Honey bee dance roxor :P

Seems that honey bees are capable of so much more than just waggle dancing!



The link they show in the end goes to a site put up by a popular ice-cream manufacturer that is devoted to conserving the honey bees. Nice idea. And I feel even better now doing honey bee research! :)

Never shout at your hard disks...

...you will only slow them down (via Federico Mena-Quintero). Amazing stuff. Funny analogy in regard to leadership principles: Never shout at your staff, you will not make them work faster!

Have your python toolchain in $HOME

In my previous post I explained how to install scipy from source on openSUSE.

What makes it particularly nice is that I can now carry most of my toolchain in my $HOME. I make python include modules from within my $HOME by setting $PYTHONPATH to something like

/home/micha/mypython/lib64/site-packages

. The good thing is that you can install any python package in your $HOME by using the --prefix option to setup.py:

python setup.py install --prefix=$HOME/mypython

For even more python goodness I tell easy_install to put everything there by having a file called .pydistutils.cfg in my $HOME with the contents

[install]
prefix=/home/micha/mypython

So everytime I easy_install a package, it is automatically put into my $HOME directory. That makes it much easier to reinstall or upgrade the system. Since most python-related stuff is now in my $HOME and not in the system, rebuilding my python-toolchain basically consists of installing python and distutils. Isn't that great :)

Update: I learnt from Brandon Rhodes that virtualenv will set up everything for you automatically. Awesome python goodness.

Installing scipy 0.7.0 on openSUSE

I had to rebuild parts of my toolchain because I messed up my OS and needed to reinstall. In the process of searching for nice numpy and scipy packages for openSuSE (which failed), I discovered that now its actually possible to do

easy_install numpy
easy_install scipy

(provided that you have the python-distutils package installed). That's great. But... it doesn't work! At least not on openSUSE. I could convince numpy to install somehow. I don't remember exactly, I think I at least needed to install gfortran, maybe also blas and lapack from the scientificlinux-repository in the build service.

For scipy then it was a little bit more work. It kept complaining that it did not find BLAS and LAPACK, even though I edited numpy's site.cfg file so that it should be aware of the location of the shared libs.

It turned out that to install scipy I had to:

1. Download BLAS sources and unpack them, e.g. to $HOME/Apps/BLAS
   
2. edit make.inc in that directory, changing the FORTRAN line to

   FORTRAN  = gfortran

   
   
3. build BLAS by calling make in the BLAS dir
   
4. DL and unpack LAPACK to $HOME/Apps/lapack-3.2
   
5. edit make.inc.example in that dir, changing the BLASLIB line to

   BLASLIB = $(HOME)/Apps/BLAS/blas$(PLAT).a

   and saving that file as make.inc
   
6. build LAPACK by typing make in the lapack dir.
   
7. Download scipy, unpack it and start the build process:

   python setup.py install

   
   

That takes quite a while. It seems it builds LAPACK and BLAS again, so maybe you don't have to build it first, but I guess you need at least to make the appropriate modifications to the respective make.inc files. Comments on that are welcome.

But most important: it finally worked :)

Update: At least I thought it worked. It didn't :D Problem was that import scipy produced a symbol not found error. Maybe adjusting ldconfig's path could fix this, but I don't have time to look into this. Installed numpy & scipy from the scientificLinux repo (link see above).

Netbeans + python = happy happy

Netbeans is now available with python support as an early access (read: beta) build. Install went smoothly, it just updated my existing netbeans 6.5 install with the python capability. Hassle-free, netbeans-style. Great!

At first glance python support looks great - I can create projects from existing sources, it allows code navigation by function names, and all that other netbeans goodness. During the next few days I'll give it a shot - I'm looking forward to finding out whether it beats Eric4...

Teaching for (no) fun

One of the nice parts about working at university is doing teaching. In my past experience teaching always was very rewarding, so I volunteered to tutor an undergrad course on the Hodgkin-Huxley cell model. I felt it would be a nice opportunity to drop out of the daily sitting-in-front-of-the-computer-the-entire-day routine, And as a side effect, it would revive my knowledge on Hodgkin-Huxley models.

Well, it got me out of my routine, but it wasn't all sunshine. Granted, some students actually were highly motivated, and the course reports they turned in were carefully prepared. It was fun tutoring them. But others just didn't care. Some of their reports stated the name of last year's tutor - suggesting that they didn't even care to change that during copy-and-paste.

Not that I care about plagiarized reports - I think a student at an university should be smart enough to figure out that they cut their own flesh when plagiarizing reports. But they also cheat on those who actually put some effort. And that's unfair. And it leaves a bad feeling for me as a teacher who volunteers out of idealism. Spoiled my fun somehow.

Wordle the antennal lobe!

Ned Batchelder posted the link to Wordle on his blog. What a cool app! It creates word clouds from any piece of text you throw at it. I couldn't resist and had to produce a wordle of my 2007 PNAS paper. Here it is:



How cool is that :)