A couple of pictures

I've had some recent requests for pictures of my dog Delia, a puli from Notadog.ca kennels. When the weather was nice, last week, we went down to the beach to enjoy some sun, and took a few pictures:



And, while I'm posting pictures, this was the weather we had yesterday. March comes in like a lamb, out like a lion.

Hardy Heron, Ubuntu 8.04 beta

So I took the bait. I can't refuse Beta operating systems. I've always enjoyed living on the bleeding edge when it comes to new and shiny OSes, so I upgraded my laptop just to see what would happen.

Well, no surprise, I broke a few things, though surprisingly, it's a pretty small list. Going from Gutsy Gibbon to Hardy Heron on my Vostro 1000 was very smooth, and required very little effort to get it up and running again, for the most part.

Compiz (3d graphics): Well, no surprise, It was somewhat of a hack to get it going on my laptop, originally, but the only thing that broke during the upgrade was a weird error about gnome-settings-daemon not being able to start. The fix:

sudo apt-get remove xserver-xgl

Unfortunately, I'd tried someone else's fix of blowing away all of the .gconf, .gconf2, etc settings in my home directory, which obviously didn't help, but now has me reconfiguring all of my settings... oh well. Just use the line above, and save yourself some of the pain.

However, removing xserver-xgl will probably kill your ability to run Compiz, and you may need to turn composite on in your xorg.conf file (/etc/X11/xorg.conf). That can be done by finding the lines:

Section "Extensions"
    Option "Composite" "0"
EndSection

and changing the "0" to "1". Tada, Compiz works again!

Wireless: This one was interesting: there's a new driver for the wireless card, so it tries to install that over what you've already got going. The new driver is much better than the old, so its a good thing, but you still need the (not-open-source) firmware from broadcom. Installing it couldn't be easier.

Follow the first 3 lines here to uninstall ndiswrapper, if you had it running before. (You don't want the new driver running at the same time as the old: this may mean you might want to take the out any lines saying ndiswrapper or bwcml43, or similar from /etc/modules.)

Follow the instructions here, to install the b43 driver firmware, although my simplified version would be:

sudo apt-get install b43-fwcutter
wget http://downloads.openwrt.org/sources/broadcom-wl-4.80.53.0.tar.bz2
tar xjf broadcom-wl-4.80.53.0.tar.bz2
cd broadcom-wl-4.80.53.0/kmod
b43-fwcutter -w /lib/firmware wl_apsta.o

You'll notice I've skipped a few steps compared to what's on the linked page. "b43-fwcutter" can be installed through apt-get, so there's no point in building it yourself, and /lib/firmware is the right place to put the firmware in Ubuntu, so you don't need to be fancy about exporting it and then using a shell variable. And that did it for me.

You may also need to go to System->Administration->Hardware Drivers to tell Ubuntu to use the b43 driver. After that, my FN+F2 key works again, and I was able to connect to my wireless network.

All is good again with my laptop.

Chip-Seq on a laptop.

Every once in a while, I get an interesting email or comment from someone, which is worthy of a blog post. I woke up this morning to a comment left on my last post:

What kind of computing infrastructure do you need to be able to handle chipSEQ datasets? I'm guessing my standard IBM T60 laptop is not going to do the trick - but what does?

So yes, I do check my email when I get up... but that's not the point. Moving along...

The simple answer is, your laptop probably can't run a chip-Seq data set with the currently available programs... but it's probably not far off. My laptop has 2Gb of RAM (after tossing two new 1Gb sticks in last week), and a dual core AMD, running at 2GHz. Ironically, it's not far from what we do use to run FindPeaks: A quadcore 2.2GHz opteron with 8Gb of RAM.

Of course, FindPeaks doesn't take up the full resources of the machine. (Though I've seen it take up to 12CPUs on one of our fancier servers.) Generally, I only allocate 4Gb of RAM to the process, which should be more than enough for several millions or tens of millions of reads. The reason it takes so much ram? Because I don't drop any of the information being held that's contained in the Eland file, and because I need to retain all of the reads in memory to do a sort.

What does it need? Generally, FindPeaks only needs the start, end and direction of each read to do the basics, however, I don't throw away any of the other information collected, in case we want to use it later. If I did that, or if I pre-sorted the reads, I could probably drop the memory requirements down by an order of magnitude or more. (No one's asked me to do this, yet, however.) Is there anyone out there who needs a laptop-runnable version of FindPeaks?

This is somewhat timely, though. For the last few days I've been playing with a companion piece of software for FindPeaks which generates UCSC-compatible BED tracks from Eland data where I've adopted a minimalist approach. It takes about the same amount of time, and runs in under 300m of RAM. That, clearly, should run on anyone's laptop.

Catching up....

I can't believe it's been nearly a month since my last post! I feel like I've been neglecting this a bit more than I should, but I'll try to rectify that as best I can.

For an indication of how busy I've been, I sat down to update my resume yesterday, and ended up adding 3 papers (all in submission) and two posters. That just about doubles what was in there previously in the papers section.

Anyhow, Next-generation sequencing doesn't stand still, so I thought I'd outline some of the things I want to talk about in my next posts, and set up a few pointers to other resources:

1. SeqAnswers. This aptly named forum has been around for a few months now, but has recently become more popular, and a great forum for discussing relevant Next-gen technology and sequencing methods. I'm especially happy to see the automated posts triggered by new literature on the subject, which are a great resource for those of us who are busy and forget to check for new publications ourselves.

2. There's one forum in particular that's of great interest: Benchmarking different aligners. This appears to be a well done comparison (if lightweight) that may be a good focus for other people who are interested in comparing aligners, and discussing it in a wider forum.

3. For people interested in ChIP-Seq, or Chromatin immunoprecipitation and massively parallel sequencing, I've finally gotten around to posting FindPeaks 3.1 on the web. I'd consider this release (3.1.3) an alpha release. I'd love to get more people contributing by using this application and telling me what could be improved on it, or what enhancements they'd like to see. I'm always happy to discuss new features, and can probably add most of them in with a relatively quick turn around time.

4. For people interested in assessing the quality of the whole transcriptome shotgun sequencing (WTSS), I'm about to break out a tool that should fit that purpose. If anyone is interested in giving suggestions on ways they'd like to see quality tests performed, I'd be more than happy to code those into my applications. (And yes, if you contribute to the tool, I will provide you a copy of the tool to use. Collaborations, etc, can be discussed, as well.)

5. A quick question, of which I'll post more in the future. Has anyone here managed to get Exonerate 2.0 to work in client/server mode on two separate machines?

6. I'll also post a little more about this in the future: building environments, ant and java. Why are people still doing large projects in perl?

7. One last thing I wanted to mention. I was going to write more on this topic, but eh... I'll let slashdot do it for me: The more you drink, the less you publish. Well, So much for keeping a bottle of tequila under the desk. Now I know what to get the competition for x-mas, though...

Cheers!