Welcome to VA4NGS. This site is the public face of an Australian Research Council funded project on visualising large scale datasets arising from next generation sequencing. The project is a collaboration between QUT (James Hogan, Margot Brereton and Daniel Johnson), the CSIRO (Sean O'Donoghue and colleagues), and Microsoft Research (Don Syme). At present, these pages are something of a placeholder, but over the coming months we will add and link to publications, reports, software and other artefacts that arise from the project. In what follows, we will tell you a little more about what we are doing, and let you know how to become involved.

Project Goals

  • To understand how scientists use visualisation to analyse and present their data
  • To identify common abstractions and representations which support insight and to embed these through visualisation design principles for NGS data sets
  • To investigate the effect of display size on the success of visualisations for NGS
  • To integrate data discovery and query-based exploration with scalable visual representations

Ultimately, much of this work will result in the creation of new software tools and libraries, and improvements in those already available. We will shortly add pages linking to our projects, tools and publications. For now, we are seeking participants for our interview studies. Please see below for details.

Interview Participants

A key aspect of our study is to understand better how biologists analyse data, and the role played by visualisation in this every-day workflow. Margot Brereton in particular is expert in applying anthropological techniques in a technical environment, working through structured interviews and think-aloud usage of visualisation tools to record how lab and computational biologists make sense of sequences. By finding common themes in the successful - and indeed, unsuccessful - use of visualisation, we hope to identify representations that support insight and discovery in complex biological data sets, and to establish design principles for the next generation of bioviz.

Our interview sessions normally last around 30 minutes, and involve an open ended discussion of work practices and tools, and an evaluation of one or more of our own visualisation tools - the protein analysis system aquaria, the Hi-C data browser Rondo, or the transcriptional regulatory network browser TRNDIff. We are based in Australia, but travel regularly, and have approval for interviews to be conducted via skype. If you would like to join us as an interview subject, and contribute to our understanding of bioinformatics visualisation, please get in touch through the channels below. We look forward to hearing from you.

This study has been approved by the QUT Human Research Ethics Committee (approval number 1500000367).

Contact

Associate Professor James Hogan.
E: j [dot] hogan [at] qut.edu.au
S: jamesmhogan