Topics › Real Science

Proteins that look like enzymes but aren't

This essay is taken from the introduction to my thesis, which is pretty much the only part of my thesis I was pleased with. It described way it's not always easy to assign a function to a protein and was used as the basis for my first paper Moonlighting enzymes in parasitic protozoa.

MergeAlign

I'm very excited that my paper (cowritten with Steve Kelly) on MergeAlign has finally come out in BMC Bioinformatics. We managed to time things well, so the website we've created - mergealign.com - is also up and fully functional.

Project:

Python Bioinformatics Tools

Various tools I've written for myself in Python to help with simple bioinformatics tasks.

Removing background from an AVI using ImageJ

I've recently been taking a lot videos of swimming cells, with the aim of calculating their velocity. In each video there is inevitably some background dirt or stuck cells, which can hinder the macro I use to automatically track cells. To deal with this problem I've written a very simple ImageJ macro (ImageJ is an excellent, free, open source image processing program) to remove static objects from an AVI or stack of images, which has proved surprisingly effective.

pH, pKa, pI and protein charge

What is acidity?

Most people know that pH is a measure of acidity, but what is acidity? Well, the Brønsted-Lowry theory states that an acid is a chemical that donates a proton (H+), while a base is a chemical that accepts a proton. The Lewis theory defines acids as chemicals that accept electrons, which is often, but not always, the same thing. For our purposes, acids are chemicals that can donate a proton, while bases (or alkaline substances) are chemicals that accept a proton.