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!

Free 3D Virtual Globe Java API and SDK

World Wind is an open source API for a virtual globe written in Java – the project is curated by NASA and released under the NASA Open Source Agreement (NOSA).

The most basic usage of the SDK displays the default globe with its default layers - it requires only 6 lines of code to instantiate everything seen here.

World Wind provides a rich set of features for displaying and interacting with geographic data and representing a wide range of geometric objects.

On the goworldwind.org pages there is a getting-started guide, impressive list of features, demos and examples.

Among the features are

• Open-source, high-performance 3D Virtual globe API and SDK
• Adds geographic visualization to any application
• Runs on Windows, Mac OS X, Linux and in web pages
• Huge collection of high-resolution imagery and terrain from NASA servers
• Open-standard interfaces to GIS services and databases
• Large collection of geometric and geographic shapes
• Uses Java and OpenGL
• and more …

I’m not sure if the common phrase “It’s not exactly rocket-science, or is it?” applies here. 😉

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.

Green Tea, Free Textbooks, Free Thinking

At green tea press, publishers of “How to think like a computer scientist” (available in 3-4 different flavours including Python, Java and C++), “Learning Perl the Hard Way” and “Physical Modeling in MATLAB” a couple of new titles are available. Among them is “Complexity and Computation” by Allen B. Downey, who also wrote “Think Stats” and runs an interesting blog: Probably Overthinking It.

This book is about complexity science, data structures and algorithms, intermediate programming in Python, and the philosophy of science…

Sounds just like some of my favourite topics rolled up into one delicious package! If one insists on the classical DTF (DeadTreeFormat) version: printed hardcopies can be purchased from Lulu.com. But the best thing is that all the titles are all available as .PDFs for free, since the textbooks can be downloaded under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

It’s also worthwhile checking out their Textbook Manifesto, concluding with the statement: “There’s just no excuse for bad books.“, and the entry on “Free Books: Why Not?“. Maybe there is a lesson for scientific publishing in general? Enjoy!

(found via SchockWellenReiter)

Always tired in the morning –

... more ... Caffeine

Coffeinated Spiders

but wide awake at night! For all you owls out there, here’s your hymn. Hearing this on the radio made my day, almost as much as the obligatory intravenous shot of caffeine before starting work.

What I didn’t know until now is that it has an effect on how spiders create their web (ah, so there’s a reason for posting this in molecules & networks) – question is if the the spider feels jittery and nervous or just a bit creative for the rest of the day… probably depends on the dose.

MLDemos – Machine Learning, visualized

Basilio Noris from the Learning Algorithms and Systems Laboratory at the Ecole Polytechnique Fédérale de Lausanne has published MLDemos – the software is available for download (for all major OSs). It works out of the box, and the first tests went really fine – I’m impressed with the visualisation of the algorithms at work!

During my PhD I’ve come across a number of machine learning algorithms for classification, regression and clustering. While there is a great number of libraries, source code and binaries for different algorithms, it is always difficult to get a good grasp of what they do. Moreover, one ends up spending a great amount of time just getting the algorithm to display the results in an understandable way. Change the algorithm and you will have to do the work all over again. Some people have tried, and succeeded, to combine several algorithms into a single multi-purpose library, making their libraries extremely useful (you will find many of their names in the acknowledgements below), but still they didn’t solve the problem of visualization and ease of use.

Also for the fellow java enthusiasts, there is Weka 3 – a collection of machine learning algorithms for data mining tasks from the Machine Learning Group at University of Waikato.

Processing 1.5.1

Processing-Books, T-Shirts etc.

is an update to the freely available programming environment – (free as in free beer: tasty, fresh, makes your brain spin). This update does not have many new features, but a lot of optimization / bug-fixing under the hood. The greatest thing about Processing is that it creates an environment where it is so much fun again to just code stuff – it’s amazing what it let’s you do after just a few hours of tinkering with it and a few lines of code. And it’s all java underneath, but keeps the depths hidden for the newbies while offering plenty more for the pros to dive into. Officially : “Processing is an open source programming language and environment for people who want to create images, animations, and interactions. Initially developed to serve as a software sketchbook and to teach fundamentals of computer programming within a visual context, Processing also has evolved into a tool for generating finished professional work. Today, there are tens of thousands of students, artists, designers, researchers, and hobbyists who use Processing for learning, prototyping, and production.”

No hype, that pretty much nails it. Of course, I myself am using it for visualisation of proteins and related data. But it’s more than just pretty pictures – the possibilities extend into the “real” world (check out arduino, 3D printing etc.). For example, the fund-raising T-shirts feature an organic structure of an early sketch of the Seed Lamps at n-e-r-v-o-u-s.com. Beyound lamps, jewelry etc. the guys at nervous system created some nice processing applets (3d subdivision surfaces, particle systems, diffusion-limited aggregation) using reaction-diffusion simulations and rendered them using sunflow.

There are quite a few videos of processing-based visulaisations (usually including code) out there demonstrating what can be done with it – think flash for java, just waaay better. Watch this space for more to come! I caught the bug about half a year ago – to me it’s probably one of the best things that happened to promote computer science in a while! If you wanted to learn programming anyway but thought that java was too much object-oriented overhead,  C(#/++/..) too scary and platorm-dependent and SCALA still to esoteric – this is it! Just what turtle-graphics was for Pascal (on the MacII) , this might do the same for java just 25years later.