Posts Tagged 3D

cubus dilabor est

This beautiful 3D animation from a team of the Stuttgart Media University reminded me of Ceasars’ “alea iacta est“, but since the cube falls apart into smaller pieces here, the line above seemed more appropriate. The video is called “Cubism”, done by Nina Wellstein, Sascha Langer, Felix Schwarz, Mark Haberpursch and Sergej Feininger:

found on Glaserei

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OpenProcessing.org

After writing a couple of sketches in processing, the urge to share it tends to become bigger. Of course processing lets you export a sketch as an application for any architecture$(windows, linux, OS/X). That has the advantage of eventually using more of the power of the local hardware, but not everybody wants to download the full program just to have a sneak-peek preview how it looks like in action. Processing also let’s you generate an applet that can be included in web-pages. In case you are not maintaining your own web-server, OpenProcessing comes in very handy in a couple of aspects.
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Molecular Animations Galore

To continue with examples in communicating “what is it all good for”: the University of British Columbia’s former “iCapture Centre” (now James Hogg Research Centre) has done a great piece on linking Asthma treatment with the underlying genetic and molecular mechanisms. (Here is Part1 and Part2)

The animations were realised by Arkitek Studios and they made a science-demoReel available.

They did some impressive work for nature on RNAi:

This series of three animations was created for Nature Reviews Genetics in 2004, built originally to live on Nature’s site temporarily, perhaps a month or so.
Seven years later, with millions of hits, it has proven to be one of the most popular things Nature has ever had on its site.
Plans are in the works to revisit the piece, since much has been learned about RNAi in the interrim. Look for the new RNAi animation by the end of 2011.

Looking forward to it!
There is also a “Nature Education Scitable“, something on Cadherin,
Stem Cells – “What are they?”, GPCR proteins, and Large Scale Biology (Human Protein Index). Enjoy!

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Relative Size of Things in the Universe

Getting the relative size and distances right is not always straightforward for us – having evolved in mediocristan of middle-earth, going a few orders of magnitude larger or smaller just blows our common sense and spatial awareness to pieces (see the impressive overview of our solar system produced and donated to me by a seven-year old). I never get tired of watching good animations of zooming in and out of the world as we know it. Decades ago, it was the Powers of Ten that gave such a view for the first time – at least it was the first movie of this kind I got exposed to (the book is here).

Hence when I came across the post below on SchockWellenReiter it prompted me to search for related videos – there is a lot of good stuff out there I wish my teachers had available when I went to school! Kantel describes the Planetenweg (planetary pathway?, opened in Sptember 2003) in the honourable old University-Town Göttingen: It represents our Solar system to scale (1:2 Billion) – Two Billion Kilometres in (outer) space corresponding to one Kilometre on the Planetenweg. Planet Earth shrinks to a 6,5 Millimetre ball (approx. a quarter of an inch) while the sun is about 75 metres away and about 70 centimetres big. You have to walk about an hour to get from the sun (close to the central train station) to reach Pluto (at Bismarckturm) … I know, it’s just a dwarf planet now … relatively speaking you are walking faster than light! To reach our next neighbouring star you’d need continue walking for about half a year, about half around the earth.

The video below is based on current data from NASA – It features a sphere denoting the area that the earliest radio-wave emissions from earth (ca. 70+ years ago) have travelled. Enjoy!

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Histone Modification Patterns …

play a predictive role in embryonic cell differentiation – this paper published this week in Science reveals a “functional “prepatternof chromatin states within multipotent progenitors and potential targets to modulate cell fate induction“. An additional discussion is in this article on genomeweb/proteomonitor by Adam Bonislawski.

It fits the picture that not only gene-regulation, cancer- and pluri-potent stem-cells rely on the state-switching machinery revolving around nucleosome/chromatin. Also Frank Holstege’s lab has a recent paper in this field (in MolecularCell – congrats!).

Hence I dug up this visualisation of the nucleosome and its lateral surface I did some time ago and put it up here. Enjoy!

Nucleosome from Michael Lappe on Vimeo.

P.S.: There is a nice expert review on the topic by M.S. Cosgrove “Histone proteomics and the epigenetic regulation of nucleosome mobility“. (PMID:17705705) (Hinted to by Robert Schneider)

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Playing with the building blocks of life

is wonderful – and you don’t need a Ph.D. to experience it and make a contribution. Even kids get to know how to make the molecule-thingy move within minutes, a simple down-to earth explanation of clashes, voids and rubberbands is sufficient – of course you have to avoid all the fancy terms from biophysics that usually impress (or shut up) the audience. To all those who take themselves too seriously as scientists, check out the story on the structure of a Monkey virus protein and their blog. The fold.it tool is available for all major platforms, and I can only recommend it. Great work! Cool for teaching and communicating the molecular basis of life. It’s still called “beta” but looks pretty stable to me. Maybe you can convince other nerds to spend some time on folding proteins rather than smashing trolls to smithereens in WoW- the fun factor is definitely there, and the science as well. Check out the video on nature “FoldIt: Biology for Gamers” which has a link to the full paper and the related News feature. An afterthought to the previous post on crowd-sourcing: Such massive online-games in science have the capacity not only to combine the CPU/GPU power of a vast number of machines, but also to integrate some of the most advanced pattern recognition algorithms on the planet: your brain.

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3D Information Visualization

A wonderful piece of an “energetic” view / visualisation of a network :
Tianamo beta is allegedly available for trying-out at this link.
Google search results never looked that good!
Since this is “beta” – when does it come out for real?
Something like this would be great not only at showing
search results, but also for bibliographies/.pdf-collections (like papers?)

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