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:10.1016/j.ijid.2015.11.001

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

Int J Infect Dis. 2016 Jan:42:24-27. doi: 10.1016/j.ijid.2015.11.001. Epub 2015 Nov 10.

Authors

S Pollett¹, M Leguia², M I Nelson³, I Maljkovic Berry⁴, G Rutherford⁵, D G Bausch², M Kasper⁶, R Jarman⁴, M Melendrez⁴

Affiliations

¹ US Naval Medical Research Unit No. 6, Lima, Peru; Department of Epidemiology and Biostatistics, University of California - San Francisco, California, USA; Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, New South Wales, Australia. Electronic address: spollett@med.usyd.edu.au.
² US Naval Medical Research Unit No. 6, Lima, Peru.
³ Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA.
⁴ Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
⁵ Department of Epidemiology and Biostatistics, University of California - San Francisco, California, USA.
⁶ Global Emerging Infections Surveillance and Response System, Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA.

PMID: 26571303
DOI: 10.1016/j.ijid.2015.11.001

Abstract

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.

Keywords: Bioinformatics; Low- and middle-income country; Phylogenetics; Training; Viral pathogens.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology*
Feasibility Studies
Humans
Income
Peru
Phylogeny*
Surveys and Questionnaires