RESEARCH PROJECTS

The projects below underpin our translational work:

Tuberculosis

A comprehensive research programme is underway that includes investigating genetics determinants in both host (Human) and pathogen (Mycobacterium tuberculosis) to understand drug resistance, and protein structure determination to inform patient-centric drug design. These findings inform the development of a scientific workflow management system to support reproducible high throughput computational experiments.

One of the projects focus on predicting operons. Operons may be important drug targets for the development of effective anti-microbials to combat the emerging, global drug resistance challenge. However, there is a shortage of known Mycobacterium tuberculosis operons. We developed COSMO, an algorithm that removes the limitations imposed by using the constraints of one specific organism’s genome and exploits raw RNA-seq data instead.  The code and examples of input and output files for testing and validation, are available at the project home page at https://github.com/SANBI-SA/COSMO

Biobanking

In collaboration with Dr Dominique Anderson at SANBI, we continue to strengthen our biobank software capabilities so that genetics data and biospecimens can be curated and stored.

RESEARCH COLLABORATIONS

1. Develop a biobank informatics management system

Collaborating Parties:

Dr Dominique Anderson – SANBI, UWC and Africa CDC

Nature and Purpose:

Development of a laboratory management system for use by Biorepositories.

Output in the last 12 months:

Baobab LIMS Lite core module has been developed.

Future Direction:

Building functionality to support Biodiversity Biorepositories

2. Analyzing genetic networks in M.tuberculosis

Collaborating Parties:

Prof Rob Warren – University of Stellenbosch

Nature and Purpose:

Identification of Operons: applying Operon finder, COSMO, to clostridium difficile.

Output in the last 12 months:

Refining COSMO for other pathogens.

3. Computational Bacterial analytical toolkit for Tuberculosis (COMBAT-TB)

Collaborating Parties:

Profs Samantha Sampson and Rob Warren – University of Stellenbosch

Peter van Heusden – SANBI, UWC

Nature and Purpose:

Develop a computational platform to store Tuberculosis -omic data and to provide a visualisation tool.

4. Biosecurity Preparedness in Africa

Collaborating Parties:

Dr Dominique Anderson – SANBI, UWC

Global Consortium on emerging infectious diseases (www.getafrica.org).

Nature and Purpose:

We aim to establish infrastructure and research capacity to respond to highly infectious emerging pathogens. 

Future Direction:

Advocating for Biosecurity Best Practice in Africa.

5. Biosecurity Preparedness in Africa

Collaborating Parties:

63 Organisations including – Africa CDC; Oxford University; Washington University; University of Melbourne; USA CDC; University of Birmingham UK; Simon Fraser University; Vancouver; Canada; Broad Institute in Boston and H3Africa.

Nature and Purpose:

The PHA4GE consortium was established to bring bioinformatics closer to public health – to build data standards.

6. African Genomics Archive

Collaborating Parties:

Africa CDC

Nature and Purpose:

To establish a data platform in Africa to manage disease surveillance data with a view to strengthen public health institutes.

Output in the last 12 months:

Prototype of the archive – AGARI.

Future Direction:

Develop a production ready server to host 5 priority pathogens for African countries.