Archive for category Visualisation

Bioinformatics Utopia

While checking out the new InterPRO (in beta stage) I came across the latest version of Utopia (available for all major OSs) :

Utopia is a collection of interactive tools for analysing protein sequence and structure. Up front are user-friendly and responsive visualisation applications, behind the scenes a sophisticated model that allows these to work together and hides much of the tedious work of dealing with file formats and web services.

The installation package (provided by the AdvancedInterfacesGroup AIG) includes

  • CINEMA – multiple sequence alignment editor
  • Ambrosia – molecular structure viewer
  • UTOPIA – support libraries and plugins

After a quick & painless installation, it seems to work out of the box. More in-depth info when I get to grips with more of the functionality.


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3D Modelling of Proteins and DNA

Judging from the gallery and videos, the Graphite – LifeExplorer is a great tool to model protein and DNA :

The Graphite-LifeExplorer modeling tool to build 3D molecular assemblies of proteins and DNA from Protein Database (PDB) files. Atomic DNA can be modeled from scratch or reconstructed from simulation.

Unfortunately, I didn’t get the Mac-Version to work on my machine (Mac OS X 10.6.8) it works only for OS X 10.7.+ (got it running on 10.7.3) – it’s definitely worth keeping an eye on:

shared by Damien Larivière via LinkedIn/Molecular Modeling in Life Sciences.

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Biophilia is an extraordinary and innovative multimedia exploration of music, nature and technology by the musician Björk. Comprising a suite of original music and interactive, educational artworks and musical artifacts, Biophilia is released as ten in-app experiences that are accessed as you fly through a three-dimensional galaxy

I still haven’t downloaded and checked out the app myself in detail, the price-tag is a bit hefty for my taste. So far I have never spend over 10 bucks on a single app, and personally find it very hard to digest more than 2 Björk-songs in a row. OK, my ears aren’t bleeding, and in this case my eyes are very much tempted by the visuals. Biophilia contains several subsections (in-apps), so one could argue it’s more than just a single app, comparable to an entire (concept?-)album. On the app-store reviews there’s some criticism of the pricing-policy, however content-wise one reviewer goes as far as claiming that “we will eventually see Biophilia as the Sergeant Peppers of music apps“. A steep claim indeed to liken it to the fab four… but even though the music is not exactly my cup of tea, I am thrilled by the unique combination of contemporary art, science and technology.

As for the scientific content, the spring 2012 issue of the quarterly newsletter published by the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB for short) features a snapshot of the video for Björk’s title “hollow”:

To accompany the song “Hollow,” Björk’s meditation on biological ancestry, [Biomedical animator Drew] Berry
created a lush landscape for DNA to replicate (and sparkle) to the music. Molecular
machines work at real-time speed, culminating in the appearance of Björk as a complex
protein structure. Many of the molecular shapes, illustrated with great depth and rich
color, were created with the help of crystal structure data from the PDB.

More of these stunning, educational and award-winning 3D animations by Drew Berry and his colleagues are available on WEHI.TV at the Walter+Elisabeth Hall Institute of Medical Research. Enjoy!

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Visualizing your Social Network

LinkedIn offers a visualisation of your network connections. While browsing and looking at the persons represented by the nodes and their proximity, directly hypothesis form in the head as to the common context (when and where one met). To me the accuracy of the layout and coloring is amazing! That the different clusters actually delineate different institutes and departments I had the pleasure to work with/at is a nice “proof-of-concept”, albeit a bit terrifying as to how much the network knows about us … if you already are at LinkedIn give it a spin to see “the community” emerging around yourself. Makes you also wonder what the guys running the social networks actually can do with the entirety of network data we dump on them. Anyway, have fun exploring your local network!

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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 and the workshop slides can be found at

Thanks to to Corinna Vehlow for feedback!

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Science: 2011 Visualization Challenge

Separation of a Cell, Andrew Noske et al. (Illustration - People's Choice)

An article describing the 2011 International Science and Engineering Visualization Challenge just appeared in Science 3 February 2012 (Vol. 335 no. 6068 p. 525, DOI: 10.1126/science.335.6068.525). Access to all materials in this section is FREE (like in free beer), especially the web-gallery of the corresponding special issue available as a slideshow is definitely worth a visit.

Each year, Science Magazine and the National Science Foundation host the International Science and Engineering Visualization Challenge. The 2011 Challenge received over 200 submissions in five categories, which were evaluated based on visual impact, effective communication of a scientific idea, and overall originality. Visualizations with the most votes from the public received the People’s Choice award.

Among the Informational Posters & Graphics I like “The Cosmic Web“, and all the videos are just awesome.
Congrats to FoldIT for making 1st Place in the “Interactive Games”-Category and thanks to Sathyapriya Rajagopal for the link!

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Goodbye to hairballs?

You probably have seen the hairballs resulting from a force-directed layout of complex biological networks. What do they tell you? Well, that the networks are rather complex. But for much more detailed analysis the classical visualizations are actually quite useless. The hiveplot  is an attempt to provide

“A scalable, computationally fast, and straight-forward network visualization method that makes possible visual interpretation of network structure and evolution.”

A laudable goal, if it works in practice for you and your data – check it out. In addition there is an R package available for creating hive plots in 2D and 3D called HiveR.

Also see Krzywinski M, Birol I, Jones S, Marra M (2011). Hive Plots — Rational Approach to Visualizing Networks. Briefings in Bioinformatics (doi: 10.1093/bib/bbr069).

Thanks to Lucy Colwell for the hint!

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