International Journal of Infectious Diseases (Jan 2016)

Feasibility and effectiveness of a brief, intensive phylogenetics workshop in a middle-income country

  • S. Pollett,
  • M. Leguia,
  • M.I. Nelson,
  • I. Maljkovic Berry,
  • G. Rutherford,
  • D.G. Bausch,
  • M. Kasper,
  • R. Jarman,
  • M. Melendrez

DOI
https://doi.org/10.1016/j.ijid.2015.11.001
Journal volume & issue
Vol. 42, no. C
pp. 24 – 27

Abstract

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There is an increasing role for bioinformatic and phylogenetic analysis in tropical medicine research. However, scientists working in low- and middle-income regions may lack access to training opportunities in these methods. To help address this gap, a 5-day intensive bioinformatics workshop was offered in Lima, Peru. The syllabus is presented here for others who want to develop similar programs. To assess knowledge gained, a 20-point knowledge questionnaire was administered to participants (21 participants) before and after the workshop, covering topics on sequence quality control, alignment/formatting, database retrieval, models of evolution, sequence statistics, tree building, and results interpretation. Evolution/tree-building methods represented the lowest scoring domain at baseline and after the workshop. There was a considerable median gain in total knowledge scores (increase of 30%, p < 0.001) with gains as high as 55%. A 5-day workshop model was effective in improving the pathogen-applied bioinformatics knowledge of scientists working in a middle-income country setting.

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