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…
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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…
Mapping Bisulphite Converted Sequence
I’ve been thinking lately about the best way to construct a mapping pipline for large sequence datasets which have been bisulphite converted. Bisulphite conversion is mostly used to detect DNA methylation, although other uses are also being found. The basic principle is that treating DNA with sodium bisulphite modifies cytosine bases such that when they…
Managing Really Large Data Sets
For a while now I’ve been working with next generation sequencing datasets. Each dataset consists of around 10 million mapped genome positions, and an experiment can consist of 10 or more datasets. When analysing this data memory usage is a major issue. Up until now our approach has been to try to store everything in…
Optimising Java Memory Usage
In the application I’m working on I have to deal with large amounts of data, which means handling tens of millions of java objects. One of the biggest problems we face is keeping the memory usage of the program under control. The main object which accounts for the vast majority of the memory consumption contains…
Exporting SVG from Java
Several programs I’ve written in Java have had an image export componet to them. Up until now the export has always only been as a bitmap image. This is very easy to do using a BufferedImage and an ImageWriter. Given a Component (all AWT or Swing widgets) and a file you can create a PNG…
Broadcom problems under linux
I’ve been trying to install Fedora 9 on a Dell PowerEdge T100 and have been tearing my hair out trying to get the network card to work. The card in question is a Broadcom Netextreme BCM5722 Gigabit Ethernet PCI Express adapter. I’ve used similar Broadcom cards in other machines without any problems, but this time…
Troubleshooting IMAP SSL
I’ve just spent a while trying to troubleshoot my SSL IMAP connection. This is the first time I’ve had to do any diagnostics since switching to an SSL secured mail connection. When my connection stopped working I got only a very non-specific error from OSX mail, and no error at all from Thunderbird (it just…