Pathogen Genome Cluster Computing

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Artistic impression of human tissue chronically infected with Trypanosoma cruzi. Credit, Castro Sila, Memorias

The high performance computing at LSHTM was funded through the Science Research Infrastructure Fund (SRIF), which is a collaboration between the UK government and the Wellcome Trust.

Pathogen Genomics Overview

Genome scale data generation has been one of the most significant paradigms in the modern history of biological science. Genomic research into the major pathogenic parasites has exemplified this trend and includes the trypanosomatids, Plasmodium, Entamoeba, tuberculosis, plague and intestinal bacteria such as Campylobacter.

Genomics has resulted in an analytical research front within bioinformatics that is increasingly converging on computer intensive mathematical models. The comparative analysis of genome data is one of these research fronts and is an extension of traditional phylogenetics. Phylogenetics calculations when reiterated throughout a genome, or phylogenomics for short, are massively computationally intensive. The computational demands of phylogenomics work is met using high performance computer clusters. The outputs of the work ultimately provide insights into drug and vaccine candidates.

Cluster Computing Technical

High performance computer clusters are meticulously managed at LSHTM. A history and software itinerary of the machine is available here.

Current and Completed Projects

  • Trypanosomatid recombination .................
  • Trypanosoma cruzi and T. brucei genomics
  • Triatomine bug population genetics
  • Campylobacter jejuni and Yersinia microarray phylogenomics
  • Plasmodium falciparum population genetics
  • P. falciparum proteome phylogenomics

Links at LSHTM

    • Microarray genomics
    • Malaria
    • Research by area
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Comments and enquiries Last updated 28th July, 2005 MWG.