Bioinformatics

Service Providers

Local labs where proteomics services are available.

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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:

Location

Gauteng

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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.

Location

Western Cape

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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

Location

KwaZulu-Natal

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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.

Location

Western Cape

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South African National Bioinformatics Institute

Conduct cutting edge bioinformatics and computational biology research relevant to South African, African and global populations.

Location

Western Cape

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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

Location

Gauteng

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Computational Biology

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.

Location

Western Cape

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Workflow Software

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

Nextflow

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"Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages"

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Galaxy

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"Galaxy is an open source, web-based platform for data intensive biomedical research"

CBIO, SUN, UWC, WITS, CHPC

 

Tool Collections

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.

Seattle Proteome Center Proteomics Tools

"The Seattle Proteome Center (SPC) is committed to providing free, open-source, software projects in support of cutting-edge proteomics research."

EBI Tools

"The European Bioinformatics Institute (EMBL-EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular data resources."

CRUX

"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"

IDM Proteomics

ProteoWizard

"ProteoWizard provides a set of open-source, cross-platform software libraries and tools (e.g. msconvert, Skyline, IDPicker, SeeMS) that facilitate proteomics data analysis"

Bio Tools

"Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences."

MaxQuant

"MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data."

IDM Proteomics, CPGR, CAF and CSIR Proteomics

H3ABioNet

"H3ABioNet has developed a number of tools and services for H3Africa and the broader bioinformatics community"

Broad Institure

"Broad Institute of MIT and Harvard, collection of genomics tools"

 

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.

krisp

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"KRISP operates high-productivity computational and storage resources for life and biomedical sciences and maintain high expertise over computational infrastructure, software development, biological data analysis and web development"

ilifu

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"A consortium of universities and research organisations have established a data-intensive research cloud, Ilifu – which means cloud in isiXhosa – and are inviting researchers in these two strategic science domains to start using the infrastructure"

CHPC

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"CHPC is mandated to provide high performance computing (HPC) resources and domain specific support to both public and private sector users"

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Public cloud computing services are available, where compute resources can be requested on demand.

Microsoft Azure

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"Azure is a complete cloud platform that can host your existing applications and streamline new application development."

Amazon AWS

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"Amazon Web Services (AWS) is the world’s most comprehensive and broadly adopted cloud platform, offering over 175 fully featured services from data centers globally."

Google Cloud

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"Cloud infrastructure solutions for SAP, VMware, Windows, Oracle, data center migration, and other enterprise workloads"

 

Bioinformatics Training

Picking up the Tabb

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"David Tabb teaches a fairly broad range of coursework. This catalog of topics may be useful for student to get the training they need.

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Training eSupport System

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"Goals of ELIXIR is to train research scientists to better use available computational infrastructures to address critical research questions"

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H3ABioNet Training

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"H3ABioNet delivers high quality bioinformatics training in a variety of formats"

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Bioinformaticians

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

Fields

  • Genomics

  • Transcriptomics

  • Differential Abundance Statistics

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Expertise

  • 16S rRNA gene amplicon sequencing

  • WGS metagenomics sequencing

  • RNAseq

  • Pathogen isolate profiling

Tools

  • Multivariate analyses: PCA, NMDS, MDS, PERMANOVA, PLSDA, RDA

  • Machine learning techniques; Random forests

  • Statistical tools for differential abundance testing

  • Nextflow

  • edgeR

  • metagenomeSeq (R)

Dr Shaun Garnett

Post-Doctoral Fellow at University of Cape Town

Fields

  • Transcriptomics

  • Proteomics

  • Differential Abundance Statistics

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Expertise

  • Liquid Chromatorgaphy

  • Mass Spectrometry

  • Discovery Proteomics

  • Statistics

  • Expression Data Functional Annotation

Tools

  • MaxQuant

  • Skyline

  • TPP

  • clusterProfiler

  • topGO

  • STRINGdb

  • ReactomePA

 

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