Talk @vizbi on phylogeny visualisation

The talks from the 2001 workshop on Visualizing Biological Data (VizBi 2011) are now available on Vimeo. There were some great talks at VizBi, especially the keynotes (the "featured videos" on the Vimeo page for VizBi).

My own (slightly breathless) talk was on phylogeny visualisation, which you can watch below.

Visualization of phylogenetics & phylogeography from Roderic Page on Vimeo.

In the talk I mention that the slides are also on SlideShare, and that is where you'll find URLs for the projects I mention. The URls aren't all that easy to get that way, so here they are:

• http://evolution.genetics.washington.edu/phylip/software.html#Plotting
• http://loco.biosci.arizona.edu/paloverde/paloverde.html
• http://www.wellcometreeoflife.org/
• http://dx.doi.org/10.1186/1471-2105-5-48
• http://dx.doi.org/10.1093/sysbio/46.3.523
• http://dx.doi.org/10.1186/1471-2105-8-213
• http://iphylo.blogspot.com/2007/06/earth-not-flat-official.html
• http://systbio.org/?q=node/184
• http://dx.doi.org/10.1080/10635150701266848
• http://www.ncbi.nlm.nih.gov/pubmed/17968069
• http://innovis.cpsc.ucalgary.ca/Research/CollaborativeTreeComparison
• http://www.perceptivepixel.com/
• http://iphylo.blogspot.com/2008/08/perceptive-pixel-taxonomy-demo.html
• http://www-ab.informatik.uni-tuebingen.de/software/dendroscope
• http://dx.doi.org/10.1126/science.300.5626.1692
• http://loco.biosci.arizona.edu/
• http://iphylo.blogspot.com/2007/08/visualising-very-big-trees-part-iv.html
• http://iphylo.blogspot.com/2011/02/live-demo-of-zooming-large-tree.html

Some VIZBI 2011 links

Given that the Twitter stream tagged #vizbi will fade away soon, I've grabbed most of the links I tweeted during VIZBI 2011 and have put them here. This isn't intended as a comprehensive list, merely the things which caught my eye, and didn't flash by faster than I could tweet.

Books

• Visual Complexity: Mapping Patterns of Information
• Visual Thinking for Design

Movies

• DNA
• Malaria lifecycle Part 1
• Malaria lifecycle Part 2
• WEHI.TV

People

• Drew Berry
• Manuel Lima
• Tamara Munzner
• Fernada Viégas
• Martin Wattenberg

Software and websites

• Arena 3D
• BioBlender
• BLAST Atlas
• Cerebral v.2.0
• Chromograms
• CloVR
• Cytoscape
• EMAGE
• embedded Python Molecular Viewer (ePMV)
• Fleshmap
• GenomeView
• History Flow
• HivePlots
• ImageVis3D
• JProfileGrid
• Many Eyes
• Molecular Maya
• Molecular Movies
• PathBLAST
• Phyloviewer
• Powerwall
• Quartz Composition of DNA
• Scribl
• Sequence Surveyor
• Shape of Song
• Sybil
• Topiary Explorer
• Vrtual Worm
• Web Seer
• Whole Brain Catalog

VIZBI 2011

I've spent the last three days at VIZBI, a Workshop on Visualizing Biological Data, held at the Broad Institute in Boston (note that "Broad" rhymes with "Code"). A great conference in a special venue that includes the DNAtrium. Videos of the talks will be online "real soon now", look for the keynotes, which were full of great ideas and visualisations. To get a flavour of the meeting search for the hashtag #vizbi on Twitter (you can also see the tweet stream on the VIZBI home page). All the keynotes were great, but I personally found Tamara Munzer's the most enlightening. She drew on lots of research in visual perception to outline what works and what doesn't when presenting information visually. You can grab a PDF of her presentation here.

One aspect of the meeting which worked really well was the poster presentations. Poster sessions were held during coffee breaks, and after the last talk of the session but before the audience broke for coffee, each author of a poster got 90 seconds to introduce their poster (there were typically around 10 posters per break). This meant the poster authors got a chance to introduce themselves and their work to the workshop audience, and the audience could discover what posters were being displayed. Neat idea.

I gave a presentation on phylogenies, which I've put on slideshare. After explaining that I thought phylogeny visualisation was mostly a solved problem (as evidenced by the large number of tree viewers available), I continued the theme of why I don't think 3D works for phylogeny (except for geophylogenies), made the pitch for building a phylogeny viewer on the iPad, and finished with my recent work on Google Maps-style viewing very large trees.

Phylogeny VIZBI 2011

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