Category Archives: Software

Mail me!

Maybe you discovered also this nifty little arrow that appears in OS X Snow Leopard Mail indicating that a date is being recognized (and can be moved to ical) or an address (ready for transfer into the address book). Continue reading Mail me!


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Please vote for my Nobel question

At the Lindau Nobel site we can submit questions to Nobel prize winners. Most of them are trivial or even boring – basically how to make a career or what rank did you have in your university studentship. My proposal to ask there: “Is another information layer on top of the known DNA sequence?” You may want vote for my question, thanks!

One of the best questions so far is “Many people consider the peer-review system broken. If you share that opinion, do you have a solution?” by Clay Barnard.

Roy Glauber, Nobel Laureate in Physics 2005: The current system is pretty poor. So now it’s not a question of spending a lot of money, as it can be resolved very easily without. Good papers last and bad papers don’t. Individuals should rate the papers, although this may not need to be done in an official way.
Sir John Walker, Nobel Laureate in Chemistry, 1997: The peer review system does have problems, but it is the best we have got and I am very much opposed to replacing it with a numerical assessment system. It is a lousy way of assessing people and the pressure to change this system comes from science bureaucrats. This is because it is scientsists making decisions about scientists’ work and the bureaucrats don’t like that; they want to have control.
Jean-Marie Lehn, Nobel Laureate in Chemistry, 1987: That’s an interesting question! I have been interested in it for a very long time. I think we need to have a control otherwise things get in the literature that should not be there …


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Optimized data security under Snow Leopard

Filevault is too much of a good thing but slowing down your system and making Time Machine backups difficult if not impossible. No security is also no option, so I thought about creating a sparse image for just a few selected datasets, like mail, calendar, passwords and adressbook. Why should I encrypt 120 Gig when only 8 Gig should be encrypted? The sparsebundle is mounting automatically using a password from the keychain.
I found it, however, difficult to create the correct links that replace the original files.
A Mac OS X hint fortunately explains, how to do that Continue reading Optimized data security under Snow Leopard


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The most significant improvement in Snow Leopard

(at least for scientists) is the possibility to annotate PDFs. Sorry, the screenshot originates from one the most stupid papers that I read over the past years but it nicely shows Continue reading The most significant improvement in Snow Leopard


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Biotorrents

A great idea – published now at PLoS ONE today and live at www.biotorrents.net– is a significant step ahead.

The transfer of scientific data has emerged as a significant challenge, as datasets continue to grow in size and demand as open access sharing increases. Current methods for file transfer do not scale well for large files and can cause long transfer times. In this study, we present BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology.

Just install a BitTorrent client, read the basics at Wikipedia, and convince your computing department Continue reading Biotorrents


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Per aspera ad astra

My MacBook Air suddenly died after 3 days of inactivity. The reasons was probably an unattended maintenance job that filled up the 80 GB HD. At least the system became unresponsive while transfering some pictures from a camera to a picture harddisk. And after a hard reset, it let not boot me anymore. This is when the nightmare started…

An already ordered 128 GB SSD did not fit the special requirements of the 1st generation MBA (that need an 1.8” ZIF 4 PATA drive with <5mm height). There seems to be only one product on market by Photofast. Unfortunately a 128 GB HD was not available for the next 4 weeks, while the 256 GB comes at an excessive price tag Continue reading Per aspera ad astra


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Change location

Here is another tech tip to overcome a frequent task – resetting printers and mailers when moving a Macbook around the world: Location X is a perfect solution with a built in autolocate function (depending on airport network! which is superior to IP detection)

Unfortunately Continue reading Change location


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Tear Down the Walls

What happens when looking at that video?

The neuroanatomy view this week in Nature

we predict[…] a macroscopic signal visible to functional magnetic resonance imaging (fMRI) in humans. We then looked for this signal as participants explored a virtual reality environment, mimicking the rats’ foraging task: fMRI activation and adaptation showing a speed-modulated six-fold rotational symmetry in running direction. The signal was found in a network of entorhinal/subicular, posterior and medial parietal, lateral temporal and medial prefrontal areas. Continue reading Tear Down the Walls


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Human language, DNA language?

A new paper in PLoS ONE argues that human languages may adapt like biological organisms. By doing a large-scale analysis of over 2,000 of the world’s languages the authors find striking relationships between the demographic properties of a language—such as its population and global spread—and the grammatical complexity of those languages. Languages with the most speakers (like English) were found to have far simpler grammars than languages spoken by few people and in circumscribed regions. This reminds me to bottlenecks in population history (and founder effects for certain DNA variants) while the authors describe this phenomenon as “Linguistic Niche”. A Hardy Weinberg Equilibrium of declension types?


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PLINK: Bug or feature?

I am struggling now for 4 weeks with some unusual behaviour in PLINK that gives me different results with a trait of the alternate phenotype files either by calling that trait directly

plink –file mydata –tdt –pheno pheno2.txt –mpheno 1

or from a loop over all traits

plink –file mydata –tdt –pheno pheno2.txt –all-pheno

It seems that I am working with different numbers at both occasions – click to enlarge the log Continue reading PLINK: Bug or feature?


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