Category Archives: Software

A Mac OSX journalling error can inhibit the boot disk to be mounted

The screenshot below shows my desperate search why my Macbook wouldn’t boot again (following a cold reset writing a large Photoshop CS5 file for more than 15 minutes).

The verbose boot mode (APPLE+S) showed some error with the journalling system, basically an error as described at the currently non functioning Apple Support Board

jnl: replay_journal: bad block list header @ 0x4bra50 (checksum 0xega0fee1 != 0x927a5993)
jnl: journal_open: Error replaying the journal!
hfs: early jnl init: failed to open/create the journal (retval 0).

Unfortunately nothing helped. Booting from an external disk just showed a normal, error-free HD in disk utility. Continue reading A Mac OSX journalling error can inhibit the boot disk to be mounted


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Optimized SSD under OSX

Having now a SSD in use for more than one year, here are my accumulated tweaks. The first one is Smart Sleep which greatly enhances sleeping/wakening time. Disabling the motion sensor (“sudo pmset -a sms 0”) doesn’t hurt but is isn’t really necessary. Mounting the SSD noatime , however, gives a measurable performance gain. And at the end, I dropped that RAM thingy as it breaks with every system update.


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R cloud computing

A recent article on WPA hacking using the Amzon EC2 cloud computing facility let me wonder whether there couldn’t be more useful projects. For example gene-gene interaction testing would be nice – indeed somebody has already setup a possibility to use R: Robert Grossman, director at the Informatics at the Institute for Genomics and Systems Biology. Great, many thanks!
What’s even better, a

… 60 Genomes dataset can be found here, as part of the public data that Bionimbus makes available to researchers. With the Bionimbus Community Cloud, the data is available via both the commodity Internet, as well as via high performance research networks, such as the National LambdaRail and Internet2 … If you are a member of the Bionimbus Community Cloud, then you don’t need to download the data but can compute over the data directly with Bionimbus. Currently, we are not making the Bionimbus Cloud generally available, but expect to do so beginning in approximately June, 2011.


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For the travelling scientist

I have still dozens of Falk paper maps in my cabinet. With the small Garmin 60 CSX, however, that includes most US and European cities, I don’t need them anymore.
But what about more remote locations where conferences are now so often located? Continue reading For the travelling scientist


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Useful WordPress maintenance scripts


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


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Why I don’t have an iphone (yet)

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)


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OSX 10.6, Macports, GD and finally Circos

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


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Keep secret

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


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The best wordpress logfile tool

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


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Spotlight indexing of Papers keywords

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


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Add thumbnails to web links on the OSX desktop

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


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