorin, MSc student
  Project title: Using FPGAs for the comparison of protein sequences

• Pravesh Ranchod, MSc student
  Project title: Parallelisation of EST Clustering

Links

We are part of the Wits node of the National Bioinformatics Network. Our collaborators are:

• South African National Bioinformatics Institute
• Professor Lynn Morris and Dr Maria Papathanasopolous at the National Institute for Communicable Diseases
• Zsuzsanna Liptak at the University of Bielefeld, and Judith Zimmerman at ETH Zurich.