Archive for May, 2012

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 blog.postmaster.gr:

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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Beyond content searching: Google’s Knowledge Graph

Google started to roll out the Knowledge Graph, intended to be more about things rather than just strings. Delivering and disambiguating related content based on semantic network associations sounds great, if this really is a step forward to move out of the filter-bubble remains to be seen. Overall, it seems to be related to the idea of a conceptual graph, and wikipedia forms a big chunk of the underlying knowledge-base.

Further details:
techcrunch.com “Google Just Got A Whole Lot Smarter, Launches Its Knowledge Graph
Googles official blog “Introducing the Knowledge Graph: things, not strings
lifehacker.com “Google Knowledge Graph Brings Smarter Semantic Results to Your Google Searches
webpronews.com “Knowledge Graph: Google Gets Tight With Wikipedia

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Happy birthday Richard !

Not that he won’t mind it was already yesterday. Since there are a couple of posts related to him on this site there is probably no need re-iterate how inspirational he was and even over 2 decades after his death still is. Just a welcome occasion to point out richard-feynman.net which has a great collection of videos, a photo gallery and quotes like this one on the ignorance of experts:

Science alone of all the subjects contains within itself the lesson of the danger of belief in the infallibility of the greatest teachers in the preceding generation … Learn from science that you must doubt the experts. As a matter of fact, I can also define science another way: Science is the belief in the ignorance of experts…

Let me refer you to this post with a bit more physics in it while leaving you with this scene from the movie “Infinity”, showing Feynman at the tender age of 6 learning a few things about science from his father.

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Weekend Music Video

In case you wondered (like me) who is doing that awesome tune used in the M$-IE-TV-ad: It’s ALEX CLARE with “TOO CLOSE”.

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Engineering Connections in an Invisible World – a Crash Course

For several years I’ve been a big fan of  Top Gear – the guys have been entertaining my inner child. Seen rationally, the petrol-based internal combustion engine is a dead end,  but getting from A to B is hardly the point, or is it? I like the irreverent, playful and fun approach to how things actually work – by taking them apart, blowing them up or whatever else seems suitable – they have an immense imagination in that department. You know, what distinguishes the men from the boys is the size of their toys. In this regard, the top gear presenters are the real grown-ups, thinking big and out of the box. Some of their projects on science and engineering are among my all-time favourites, so I am happy to see Richard “Hamster” Hammond back on the screen again.

First, there’s the recently launched “Crash Course” :  

And then I have to mention his series “Engineering Connections” on the National Geographic Channel where Hammond

looks at how engineers and designers use historic inventions and clues from the natural world in ingenious ways to develop new buildings and machines.

And if you still can take some more, there is some really stunning footage in the “Invisible worlds” –  series (2010). Definitely something to go into my DVD collection, here’s a teaser:

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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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Play more …


The Federation of American Scientists (FAS) Learning Technologies Program (pre-)launched the Science Game Centerto demonstrate to teachers, scientists, museums, and parents the myriad ways games can be used to improve education in math and science“. Next to Phylo and Fold.it (which I mentioned around here before) are several entries listed I haven’t seen yet. It may be due to the movie “Fantastic Voyage” that made a lasting impression on me as a kid that “Immune attack” immediately caught my attention. After all, I’d rather kick some pathogenic butt than blowing up poor aliens in space. Good hunting!

P.S.: Reminds me of this quote by 137th Gebirg on battlestarforum.com

“I may appear unoccupied to you, but at the molecular level, I’m really quite busy.”

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