Archive for category Computers & Code

N.O-T/MY-D/E.PA/R.T-ME-N/T. 2.9-C/3

29C3 - 17720

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The 29th Chaos Communication Congress (29C3) was held a couple of weeks ago under the title “Not my department” at the Congress Center in Hamburg, Germany.

Being among thousands of fellow nerds with so much going on was breathtaking. My most lasting impression was to see how many important non-technical aspects like philosophy, law and health were tackled in some of the talks and discussions with a refreshing hacking attitude. Clearly, the scope is expanding well beyond the limits of what is traditionally considered the comfort-zone of us nerds. As there were 3 tracks running in parallel, it was just impossible to attend everything, but fortunately, the video-streams are available on CCC-TV. Some of the talks that got me thinking are Applebaum’s opening keynote, “Hacking Philosophy“, “Best of … Verfassungsschutz“, “Hacking the law“, and “Enemies of the State“. Not to forget the wonderful discussions at the bar later, affectionately called “10-forward“. Hope to be there for the 30C3 again …

imagine the world as it should be – and then: code it up!

Here is where the title comes from: “… once the rockets are up, who cares where they come down? That’s not my department! – says Wernher von Braun” by Tom Lehrer:

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Introductions to Graph Databases and Theory

As said before, I am getting deeper into graph-databases, specifically “neo4J “. The pace of development is breathtaking, it’s hard to keep up with the new versions and amazing features. In preparation of attending a “Cypher Hands On” (Meetup-Graph), I finally got round to updating to the latest 1.8M03 Milestone. By now, there are a couple of nice introductory videos available:

You might want to check out the videoGraphy @ neo4J. I also recommend the following Intro to Graph Databases (on vimeo) which has a nice explanation on what the buzz/whole point is all about plus some real world examples and history:

To deepen our understanding of the graph-theoretic foundations, I came across these books via

Graph Theory and Complex Networks: An Introduction” by Maarten van Steen. It is very interesting to note that this book is also available electronically as a personalised PDF. As the author notes: “When you write a book containing mathematical symbols, thinking big and acting commercially doesn’t seem the right combination. I merely hope to see the material to be used by many students and instructors everywhere and to receive a lot of constructive feedback that will lead to improvements. Acting commercially has never been one of my strong points anyway”.

– Reinhard Diestel: “Graph Theory“.

Working with #neo4j and #cypher I must take care not to: 1. get all addicted; 2. use it as a golden hammer for everything since it’s fun! @pavlobaron

It is fun, indeed. Enjoy!

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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 and

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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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Nobel Prize in Computing

Pearl‘s book on “Causality” has been on my shelf for a while now. I also read it, a few times, but never managed to get through it in one go, cover to cover. Consequently, I haven’t come to grips with all details, implications and equations yet. No reason to worry about my intellectual capabilities, it’s quite fundamental and takes time to sink in. Now Judea Pearl has been awarded the 2011 ACM Turing Award – Congratulations!

The annual Association for Computing Machinery (ACM) A.M. Turing Award, sometimes called the “Nobel Prize in Computing,” recognizes Pearl for his advances in probabilistic and causal reasoning. His work has enabled creation of thinking machines that can cope with uncertainty, making decisions even when answers aren’t black or white. […]
The UCLA computer science professor is widely credited with coining the term “Bayesian Network,” which refers to a statistical model ACM describes as mimicking “the neural activities of the human brain, constantly exchanging messages without benefit of a supervisor.” Bayesian networks have been used to, among other things, analyze biological data for studies of medicine and diseases.

Here is a chance to see him talk for yourself:

“I compute, therefore I understand” – More videos are here on theScienceNetwork.

found via Judea Pearl, a big brain behind artificial intelligence, wins Turing Award. See also on the ACM NEWS “Judea Pearl Wins 2011 ACM Turing Award“.

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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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Drawing Formulas

One of those nifty little tools that just make life easier: WebEquation by VisionObjects.

Just draw your formula, and it returns the corresponding LaTeX or MathML code. For me, it works great with a cheap graphics tablet, feels a bit more cumbersome (but ok) with the mouse – but still waaay better than messing around trying to convince LaTeX to let that darn’ formula say what you really want it to say. As an example, I just did Euler’s identity in a couple of seconds. For all of us who don’t do this on a daily basis 😉

Found via SchockWellenReiter.


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