Bioinformatics paper published

So I had my last postdoc work published in the eponymous journal Bioinformatics. The advance access version is available here:

http://bioinformatics.oxfordjournals.org/content/early/2010/10/04/bioinformatics.btq557.abstract

TURNIP is a detection algorithm for finding small-scale variation in hard-to-assemble tandem repeat DNA, written in Perl. Learn more by reading the paper, or visiting the TURNIP site for documentation. The sources will be released very shortly!

I found my blog again!

After much time away (OK I forgot I had a blog. Then I forgot my login) I'm back!

I'm sure you're all agog by my veritable bloggurection by now so here's an update to bring you down to planet b0ggler.

Married @ an awesome place to an awesome woman !
New job @ The Genome Analysis Centre !
Band stuff @ End Soteria !

Lots of coding still underway. Still doing stuffs with the Fluxion data integration framework but mainly focussed on the integration layer now. Continuing to build MISO, our new open-source lab information management system (LIMS) for next generation sequencing platforms, e.g. Illumina, SOLiD, 454.

Catch up with me on IRC - fr0ggler @ irc.freenode.org ##java

Disabling the K810i web browser button

Goddamnit if I don't get annoyed with the stupid web button on the Sony Ericsson K810i. Every time I take my phone out of my pocket, it's magically unlocked itself and happily sits on the internet due to the fucking dumb web button on the left hand side of the front of the phone.

There's no way to change the functions of these buttons, and you can't disable the button itself, so I thought a cunning way would be to make an internet profile that points to nowhere. So, the phone would just say it isn't able to connect using the profile, and when I do want to use the internet (very rarely I might add), I can just select one of the working GPRS profiles.

So, under the Connectivity Settings menu, go to Internet Settings, then Internet Profiles. Create a new profile, named anything you like, and then it'll ask you which Data account you wish to use for the profile. Make another blank data account with no APN, Username, Password etc settings. Use this dummy account for your dummy profile.

Woot! No more internet going off in your pocket! And you can always simply change your internet profile back when you do want to use the net.

It's new! Kinda.

Not long to go on the ComparaGRID project, but loads left to do with Pussycat.

Most stuff works as it should, but a load of refactoring will need to be done once we start getting some real results out from the publishers and run through Matt's Runcible rules processing engine. Looking forward to it.

Also looking forward to band practice tonight - stuff seems to be going well with Messrs Chim, fr0g, Dibs and Barquois. Just need a vocalist, and a DiMarzio D-Activator pickup for my Ibanez. Christmas is coming. Goose is getting fat. Go on, have some more cholesterol. And some burgers. You big fatty.

Spoke too soon

OK the machine in question to be upgraded from RH9 to FC was getting far too many segfaults for my liking, so I downloaded the first FC5 iso and booted up memtest86. Turns out one of the 512MB sticks is TOTALLY screwed. I left the tester for about 4 minutes, and it found cumulatively 67000 errors, approximately. Took the stick out, but by this time, I had already nuked the root directory so it's back to the start I go.

So, after much swearing, I tried the FC5 netinstall from CD 1. Needless to say, what should have been an easy job turned out to be a day long nightmare. Trying to grab headers and packages from CD1 and a nice quick Swedish FC repo proved to be too much for the box and just hung each time it got to "Starting installation...". I Alt+F'ed to the debug terminals to find db4 errors with the rpm DB. I nuked the /var/lib/rpm/__db.001 .002 and .003 files and moved the Packages file - the errors went, but the hangs didn't go away.

I gave up.

I'm getting the FC5 DVD iso as we speak. Fucking thing.

Upgrading Red Hat 9 to Fedora Core

I'm currently doing upgrading Redhat 9 to Fedora Core on my work PC due to problems with multi-processor machines outlined in Sun's Java JDK 1.5 release notes.

I'm getting Tomcat hangs and intermittent JVM segfaults so decided it's time to get shot of the aging RH9 install on our dual-P4 server.

The process should be quite simple via the YUM tool, as per these instructions, using a hand-crafted /etc/yum.conf like the one below. It was quite a task finding repositories with available FC1 packages, but I managed to use the following repos to good effect:


# Yum config file from http://www.xades.com/proj/fedora_repos.html
# Put this file at /etc/yum.conf

[main]
cachedir=/var/cache/yum
debuglevel=2
logfile=/var/log/yum.log
pkgpolicy=newest
distroverpkg=fedora-release
tolerant=1
exactarch=1

[base]
name=Fedora Core $releasever - $basearch - Base
baseurl=ftp://ftp2.newnet.co.uk/pub/fedora/linux/core/$releasever/$basearch/os/

[DAG repo]
name = Fedora Core $releasever - $basearch - DAG repo
baseurl=http://apt.sw.be/fedora/$releasever/en/$basearch/dag/

[livna-stable]
name=Livna 3rd party packages with questionable (in USA) licenses -- use at your own risk
baseurl=http://rpm.livna.org/fedora/$releasever/$basearch/yum/stable


After a quick yum update as root, the main problems existed between RH9 packages that need libcom_err.so.3 (part of kr5-libs) and FC1 versions which don't. The DAG repo took care of packages like subversion and neon, but I was still left with a niggling postgres dependency.


package postgresql-libs needs libcom_err.so.3 (not provided)
package postgresql needs libcom_err.so.3 (not provided)
package postgresql-server needs libcom_err.so.3 (not provided)


I was also left with these little monkeys which were easily resolved by removing (rpm -e package_name) arts, redhat-config-securitylevel and all Mono packages left over from an install I never used.


conflict between xmms and arts
package redhat-config-securitylevel needs lokkit (not provided)
package mono-winforms needs mono(System.Web) >= 1.0.5000.0 (not provided)


So, I removed xmms. lokkit needs redhat-config-securitylevel which needs firstboot, so I just removed all these three as FC has no need for them anyway.

All went pretty smoothly after removing these troublesome packages, so now I have a working FC1 install from RH9! Now to upgrade to FC5 ;)