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.


HGT work Wins ISMB2011 Outstanding Poster Award

This is a piece of SHAMELESS self-promotion! I was lucky enough to win the Outstanding Poster Award for my work on horizontal gene transfer at ISMB2011. With over 2000 delagates attending and 800 posters, this was a really great honour. Since this website is both a blog and an archive of bits and pieces to …

Del rate

RECOMB 2011 Poster

F1000 is a great way to extend the lifespan of a poster following a conference. This was my poster submission for RECOMB 2011 in Vancouver. I was at stand 84 presenting “Horizontal Gene Transfer Of Protein Domain Architectures” by Adam Sardar & Dr Julian Gough.


Morphogenesis Undergrad Masters Project

I just thought that it might be an idea to pop my undergrad final-year project up online. This was the project that eventually led me to join the Bistol Centre for Complexity Sciences, spark my interest in mechanisms that provide biological form and focus on mathematical/computational biology. It was therefore a pretty important time in …

Photonic Butterfly

Photonics Undergrad Research

My-first-research project was in Toronto, a very formative time for me as a scientist. I was in the lab of Prof. Geof Ozin, a British ex-pat materials scientist. I loved it and really thought that I was going to become a solid state chemist! How things change. Anyway, my project was on biochemically tuneable photonic …