Actually the dog is somewhat irrelevant – it’s what comes with it which matters. One of the side-effects of dog ownership is that you get to spend an hour or so a day out walking, which means you have an hour or so with your own thoughts and no distractions. I’m sure everyone has experienced…
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Choosing the best format for raw sequence data
Introduction In the current Illumina pipeline raw sequence data is generated in qseq files, but can optionally be converted to the more standard FastQ format for use with other analysis programs. The FastQ files produced are uncompressed text files and take up a considerable amount of space in our storage system. We’ve therefore been thinking…
Selecting large random integers in Perl
We had a very odd bug in a simulation we were writing recently. We were supposed to be sampling from a large pool of possible data, but were getting a very weird distribution of values. After much debugging we found a most unusual cause. Here is the pop quiz – read through the short script…
Recovered from defacing
Anyone visiting the site in the last couple of days may have found that I appeared to have simultaneously developed a fanatical interest in middle eastern politics, and a very poor taste in music. Whilst it’s very convenient to have a simple to use blogging engine such as WordPress to use, I guess the downside…
How good is ‘good enough’ for research software
There are two linked problems which seem to face me with every piece of software I write for research use: When is the software complete enough to write a paper on it How to manage the versions and project description I think that although similar questions arise within software written for general use, their answers…
Where do you analyse next gen sequence data?
We had an interesting discussion at the Bioinfo-core workshop at ISMB2010. The discussion centred around the best way to handle the logistics of making sequence data available to using a sequencing service. The problem is that the data is so big that even if you have a large central store you run the risk of…
First impressions of iOS4 on new iPod touch
My original first gen iPod touch has been, without doubt, the best gadget I’ve ever purchased. It’s been used daily for almost 3 years now as an MP3 player, email client, TV, photo album, and PDA. However the headphone socket has only played out of one ear for about 6 months, and about a month…
Copying OpenOffice formulas to a whole column
In my entire working life the single biggest increase to my productivity came the day that I found out that double clicking on the little box at the bottom right of a cell containing a formula would copy that formula to the entire column. Prior to that, on a bad day, I could spend half…
Overestimating DWIM in Perl
I hit a bug in a script I was writing this week which reminded me that sometimes you can put too much faith in perl’s ability to ‘do what I mean’ (DWIM). It took me a couple of minutes to see what was going wrong here – see if you do any better. #!/usr/bin/perl use…
Sound Level Monitoring in Java
For a project I’ve been working on I needed what I thought should be fairly easy to make – a simple widget to monitor an input sound level. I’d never worked with the full javax.sound API before, but assumed that there would be ample documentation to do what I needed. Having started on the project…