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 and data. I’ve been thinking that this is a movement…
Author: Dave Lunt
KCite plugin for WordPress blog referencing
I’ve been trying out the KCite plugin for WordPress. This has been created to make WP a better scientific publishing platform- and so far I’m really impressed. Install the plugin in the usual way, there’s nothing really to set up, just start using it. To add a reference[cite]10.1093/gbe/evr090[/cite] you have to include a shortcode in the…
How many species are there really?
Rod Page at iPhylo draws attention to a new paper in Systematic Biology (Costello et al 2011) estimating the total number of species. They come to a much lower figure than a previous paper (Camilo Mora et al 2011). Rod said something interesting that linked in to my thoughts on species numbers. “The fuss over…
Why can’t Nature just copy and paste?
I just noticed that an old publication of mine has a typo in the title on the Nature website “Animal mitochondrial DMA recombination”, anyone want to guess what the error is? Web of Science has the correct title, Pubmed has the correct title, and it used to be correct on the Nature website, but somehow…
Genomics and ethics
There is a really interesting take on the ethics of human genomics from Dienekes’ Anthropology Blog prompted by the aboriginal genome recently released. I can’t say I disagree with anything. Potential bad ethical outcomes of genetic sampling are very rarely clearly explained and just left hanging in the air as something that must be true….
Calculating intron density
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 size Xbp” is usually all we get. This sort of…
Bio-Linux in a VirtualBox
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 with installations of software packages and wanted to see how…
Dr Bill Jordan
Bill Jordan was an evolutionary biologist at the Institute of Zoology in London who tragically passed away in May this year. He worked in many areas of evolutionary genetics but particularly in those relating to adaptation. He was a first-rate scientist, very sharp, very practical. He was also one of the nicest, most entertaining, most…
The Eighth Day of Creation and the weight of knowledge
There have been several obituaries for Horace Judson recently [1][2], and today Larry Moran in an excellent Sandwalk blog post talked about the lack of knowledge of the history of their field by molecular biologists modern researchers are completely unaware of the history of their field. That’s partly because the work on bacteria and bacteriophage—where…
Manuscript writing with Google Docs
I hope I’m going to submit my PhD student’s first comparative genomics paper very soon. Three of us have written the manuscript collaboratively using Google Docs. GDocs is an online word processor and although I’ve used it quite a bit before, this is the first time I’ve used it to write a manuscript with colleagues….
EvoPhylo 