Crowd-sourcing killer outbreaks: Nice video from the BBSRC and Arran Frood
The BBSRC have done a nice job making a short video about the E. coli O104:H4 outbreak crowd-sourcing project, featuring little old me as well as the far more telegenic Lisa Crossman. Check it out, it’s got some spooky music too. Also please check out the OpenAshDieBack crowd-sourcing project currently ongoing, coordinated by the chaps [...]
A chat with Oxford Nanopore’s Clive Brown at AGBT 2013
Don’t judge me, reader, because I’d skipped a session at AGBT to go and have a swim in the sea. A man can only spend so much time in dimly-lit, low-ceilinged hotel conference rooms, popping low-sugar sweets, before the will to live ebbs away. On returning to the conference, passing the bar I spotted a [...]
Loman’s law of bioinformatics
Loman’s law of bioinformatics states: If you haven’t found at least one serious bug in the bioinformatics pipeline you are re-using then you don’t yet understand it. Loman’s second law of pipelines: By the time you’ve got someone elses pipeline working to your satisfaction you could have written your own.
Generating MLST profiles from short-read data
There are now several available options if you want to call MLST profiles from whole-genome data. DTU MLST Server The web server at the Center for Genomic Epidemiology at the Danish Technical University is probably the easiest option, with the advantage that it will accept both raw read files and assemblies. It worked well when [...]
Getting Windows 7 running on KVM as a guest OS (Ubuntu LTS 12.04)
There are surprisingly few resources on this on teh intarwebs, so just some notes for my future self and anyone else attempting it. If you are wondering why I want to run a Windows 7 virtual machine – it’s because we need a server to run the MiSeq reporter and RTA on, in order to [...]
All the Tweets from #MMGC 2012
Rapid Next-Generation-Sequencing Conference for Public Health and Clinical Microbiology was held in Münster last week. The title is pretty self-explanatory. It is probably the first meeting since last summer’s E. coli outbreak in Germany to allow epidemiologists, microbiologists and genomicists to get together and discuss the impact the rapid release of genome data had on [...]
Oxford Nanopore megaton announcement: “Why do you need a machine?” – exclusive interview for this blog!
Sometimes this genome blogging lark really pays off. Yesterday was one of those days as I got a sneak preview of the big announcement at AGBT, and 20 minutes to speak with Oxford Nanopore’s Dan Turner (Director of Applications), Clive Brown (Chief Technical Officer) and Zoe McDougall (Director of Comms). The downside of course was [...]
2011: Review of a Remarkable Year
2011 has been a remarkable year for me, during which I have travelled widely, met lots of interesting people, recruited substantial grant funding and had a paper published in the journal with the highest impact factor of them all! So, at the risk of producing one of those cheesy round-Robin letters that get stuffed in [...]