Posts Tagged Source

Nobel Prize in Technology

The 2012 Millennium Technology Prize (Technology Academy Finland) will be awarded to Linus Torvalds and Dr Shinya Yamanaka.

Linus Torvalds initiated LINUX about 20 years ago (as mentioned previously, see here).


Dr. Yamanaka pioneered work on induced pluripotent stem cells (iPS cells or iPSCs), using a combination of c-MycKlf4Oct-3/4, and Sox2.

As a bioinformatician, I cannot help but point out that ComputerScience and stem-cell research are sharing such a prestigious award. Somewhat a confirmation of the idea that combining the two in a fruitful way is a very good idea, indeed. And in this context I’d like to mention Hans Schöler, whom I had the pleasure to listen to recently. In his excellent work he demonstrated that Oct4 plays a key-role in reprogramming. The structural underpinnings he presented were simply brilliant – see the PDB molecule-of-the-month article on “Oct and Sox Transcription Factors” as a substitute.

(found via heise.de and zdnet.com)

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Democratization of Science

If anything, then it’s the MultipleSequenceAlignment (MSA) problem (in combination with the folding problem) which defines the core of bioinformatics. At least from my perspective, since that’s from where I started out my adventures in the field. Already fold.it successfully demonstrated for protein folding that it is possible to tackle hard problems by crowd-sourcing, a.k.a. Citizen Science. After all, the pattern recognition software installed on the wetware between your ears is highly evolved and can complement pure in-silico calculations. With Phylo researchers from McGill university have taken this approach to the sequence level:

Phylo is a challenging flash game in which every puzzle completed contributes to mapping diseases within human DNA.

Although the call for CitizenScience is not entirely new, it is boosted by such developments over the internet significantly. Who said that science and fun do not go together and can only be done while wearing a labcoat and operating extremely expensive machinery (?) – quite the opposite!

Biochemist Erwin Chargaff advocated a return to science by nature-loving amateurs in the tradition of Descartes, Newton, Leibniz, Buffon, and Darwin — science dominated by “amateurship instead of money-biased technical bureaucrats”.

Now that’s some company to be proud of. And I can’t say I completely disagree, albeit I’d like to think the two are not necessarily mutually exclusive (for-the-love-of-it vs. for-profit). If you’d like to get started, check out the tutorial video below and have fun aligning!

Reference: “Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment” by Alexander Kawrykow, Gary Roumanis, Alfred Kam, Daniel Kwak, Clarence Leung, Chu Wu, Eleyine Zarour, Phylo players, Luis Sarmenta, Mathieu Blanchette and Jérôme Waldispühl (2012) PLoS ONE 7(3): e31362. doi:10.1371/journal.pone.0031362

P.S.: For recent developments on the algorithmic frontier see this one by the Söding group (@LMU Munich, http://toolkit.genzentrum.lmu.de/hhblits/)

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment” by Michael Remmert, Andreas Biegert, Andreas Hauser & Johannes Söding (Nature Methods 9, 173–175 (2012) doi:10.1038/nmeth.1818)
“HHblits is the first iterative method based on the pairwise comparison of profile Hidden Markov Models. In benchmarks it achieves better runtimes than other iterative sequence search methods such as PSI-BLAST or HMMER3 by using a fast prefilter based on profile-profile comparison. Furthermore, HHblits greatly improves upon PSI-BLAST and HMMER3 in terms of sensitivity/selectivity and alignment quality.”  

The entire suite of programs is available for all major OSs.

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deBugging Code


Just recently, I found this REAL bug sitting on the edge of my screen while coding – the (admittedly quite nerdy) irony of it is hard to miss. Rest assured, I ‘guided’ it away from ‘the system’ to the outside as gently as possible, resisting any impulse to to squash it using the keyboard on the spot. You know the rule, “Never touch a running system”, and unfortunately double-clicking and pressing <DEL> didn’t seem to work here.

A more funny (and nerdy) take on debugging code is this video by Atlassian called “Software Bugs” that made my morning:

“All bugs welcome! … create some buzz, … and when the spider gets here, I guess we can start talking web development”

Some more in-depth understanding of the issues involved is provided in this talk by Prof. Stephen Freund on “Stopping the Software Bug Epidemic” – he also touches on the halting problem, memory leaks and parallel code execution.

Although the talk is very informative throughout while presenting the basic issues in an entertaining way, I wonder why he didn’t mention the “Dining Philosophers Problem” – I guess it’s hard to trace deadlocks by automated checkers? In addition, he only refers to the (ancient) waterfall-modell of software engineering. Some comments on how more modern development philosophies (eXtreme programming, agile etc.) fit into the picture would have been nice. Anway, Happy deBugging!

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Watching them watching us

Collusion is a plug-in for FireFox that visualises the sites that track your movements on the web – and then displays the results for you as a directed graph. Each node represents one particular web-site, each edge a “tracking through” relationship. After installation, collusion summarizes the data on the trackers. After a bit of the usual browsing you might be in for a bit of a surprise as you can almost see your digital footprint grow in real-time. No worries, it just displays the data that is gathered by companies on you, so it helps to get a better idea what your rights to electronic self-determination might entail.

Privacy Policy: When you’re using the add-on, we collect sites you visit solely to show you how they’re connected. We don’t keep them and don’t give away the information to anyone except you.

It is quite educational to see what the central nodes are – google of course, as you might expect, is one of them. But ever heard of ScoreCardResearch?

See also the collusion blog for more background info and links to the (open source) code – additional references are lifehacker.com: “Collusion for Firefox Shows You Who’s Tracking You on the Web In Real Time” and (german) heise.de: “Add-On für Firefox visualisiert Webseiten-Tracking” (Permalink)

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Computational Geometry Algorithms Library

Last week CGAL-4.0-beta1 was released – as with most X.0 and beta releases of any kind of sofware, this is not yet intended for use in production. Howevever, previous releases look quite stable.

The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as: computer graphics, scientific visualization, computer aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, mesh generation, numerical methods… CGAL can be used together with Open Source software free of charge.


Also, a Book on “CGAL Arrangements and Their Applications” just became available (Springer).

The list of features packed into the kernels is impressive and too long to be summed up in a few lines – see here for the Package Overview – I am sure you’ll find quite a few items of interest. Especially the spatial sorting functions and matrix searches sound very useful to me. In addition, there is support for 3rd party software such as the Boost Graph Library. So much to check out – here are some tutorialsmanuals and videos on CGAL … For example the dynamic 3D Voronoi demo below.  Have fun!

Thanks for hints to Kasthuri Kannan and Chris Sander.

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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. 😉

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Networks and Presentations: déjà VUE ?

The Visual Understanding Environment (VUE) is an Open Source project based at Tufts University. The software seems quite mature (current release v3.1.1)  and strikes me as a crossover of a graph visualisation/layout and a mind-mapping tool, resulting in a different way of sharing and presenting information – think prezi.

VUE, the Visual Understanding Environment, is an open source concept mapping tool, licensed under the Education Commons License. Although originally developed with a focus on educational needs, VUE has grown to be used by people in many organizations working on engineering, graphic design, creative problem solving, construction, writing, and more. VUE 2 introduced the melding of the map with presentation tools, allowing people to advance from the linear nature of traditional slide paradigms to a more flexible model allowing presenters to walk their maps in dynamic and visually controlled manner.

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