We are still largely missing the benefits of reproducibility in phylogenetics. I think that this makes our lives unnecessarily difficult and makes us particularly poorly prepared to confront modern data-rich phylogenetics. In this first post “Why” I want to talk about why we need reproducible phylogenetics. Then, in part two, “What“, I’m going to talk…
Author: Dave Lunt
A question about my use of ELNs
I received an email from Alex Lang and he asked about my current use of Electronic Lab Notebooks Hi Dave, I’m a physics graduate student who just started using a WordPress based ELN. I really found your thoughts on ELNs helpful, especially: http://www.davelunt.net/evophylo/2009/03/wordpress-as-eln/ https://speakerdeck.com/davelunt/electronic-lab-notebooks-for-ug-students Since someday I want to be a PI, I had some…
Jobs at EvoHull
We have two jobs open at the moment in the Hull Evolutionary Genetics group @EvoHull. Both are, I think, quite exciting; not your standard postdoc positions and the group is looking forward to getting two new colleagues. 1-Year Lectureship in Evolutionary Biology This is maternity cover for Dr Domino Joyce. You will be covering teaching in…
Pride before a (data) fall
I’m pretty proud of some parts of my workflow: electronic lab notebook, reproducibility, open data files, (semi-obsessive) automated data backups etc etc. But pride often comes before a fall. I had a bad experience this week where I thought I had lost some important phylogenetic data files (I found them eventually), and I’m writing this…
Professor Godfrey M Hewitt
10 JANUARY 1940 – 18 FEBRUARY 2013 I was asked to write a piece about my PhD supervisor Godfrey Hewitt for the UK Genetics Society magazine, and have reproduced a version here. I’d been putting off writing about Godfrey since he died in February, making excuses to myself, so a big thank you to the…
Steve Jones should publish more
In today’s Guardian newspaper geneticist Steve Jones has a short column replying to a 7 year old child who had asked “Will humans evolve into a new species?“. Jones is known in the UK as the media’s favourite geneticist and evolutionary biologist; he is a frequent guest on media shows and contributor in print media….
How can we ensure the persistence of analysis software?
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 situation and action that is needed right now. Casey Bergman…
Rewriting the invention of DNA barcoding
Today I got an email from David E. Schindel, who is the Executive Secretary of the Consortium for the Barcode of Life, announcing Google funding for DNA barcoding. The project aims to create a reference library of endangered species COI sequences so that DNA barcoding can be used as a tool against wildlife trafficking. Good for…
Printing out GenBank- Nucleotide Sequences 1984
I have in front of me a copy of the book “Nucleotide sequences 1984 Part 1 A compilation from the GenBankTM and EMBL data libraries” published by IRL Press. Wow, what a surreal book for anyone used to dealing with sequence databases today. The idea that DNA sequences would be printed out, in an actual book…
Open social reference management
Mendeley, Zotero, Papers, Citeulike, and others are all playing the social reference management game. You store your PDFs in their excellent programmes and then you can start to be social; form groups, browse subject categories, subscribe to other people’s reference lists. My question is this: is the current implementation the best way forward for us, the…
EvoPhylo 