I've been thinking about sustainable and accessible archiving of bioinformatics software, I'm pretty scandalized at the current state of affairs, and had a bit of a complain about it before. I thought I'd post some links to other people's ideas and talk a bit about the...
I've been reading a lot recently about reproducible research (RR) in bioinformatics on several blogs, and Google+ and Twitter. The idea is that it is important that someone is easily able to reproduce* your results (and even figures) from your publication using your provided code...
Moss, Stephen P., Domino A. Joyce, Stuart Humphries, Katherine J. Tindall and David H. Lunt (2011) Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage. Genome Biology and Evolution doi: 10.1093/gbe/evr090, (PDF) We have developed a bioinformatics pipeline for the comparative evolutionary...
I have a project going at the moment to examine changes in intron diversity, size and location in animal genomes. I am always a bit frustrated with the way introns are treated in many genome characterisation papers- "the genome contained Y introns with mean intron...
For those of you who haven't come across it before Bio-Linux is an operating system set up for bioinformatics with a huge number of programs pre-installed. It can be obtained (for free) from the NERC Environmental Bioinformatics Centre. I've spent quite a while recently messing...
I'm not a very competent perl programmer. Even writing the word programmer here makes me slightly embarrassed. I do carry out frequent sequence conversions and manipulations with perl scripts I've put together though. Sometimes when I need to run a script many times I've found...
In order to really get information out of building phylogenetic trees (especially large ones) some thought has to be given to how to annotate the tips (OTUs).The two programs that seem to do this in a powerful way are ARB and Treedyn. I also want...
