Services

The UCT Computational Biology Division hosts a number of bioinformatics tools, in-house and external, and services for researchers at UCT. CBIO has a Galaxy installation for developing and running bioinformatics workflows and can provide support for creating custom pipelines or packaging new modules into Galaxy.

 

For more details on bioinformatics service requests please see: Bioinformatics Service Requests.

 

The group members are open to collaborations from researchers within and outside of UCT. Our policy for collaborations is that the group member involved is acknowledged for significant contributions to projects through authorship on publications. We strongly advise that bioinformatics collaborations are developed at the start of the project rather than after data has been generated.

Data analysis support can be provided for:

Tools and resources

CBIO Tools

  • PINV (web-based protein interaction viewer) 

PINV is an open source, native web application that uses the latest generation of web technologies to offer an interactive view of protein-protein interactions which is easily accessible from any modern browser. PINV enables researchers to explore preloaded or their own data using different methods. The visualization can be manipulated to highlight the proteins or interactions of interest. The resulting graphic can be exported into common graphic formats so it is suitable for publication and sharing purposes.

PINV ScreenShot

  • Local Galaxy servers

CBIO has a Galaxy installation for developing and running bioinformatics workflows and can provide support for creating custom pipelines or packaging new modules into Galaxy. To see a list of the tools developed in house please go here.

 

The University of Cape Town also hosts a Galaxy instance. To get access to the instance please follow the instructions here. This instance is fully integrated into the UCT HPC environment and this means that enough storage and computational power are available for doing NGS data analysis. Currently the instance does not support the CBIO specific tools.

  • eBioKit

The eBioKit is a system running multiple open source web services on an Apple Mac-mini where all databases are stored locally. This reduces the need for a fast internet connection while giving the users an opportunity to incorporate their data sets in widely used web services. As the eBioKit is a work in progress, more services will be available in the future. The following applications are currently installed:

 

EnsEMBL, BioMart, NCBI Blast, Galaxy, Jalview, wEMBOSS, MRS, RSAT, Yasara, PLINK, Weblogo and MEGAN

 

Our local instance is hosted here . Please note that the instance is only accessible within the UCT network.

  • ProbeSearcher

Find the right chip for your experiment.

  • IT-GOM (Integrated Tool for IC-based GO Semantic Similarity Measures)

This tool provides the information content (IC) of GO terms, semantic similarity between GO terms and GO-based protein functional similarity scores. Users can input UniProt accession numbers or GO IDs.

  • SDT (Species Demarcation Tool)

The program allows the demarcation of new virus species based on sequence pairwise similarities. It takes as input a FASTA file of aligned or unaligned DNA sequences and aligns every unique pair of sequences, calculates pairwise similarity scores, and uses a rooted neighbour joining phylogenetic tree to cluster closely related sequences based on similarity scores.

 Supported Tools

  • R-Project Mirror

A local mirror of the R-Project Web Site and CRAN source repository can be accessed here.

  • Web Portal for Microarrays

The webportal for microarrays is aimed at researchers working in the microarray arena and will guide you through the microarray experiment from design to data mining.

  • BioEdit 

BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program. Download it here or directly from the site.

  • BLAST2GO Local Web Service

Blast2GO is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. More information on how to access our BLAST2GO local database and web service. 


 

 

CBIO tools