Posts Tagged Open

Weekend Science Videos: Views from and into the (night) sky above us

A message from space to our blue marble:

And here is the executive summary: “Our Story in 1 Minute” (somewhat reminiscent of the BigBangTheory Intro Sequence) by melodysheep

The following footage taken from the International Space Station left me speechless anyway: “View from the ISS at Night” by  (fullscreen view is a must)

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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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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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Free Ivy-League Education

 After I mentioned theScienceNetwork in the previous post and you might already be aware of sites such as SciVee.tv, labtube.tv and iTunes U it’s time to share some recent links in the area of online-courses:

First, with a biological focus, there is iBioSeminars accompanied by iBioMagazine – let me just highlight this talk by David Baltimore.

On the computational side, there is udacity which was started by former Stanford professor and Google fellow Sebastian Thrun. He developed a vision for “University 2.0” under the motto of “democratizing higher education”. After having experienced that he could reach out to more people in a better way by a single online course than he could have by traditional teaching (even in huuuge overcrowded lecture halls) during the next couple of years he just couldn’t go back to the olden ways. He really has a point in dumping his professorship I heartily agree with, and that’s an understatement. I highly recommend to check out his talk at DLD (hosted by the gorgeous Maria Furtwängler), here is a teaser-trailer for the CS101-class “Building a Search Engine”:

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(You might want to check out this previous post on the online courses at Stanford)


To round things up, at the moment there is a free introductory course on Machine Learning “Learning from Data” ongoing at Caltech by Professor Yaser Abu-Mostafa covering basic theory, algorithms, and applications. Registration is still possible, the previous lectures are available here.

Video et studio, ergo sum.

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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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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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Europe’s science cloud: Helix Nebula

… a consortium of leading IT providers and three of Europe’s biggest research centres (CERNEMBL and ESA) announced a partnership to launch a European cloud computing platform. ‘Helix Nebula ‐ the Science Cloud’, will support the massive IT requirements of European scientists, and become available to governmental organisations and industry after an initial pilot phase.
The partnership is working to establish a sustainable European cloud computing infrastructure, supported by industrial partners, which will provide stable computing capacities and services that elastically meet demand.

Building an efficient scientific cloud infrastructure in europe is a good thing, considering the onslaught of data from genomics, high-energy physics and sattelites. But I somewhat can’t shake off the uneasy feeling that the big-science flag-ship projects don’t leave any room for grassroots developments anymore, i.e. movements like the WWW when it took off in the mid-nineties. Along these lines, I’d rather (or at least equivalently) see the LinkedOpenData (as advocated by Tim Berners-Lee for several years) agressively being pushed forward and funded appropriately, the pay-offs are hard to (over-)estimate. But anyway, here are some links to make up your own mind:

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