I have finally got around to migrating fully to mrgraeme.com. I hope it doesn’t inconvenience anyone. Please let me know if you have any issues!

  Predicted 0 Predicted 1 Actual 0 True Negative False Positive Actual 1 False Negative True Positive   Accuracy Error Rate ( True Negative + True Positive ) / Number of observations ( False Negative + False Positive ) / Number of Observations Sensitivity Specificity True Positive / ( True Positive + False Negative )…

I am currently working to remove some of the thornier dependencies for BAYSIC (source) and though we have just about managed to replace VCF merge (which has been especially ill behaved for us) we have decided that for now R2jags is still our best bet for Gibbs sampling. I know some people have a bad…

Download the latest / required version of BWA: http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.12.tar.bz2/download Unzip the downloaded file and navigate to the resulting directory: tar -xvf bwa-0.7.12.tar.bz2 cd bwa-0.7.12 BWA doesn’t come with a ./configure file so we can just run make Which should compile everything nicely and result in a executable bwa binary file in the bwa-0.7.12 directory.  Once…

Having spent some time trying to grasp the underlying concept of the Greedy Motif Search problem in chapter 3 of Bioinformatics Algorithms (Part 1) I hoped to cement my understanding and perhaps even make life a little easier for others by attempting to explain the algorithm step by step below. I will try to provide…

Hi soon-to-be Git fans! This guide is for people who kind of know what Git is but perhaps haven’t had much experience in using it. The first thing to do is to install Git if you haven’t already. Everything you need to do that is over at http://git-scm.com/. If you are installing on Windows make sure…

After so much time studying for MIT6.00X and running through Rosalind problems I was rather frustrated to find the first exercise in An Introduction to Bioinformatics Algorithms below a bit tricky… Design an algorithm that performs only 3n/2 comparisons to find the smallest and largest numbers in a list As a linear search would end up performing…

My meatiest lingering life regret has been that I spent most of my Artificial Intelligence major at the student union pub… My second most meaty regret has been that programming lectures were the worst casualty of my determination to drink rather than learn. Well, they say that life is all about second chances (do people…

I realised today that I have never created a Pascal Triangle generator! So instead of packing or cleaning or painting or what not I decided to create a generator with as few lines of JavaScript as I could manage. Time well spent!

I put this little infographic (admittedly more graphic than info) together last week. All hand (mouse?) crafted and definitely one of the projects I have worked on this year!