title: Feasibility and effectiveness of a brief, intensive phylogenetics workshop in a middle-income country.
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.
authors.affiliation: 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.
authors.forename: S
authors.initials: S
authors.lastname: Pollett
authors.affiliation: US Naval Medical Research Unit No. 6, Lima, Peru.
authors.forename: M
authors.initials: M
authors.lastname: Leguia
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA.
authors.forename: M I
authors.initials: MI
authors.lastname: Nelson
authors.affiliation: Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
authors.forename: I
authors.initials: I
authors.lastname: Maljkovic Berry
authors.affiliation: Department of Epidemiology and Biostatistics, University of California - San Francisco, California, USA.
authors.forename: G
authors.initials: G
authors.lastname: Rutherford
authors.affiliation: US Naval Medical Research Unit No. 6, Lima, Peru.
authors.forename: D G
authors.initials: DG
authors.lastname: Bausch
authors.affiliation: Global Emerging Infections Surveillance and Response System, Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA.
authors.forename: M
authors.initials: M
authors.lastname: Kasper
authors.affiliation: Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
authors.forename: R
authors.initials: R
authors.lastname: Jarman
authors.affiliation: Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
authors.forename: M
authors.initials: M
authors.lastname: Melendrez
mesh_terms: D019295:Computational Biology; D005240:Feasibility Studies; D006801:Humans; D007182:Income; D010568:Peru; D010802:Phylogeny; D011795:Surveys and Questionnaires
keywords: Bioinformatics; Low- and middle-income country; Phylogenetics; Training; Viral pathogens