End of a year and time for some maintenance work.
And yes, I found a nice plugin to convert all useless pages to posts (sorry, there is no download page here anymore, it’s all in the blog hierarchy).
It would be also nice to check my 3056 links over the past 4 years and it looks good, what the link checker says Continue reading Useful WordPress maintenance scripts
Just recently I read an interesting blog entry of another internet veteran. I am reprinting here the main argument
The iPhone vision of the mobile Internet's future omits controversy, sex, and freedom, but includes strict limits on who can know what and who can say what. It's a sterile Disney-fied walled garden surrounded by sharp-toothed lawyers. The people who create the apps serve at the landlord's pleasure and fear his anger. Continue reading Why I don’t have an iphone (yet)
I need live circos plotting for an upcoming seminar next year.
After installing the most recent xcode, a new macports and a fresh GD library, I issued on the command prompt
sudo port selfupdate
sudo port install gd2
which perl
sudo perl -MCPAN -e shell
cpan> install MD5
cpan> install YAML
cpan> install CPAN
cpan> reload cpan
cpan> install Clone
cpan> install GD
cpan> install GD::Polyline Continue reading OSX 10.6, Macports, GD and finally Circos
There is a new Edge Special Event about the Hillis’s question “WHO GETS TO KEEP SECRETS?”
The question of secrecy in the information age is clearly a deep social (and mathematical) problem, and well worth paying attention to.
When does my right to privacy trump your need for security?; Should a democratic government be allowed to practice secret diplomacy? Would we rather live in a world with guaranteed privacy or a world in which there are no secrets? If the answer is somewhere in between, how do we draw the line?
With all the wikileaks hype over the last year, the Edge essay is la perfect supplement to our last paper about anonymity in genetics – check out BMC Ethics “Caught you: Threats to confidentiality due to the public release of large-scale genetic data sets“.
What we didn’t mention in this paper are more complicated statistics like stochastic record linkage – more on that in RJournal 2/2010, p.61 ff
After using many different plugins for the analysis of the server log, I finally reverted to analog. I am updating first the local logs using the “Superflexible Synchronizer” before starting a highly configured analog analysis. A few really important options (on the Mac!) are: Continue reading The best wordpress logfile tool
So far, spotlight indexing of Papers’ keywords is not possible (while being planned for a future release according to an email that I received today from one author). In the meantime, here is a workaround.
1. Export the whole Papers database as tmp.csv
Continue reading Spotlight indexing of Papers keywords
Here comes another mac tip as it is always annoying to move a link on the desktop but loose its associated favicon. Fortunately there is a small program that monitors the desktop (or any other directory) by launchctl and restores the icon. Checkout etWeblocThumb
I tried out everything but only one trick worked. Continue reading R timeout with read.table() and large datafiles
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!
There are certainly a zillion ways how to do create a nice background for your Mac. Here is my favorite method of a weather forecast, an individual calendar and the most recent emails. I created just three geeklets and loaded them in Geektool. Continue reading A living desktop for Snow Leopard
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 …
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
(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
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