Bioinformatics
Welcome to Stellenbosch University

​South African Tuberculosis Bioinformatics Initiative

Training

​Stellenbosch University is committed to training the next generation of bioinformatics and biostatistics researchers. The South African Tuberculosis Bioinformatics Initiative (SATBBI) investigators are actively seeking students for MSc  and PhD training.

Student Opportunities

Professor Tabb seeks a student for a new push in automated flow cytometry data analysis. Many algorithms have been created for automated gating and classification of flow cytometry data. Which of these systems would be suitable to streamline data analysis at the Stellenbosch University Flow Cytometry Unit? A student would learn skills in both flow cytometry and software development / evaluation.

Professor Tromp seeks students with diverse interests related to bioinformatics.

One topic is high-throughput computing. Many of the problems in molecular biology are amenable to multithreaded processing (using multiple processor cores) or multiple discrete processors. The student would seek to implement workflows for high-throughput sequencing data on the high-throughput computing facilities of Stellenbosch University.

Another topic is statistical learning methods (machine learning). Some bioinformatic problems are not amenable to standard statistical analyses, but are amenable to statistical learning methods such are random forest and support vector machine analyses. The student would seek to apply these methods to existing data sets and develop analytical pipelines for similar data sets.

The qualifications we seek in potential graduate students begin with Honours training in a field associated with biology, chemistry, math, statistics, or computer science disciplines. Programming skills are not a prerequisite, but exposure to programming is certainly useful.
 

Tutorial Opportunities

SATBBI personnel conduct a month-long training in biostatistics and bioinformatics as part of the Honours course for Molecular Biology and Human Genetics. Slides and MP3 recordings are available upon request.

Professors Tabb and Tromp visit the Stellenbosch main campus one Friday a month to discuss projects that could benefit from their assistance. Contact Suzette Els to schedule a half- or full-hour meeting.

Professor Tromp visits the University of Cape Town Medical School on alternating Fridays to participate in the SATVI work-in-progress presentations and to consult with researchers on bioinformatics problems. Set up an appointment with him by email if you would like to visit with him.

Professor Tabb spends Tuesday of each week at the University of Cape Town Medical School to take part in the Blackburn Laboratory community proteomics meeting. Set up an appointment with him by email if you would like to visit with him.

 

Bioinformatics Honours Projects Proposals


SATBBI is committed to achieving the Transformation and Diversity goals of Stellenbosch University.