Infectious Disease Epidemiology, Imperial College London
Doi
Abstract
The ever-increasing generation and submission of DNA sequences, and associated
biological data, to publicly available databases demands software for the analysis of
the biological meanings held within. The web provides a common platform for the
provision of tools enabling the concurrent deposition, visualisation and analysis of
data collected by many users from many different locations. Open programmatic web
standards allow the development of applications addressing diverse biological
questions and, more recently, are providing methods enabling functionality more
traditionally associated with desktop software to be provided via the internet.
In this work I detail the development and use of web applications addressing different,
but not exclusive, areas of infectious disease microbiology. Firstly, an application
utilised by a group of researchers (including myself) to undertake a comparative
genetic analysis of the capsular biosynthetic locus from serotypes of the pathogen
Streptococcus pneumoniae is detailed. Secondly, an application widely used by
communities of researchers and public health laboratories for the assignment of
microbial isolates to strains via the internet: mlst.net is described. Thirdly, I describe a
generic electronic taxonomy application for assigning strains to bacterial species,
exemplified using sequences from the viridans group streptococci, the taxonomy of
which is notoriously difficult to define. Lastly, I describe the use of web mapping
tools for molecular epidemiological databases, such as mlst.net, and further detail
their application to the European distribution of genotypes of Staphylococcus aureus,
to catalogue the global distribution of the emerging amphibian fungal pathogen
Batrachochytrium dendrobatidis and to provide geocoding tools to encourage users to
submit and explore their own data in the geographical context they were collected.
Each application has been designed with generality in mind and through reference to
user workflows and biological examples, I demonstrate the extensibility and general
applicability of current web development methodologies to enable the provision of
applications addressing a diversity of biological questions
