Visualizing Biological Data

The VizBi-2012 Conference took place in Heidelberg this week – unfortunately I couldn’t attend it. Nevertheless, I received a bit of summary and feedback: The talks will be made available online, I am looking forward to check out a few of them (i.e. Jim Robinson, Jernej Ule). Ivet Bahar (ProDy) and Valerie Daggett (Dynameomics) gave an interesting overview on Molecular Dynamics.

The conference was preceeded by a several tutorials on Monday. Among them on was one on Processing.js (which has been mentioned around here a few times before) and one on D3.js. Both are based on JavaScript and generate cool Visualisations for the Web. D3 only recently got onto my radar, it’s document driven approach seems quite powerful. So it’s definitely worth a look –

see some more examples (like the force-directed layout on the right) on http://mbostock.github.com/d3/ and the workshop slides can be found at http://bost.ocks.org/mike/d3/workshop/.

Thanks to to Corinna Vehlow for feedback!

Visualizing collaborative networks

Moritz Stephaner and Christopher Warnow used data from SciVerse Scopus (>94,000 publications in total) to map the collaborations of Max-Planck Researchers (inside and outside the MPG) over the last decade. A nice combination of (social) network logic and geography!

The network view shows the Max Planck Institutes and their connections. The size of the circles represents the number of scientific publications for each institute, and the width of the connecting lines the number of jointly published papers between two institutes.

Everything looks like a graph …

Gephi is a free and open-source and multiplatform (Mac, PC, Linux) Graph Vizualisation software claiming to be just “Like Photoshop™ for graphs”.

There is active development in the community, current stable release version is 0.8 beta and a corresponding toolkit.

Understanding Schematics

While tinkering with my arduino-board (a project loosely related to processing) I came across this video on Make: explaining the basics of electronic schematics.

 

It reminded me of this wonderful and thought-provoking article by Y.Lazebnik “Can a biologist fix a radio?–Or, what I learned while studying apoptosis.” (see here for the .pdf).

Another example of how complexity arises from combining relatively simple building blocks, and how we go about understanding and reverse-engineering complex systems in different disciplines.

(found via SchockWellenReiter)

Weekend Music Videos

This one is more about the visuals than the music: The networks mapped onto spheres, a human body and the planet – all rolled into one! Just stunning. On top of that, it’s got “chemistry” in the title and is done mostly in processing. That’s several reasons why this should go onto this blog … Have fun!

Interpol – Rest My Chemistry Video from Aaron Koblin on Vimeo.

Worthwhile to check it out in fullHD on vimeo – which also might run it more fluently.

OpenProcessing.org

After writing a couple of sketches in processing, the urge to share it tends to become bigger. Of course processing lets you export a sketch as an application for any architecture$(windows, linux, OS/X). That has the advantage of eventually using more of the power of the local hardware, but not everybody wants to download the full program just to have a sneak-peek preview how it looks like in action. Processing also let’s you generate an applet that can be included in web-pages. In case you are not maintaining your own web-server, OpenProcessing comes in very handy in a couple of aspects.

Data Visualisation

http://numberpicture.com/

http://jess3.com/ is a creative agency that specializes in data visualization. On their site on information aesthetics. (Where form follows data) I came across this article on numberpicture.com.

A potentially useful feature is that custom-made templates can be added through the use of Processing.js (that’s the little, more outgoing twin-sister of processing).

“Number Picture is a web application that enables you to come up with, easily create, and share fresh and interesting tools for visualizing data – that others can then use to visualize their own data.” Very interesting- a breeze of crowd-sourcing and open-access/open data in visualisation. Sounds good to me!

On their page I learned that the classical pie-chart was invented in 1801 (for historical context: at that time, the French Revolution was just over and Napoleon ruling) – and that PictureNumbers just went live less than 2 weeks ago – so this is hot stuff, fresh from the oven. If you have tested a piece of the cake, please let us know (comment!) before you decide to take over the bakery.