BiVi 2015

It’s the first year someone from InterMine has attended BiVi (Biology Visualisation), which is in its second year of a (currently) three-year plan to create a community around biology visualisation.

The atmosphere was pleasantly thriving, with probably 20 or 30 attendees from Cambridge, Edinburgh, London, Oxford, and even Institut Curie in France. I think it was safe to say that most of the attendees were people with a computer science background who worked in biology-related fields, although that wasn’t a strict rule.

Two themes were particularly popular this year:

  1. 3d molecule visualisation. Multiple different talks / groups of BiVians had exciting developments to show us, from Hapitimol, a visualisation with haptic feedback, to EZMol, with an easy-to-use wizard to produce visualisations, Foldsynth, a physics based engine from Goldsmiths, MARender, a Javascript-driven biomedical imaging library, and BioBlox, which gamifies protein docking to allow crowd-sourced research.
  2. Usability. Biology is a rich, complex field. Computer people making tools for biologists need to keeps things easy to use. EZMol, mentioned above, was created due to a notable lack of simple usable 3d visualisation tools. Our upcoming InterMine 2.0 release is another push towards creating a better user experience.

One of the most impressive tools demonstrated was Zegami, a tool to annotate, view, and filter images. It may have started as a biological tool, but it’s equally functional for your holiday snaps or for sorting and filtering Netflix movies. It’s a shame we don’t really have any image data in InterMine (well, in Fly or HumanMine at least) given how cool it looked.

Example from South Australian Museum invertebrates.

A few other tools / demos of note included:

  • Reactome pathway browser, which is fully embeddable into your own web app.
  • Jalview, ‘a free program for multiple sequence alignment editing, visualisation and analysis’. The main Jalview dev is also one of the organisers of the VizBi biology vis conference, next taking place in Germany.
  • Aequatus-vis uses Ensembl web services to visualise homologous gene families.

On day 2, I gave a short talk on the future of InterMine, focusing on why we want to revamp our UI, and what we think we’re doing better in InterMine 2.0. The slides are available on Google Drive (better format) or Slideshare.