PerlBrew DBD::mysql – Configure failed

Quick post on a issue that I had trying to install DBD::mysql in my PerlBrew installation on Natty-Ubuntu. PerlBrew (PB) is AWESOME – it gives you your own little universe of perl, completely installed in user space, so you have no need of sudo privlidges. Say your sysadmin doggedly refuses to update beyond 5.8 to …


Making Maths Look Good On A Blog

I set this blog up a little while ago, but have taken ages with getting going and actually writing articles. Why? Well a big factor was that I wanted to have a blog that contained maths – but I just couldn’t find any easy way of embedding maths in my blog that both looked good …


Parsing a Newick Tree Using Perl Regex

A newick tree is a way of representing a tree, with branch lengths and internal node names, as a single string. An example is: (A:0.1,B:0.2,(C:0.3,D:0.4):0.5); Which would correspond to the tree below (notice how the braces show the groupings of nodes and the colons act as delimiters for showing branch length):   These come up ALOT in computational biology, …


All my code is now on github

I have a comment that I’d like to share on the nature of reality: git and github are awesome All of my code is (or shortly will be) hosted by github at: I hope that it helps someone else with their research/work.