Archive for February, 2012

Dear Elsevier Employees, With Love, From @FakeElsevier.

Came across this via the satirical twitter-stream http://twitter.com/#!/FakeElsevier – in part the argument is very much along the lines on CargoCult Science I wrote last year (i.e. https://cistronic.wordpress.com/2011/05/19/free-science-no-more-cargo-cult/)

Admittedly, this is my first attempt at reblogging … let’s see how this works out.

P.S.: See the comments for additional info …

The Real Fake Elsevier

An Open Letter.

A little background

As anyone who is reading this probably already knows, the publishing giant Elsevier has recently placed itself at the center of a shitstorm of animosity from the research community, thanks in part to its vocal (and financial) support of the Research Works Act (RWA). Currently, the National Institutes of Health mandate that the research products they fund with tax dollars must be made freely available to the public; the RWA would make such mandates illegal, enabling Elsevier to keep research papers resulting from taxpayer-funded research behind paywalls for as long as they like. There’s some douchey attempted subterfuge in the language of the bill about not locking up the research results themselves, but make no mistake: research papers are our output as researchers, and they are what makes up the scientific literature. While manipulating the legislative process for financial gain would be galling by itself…

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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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Science: 2011 Visualization Challenge

Separation of a Cell, Andrew Noske et al. (Illustration - People's Choice)

An article describing the 2011 International Science and Engineering Visualization Challenge just appeared in Science 3 February 2012 (Vol. 335 no. 6068 p. 525, DOI: 10.1126/science.335.6068.525). Access to all materials in this section is FREE (like in free beer), especially the web-gallery of the corresponding special issue available as a slideshow is definitely worth a visit.

Each year, Science Magazine and the National Science Foundation host the International Science and Engineering Visualization Challenge. The 2011 Challenge received over 200 submissions in five categories, which were evaluated based on visual impact, effective communication of a scientific idea, and overall originality. Visualizations with the most votes from the public received the People’s Choice award.

Among the Informational Posters & Graphics I like “The Cosmic Web“, and all the videos are just awesome.
Congrats to FoldIT for making 1st Place in the “Interactive Games”-Category and thanks to Sathyapriya Rajagopal for the link!

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Weekend music video

Five people singing and playing one single guitar –

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Goodbye to hairballs?

You probably have seen the hairballs resulting from a force-directed layout of complex biological networks. What do they tell you? Well, that the networks are rather complex. But for much more detailed analysis the classical visualizations are actually quite useless. The hiveplot  is an attempt to provide

“A scalable, computationally fast, and straight-forward network visualization method that makes possible visual interpretation of network structure and evolution.”

A laudable goal, if it works in practice for you and your data – check it out. In addition there is an R package available for creating hive plots in 2D and 3D called HiveR.

Also see Krzywinski M, Birol I, Jones S, Marra M (2011). Hive Plots — Rational Approach to Visualizing Networks. Briefings in Bioinformatics (doi: 10.1093/bib/bbr069).

Thanks to Lucy Colwell for the hint!

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