I have just read Sean Eddy’s thought provoking blog post on the problems with how biology is handling high throughput sequencing which you should definitely read. One of his themes is that bioinformatics is going to be a key part of the 21st century biologists toolkit, and that biologists doing sequencing experiments should be able to tinker…
This post is about reproducing analysis from a paper, the first step in this is obviously get the data. In this case, the data is from the Sanger and the primary I’m interested in Salmonella Typhimurium ST313, a potentially invasive strain that is possibly in the process of genome reduction leading to human host restriction.…
I had two experiences recently that I’m sure many other people who use twitter have also had. I was reading about the poisson distribution and there was a great set of lecture notes from a Prof at Oxford University (which are on the first page of google results for ‘poisson distribution’). However, there seems to have…
So, I’m supposed to be writing my speech for my brothers wedding which is a week today (EDIT: which went very well, thanks for asking ;-), mazel tov James and Morgan), but I thought it would help me get in the zone to write a quick blog post. Hopefully I will remember not to put…
TL;DR HelixIO is a slick platform for telling you what is in your fastq sample – very useful for microbiologists! Will be interesting to see how it stacks up against KmerID in a larger number of samples. Interesting ycombinator thread HelixIO have recently launched a public beta of their intriguing bioinformatics platform for ‘fast, portable…
I think some biologists have a bit of a blind spot for bioinformatics when it comes to critical thinking. There may be a bit of a ‘well, the computer says this, therefore it is true’ attitude. I think that any biologist who is interacting with bioinformatics/NGS results should take the following steps: 1. Take a…
Tomorrow I’m going to Westminster Kingsway College in central London to talk to 11-18 year olds about careers in science, technology engineering and maths (STEM). The organisers have given us some questions the kids might ask and I thought that working through a few on here would help me get my thoughts together. I’m not…
This post is by Lauren. Two weeks in Michigan by a lake in the spring time – bliss! PLUS I got to test out my bioinformatics skills and learn all the areas where I am severely lacking, this was really driven home to me when on the first day we were asked to do a…
Biologists often want to see annotated genomes so they can start digging into the genome using tools like Mauve and Artemis. First off though, I think it is really important to provide the ‘whole-y genome’ disclaimer (h/t Neil Perry). Before letting the biologist loose on the genome it is vital that they really meditate…
I got a PHE fellowship to come and visit Bill Hanage at the Harvard School of Public Health. While I was going to rely on my English accent to convince everyone I’m intelligent, half the people in the group are English so I thought I better do some work. One of the English expats is…
Bits and Bugs 