Developing an F# Bioinformatics Application with HTML5 Visualization

  • Adam Granicz IntelliFactory
September 15, 2012 2:45 - 3:05 PM


With proprietary plugin-based containers like Flash or Silverlight gradually losing ground, an increasing number of web applications are beginning to seek web standards compliance, and to utilize HTML5 to deliver rich and interactive client-side functionality and end-user experience. Indeed, modern browsers continue to invest heavily in establishing standard support for various HTML5 features, making HTML5 an appropriate choice for an ever-growing crowd of web developers.

Earlier this year at IntelliFactory, we completed a pilot project missioned to create a custom, innovative, and highly interactive bioinformatics web application using F# and our WebSharper technology. This application set out to serve the bioinformatics research community, and to deliver, among others, an interactive visualization of the gene sequence of a particular bacterium, with various mutations available for further research and laboratory use. The application consumed a large amount of bio data and integrated various advanced HTML5 visualizations, such as full functional gene ontology, a KEGG orthology, and a phenotype map, making it a useful web resource for researchers and laboratory staff alike.

In this talk, I will present our experience report on developing this bioinformatics application, the practices and guidelines related to client-based visualization projects we distilled while developing it, the challenges we met on the way, and how we solved these challenges. Many bioinformatics algorithms are amenable to functional programming, but as a full-blown web application with advanced visualization this project yielded a great deal of details that we hope will be useful for other attendees.

Adam Granicz

Adam Granicz is a long-time F# insider and key community member, and the co-author of four F# books, including the upcoming edition of Expert F# 3.0 with Don Syme, the designer of the language. His company IntelliFactory specializes in consulting on the most demanding F# projects; shaping the future of the development of F# web, mobile and cloud applications; and developing WebSharper, the most mature web and mobile development framework for F#. You can follow him on Twitter at @granicz, or find him on FPish, the largest online functional programming community.