Local labs where bioinformatics services are available.
University of Pretoria Center for Bioinformatics and Computational Biology
This unit forms part of The Genomics Research Institute and The African Center for Gene Technologies. They offer training, support, and research in the areas of Bioinformatics and Computational Biology, specifically:
Center for Proteomic and Genomic Research
High-throughput experimentation generates vast amounts of raw data. In order to assist you in handeling, analysing and interpreting this information, the CPGR offers standard bioinformatics services for genomics and transcriptomics.
Krisp Bioinformatics Services
KRISP is a competence centre in bioinformatics and computational biology. The group employs skilled personnel that provides infrastructure, support and technological R&D for life sciences and clinical research
South African Tuberculosis Bioinformatics Initiative
As tuberculosis research in South Africa has become increasingly reliant on molecular biotechnologies, the volume of data produced has grown considerably. The South African Tuberculosis Bioinformatics Initiative (SATBBI) was created in response to this growth, creating a group of bioinformatics researchers engaged with the tuberculosis research community in South Africa.
South African National Bioinformatics Institute
Conduct cutting edge bioinformatics and computational biology research relevant to South African, African and global populations.
Sydney Brenner Institute for Molecular Bioscience
A burgeoning multi-disciplinary research institute dedicated to investigating the molecular and genomic aetiology of diseases among African populations
The Computational Biology (CBIO) division at the University of Cape Town (UCT) is the centre of bioinformatics activities at the university. It forms part of the Department of Integrative Biomedical Sciences and is located within the Institute of Infectious Disease and Molecular Medicine (IDM), in the Faculty of Health Sciences. The division carries out research in a number of areas, and provides training and services in the discipline.
Bioinformatics analysis expecially of NGS data may require a number of step involving different software processing step, conversion of file formats to reach a desired result. In order to prevent needing to re-invent the wheel everytime a analyis needs to be performed, data analysis workflows have been constructed using recognised and accepted software. Furthermore workflow software has been developed to make it easier to construct workflows from existing software
One peptides have been identified and relative protein abundances determined, statistical tests determine which of the protein as significantly differentially expressed between biological conditions and require further study.
"The Crux mass spectrometry analysis toolkit is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data"
High-Performance Computer Clusters
Due to the large volumes and complexity of omics data, it is not always possible to analyse this data on standard desktop computers. Large computer clusters of often required, which are able to store large volumes of data and process data rapidly in parallel. There are a number of local HPC cluster available through academic institutions.
Public cloud computing services are available, where compute resources can be requested on demand.
Bioinformaticians are available to assist you with your project.
The earlier you contact them the more assistance they will be able to offer. In particular, the experimental design is critical in ensuring the success of any project. Contacting a statistician and ensuring your experiment has enough statistical power will go a long way to ensuring its success.
Selecting the best technology for your project will ensure you get the best results for the your project. Omics research is costly, choosing the most appropriate technology for you experiment and budget is therefor critical.
It is best to first run a pilot study and having an expert check the quality of the results before continuing with the bulk of the analysis. The pilot project will also allow you to familiaries yourself with the sample analysis process, the data generated and the means of analysis, before embarking on the main project.
Once you have produced the data, you will realise omics technologies produce mountains of data. It often requires some expertise in handling big data, to deal with the amounts of data produced. Fortunately we have tools and resources to store and process your data making it easy for you to understand. Contact our team of expert bioninformaticians for assistance on all levels of your project.
Dr Katie Lennard
Bioinformatician at the Institute of Infectious Diseases & Molecular Medicine
Differential Abundance Statistics
16S rRNA gene amplicon sequencing
WGS metagenomics sequencing
Pathogen isolate profiling
Multivariate analyses: PCA, NMDS, MDS, PERMANOVA, PLSDA, RDA
Machine learning techniques; Random forests
Statistical tools for differential abundance testing
Dr Shaun Garnett
Post-Doctoral Fellow at University of Cape Town
Differential Abundance Statistics
Expression Data Functional Annotation