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Python in Viral Bioinformatics Research

Description

The field of bioinformatics -- using computer technology to store, process and analyze biological data -- is relatively new, but is expanding rapidly. Many free and commercial tools, both online and stand-alone, are available. This presentation will describe the approach and tools developed in our research group at the University of the Witwatersrand. Although we research hepatitis B virus, many of the tools can be used with any biological sequence data (DNA, RNA or amino acids).

The tools cover several aspects of typical laboratory research, including tools to process sequence data, automate analyses and report variations in sequences. The tools were developed to be quick, lightweight solutions, which could easily be used routinely by researchers without extensive computer skills. Many of the tools have been developed in direct response to a specific need.

Topics covered will include the design approach (online, CGI-scripts, no frameworks) and the reasons for this approach, as well as the experience of working as the only bioinformaticist in a wet laboratory. Mention will also be made of other resources, such as R and SQL, in addition to Python.

Several of the tools have been described in published papers. The tools are all freely available online (http://hvdr.bioinf.wits.ac.za/tools) and source code for most of the tools is available via GitHub at the following address: https://github.com/DrTrevorBell

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