Mailund on the Internet

…or maybe I am just not ready to use it there…

Actually, I have been using Linux for more than 10 years and, until I bought a Mac this year, exclusively since 1995.  Generally, I am very comfortable with Linux, but I made a major mistake when I bought my latest office machine about a year ago.

I bought a Dell ’cause I figured that since Dell sells machines with Ubuntu pre-installed (in the US and UK but sadly not in Denmark) the hardware would be supported by Linux.

Not so!

This machine has an ATI Radeon HD graphic card, and Linux support for that is practically non-existing.  ATI has a driver for it that you can install, and with that I managed to get an acceptable — but by no means very good — performance. 2D graphics at least.  3D graphics rarely worked.

I begged Kristian Høgsberg for help.  He is a friend of mine who works at RedHat, making eye candy for Linux. I figured he would have some suggestions.

He suggested I switched from Ubuntu to Fedora, ’cause he wouldn’t know how to help me with a competing product.

I figured he was joking, but still, I switched.

In Fedora, I actually managed to get the ATI driver working.  Not perfectly, but a lot better than I had managed before.

Now, a few days ago, it stopped working.  I’m not sure what happened. I didn’t fiddle around with the setup or any thing, but maybe updated package or something broke the setup.  Break it did, to the point where enabled Compiz meant the screen would just gray out and where disabled Compiz was painfully slow.  Like you wouldn’t imagine.  Moving a window across the screen would take several seconds.

In frustration and  desperation I re-installed Fedora yesterday.  I was hoping I would get it back to the state it was a few days ago.  That didn’t work, but I did manage to delete a week’s work that I hadn’t backed up.  Way to go, Dr. Mailund, way to go!

I caught Høgsberg on Jabber and asked for help again.  He suggested that I buy a nVidea graphics card. That is probably the right choice.

Anyway, I don’t have time to try to fix my Linux.  I need to analyse some data before a meeting in Iceland next week and I’m leaving Friday.

I need Linux for it, though, ’cause I haven’t managed to compile the software I need on my Mac.

I guess I’ll just ssh to the Linux box and work that way.

Ok, I tried my fix to the BiRC webpages, but I am not sure I should have.  After the server process was restarted, all the auto-generated files were gone, and now I don’t know how to get them back.

The good news is that loading the pages will no longer crash your browser.  The gigantic files are the ones that are completely missing now.

The pages without the stylesheets look like crap, though.

If you go to BiRC’s homepage, and I suggest you don’t right now, you will experience an extremely slow load time. If you are lucky, your browser will crash. If you are really lucky, your computer will crash.

We have this problem, you see. The CSS file is 31Mb and the Javascript file is 28Mb.

It seems that every time the page has a hit, a few lines are added to each of these files. Why this happens has been bugging us a little while.

We are using a CMS developed in-house. It’s called Skeletonz and is developed by Amir Salihefendic who was employed as student programmer at BiRC a few years back, where he developed Skeletonz. Generally, it is working fine and we are very satisfied with it, but it is beta and since Amir left BiRC we haven’t had much support on it.

Anyway, back to the mystery of the growing files…

We have suspected the blog plugin for a while.  The lines added to the files concerns the blog, so that makes sense. However, the problem didn’t go away when I disabled the blog, so I didn’t think it was the blog anyway…

Now I think it is again.  I think it was enough to install the blog plugin.  I’ve found a bit of suspicious code I think is causing the problem.  I do not have the access rights to change the code, but I’ll get that and try my fix tomorrow or next week.

It is a bit embarrassing that an informatics group has been unable to have a homepage up and running without problems, but there you go.  I just hope we’ve solved the problem now…

Take a look at this post from Genetic Future.  It concerns the genetic population structure of Europe, and it seems that the genotypes can be used to pretty accurately predict the geography.  Of course I expected a lot of population structure when considering all of Europe, but I am a bit surprised that there is this much structure between, e.g., Swedes and Danes.

I haven’t read the paper refered to yet — I will print it when I get to the office tomorrow — but this is pretty cool.

What does this mean for association mapping, by the way.  Is the HapMap CEU sample based tagSNPs equally good for all Europeans, or what?

Yeah, yeah, I know I have been silent for a while again. There was a little vacation time and then BiRC moved to a new building. I am sitting in my new office now where I’ve finally arranged everything the way I want it (except for the blackboard where I need someone to drill some holes).

My new office is about twice the size of the old one, so now I have room for both my comfy chair and my old sofa. The sofa is from my flat when I lived downtown and I moved it to my office when I moved from my flat to my current house. I haven’t had room for it in my own office for a while, though, so others have had the pleasure of having it. Now it is back with me. Excellent if I feel like taking a nap at work.

From my window I can see the old BiRC building. I don’t know what it will be used for in the future, assuming they do not just tear it down. It is an old building and it is not in a particularly good shape any more.

Sorry about the picture quality, by the way. The pictures were taken by my cell phone and the quality is lousy.