Last month I was invited to give a talk on using alchemical free energy methods to predict antimicrobial resistance at a workshop in Göttingen organised by the Max Planck Institute for Biophysical Chemistry on behalf of BioExcel. You can read more about the meeting, which I hope will become a biennial event, here.
The M. tuberculosis genome is pretty small, only 4.4 million nucleotides, so storing all that as plaintext means each genome is 4.2MB, but when you have tens of thousands of genomes it starts to add up, particularly as I want to keep my data tree on my workstation so I can view the images produced […]
Last week on Thursday and Friday I helped run a Software Carpentry workshop in the Department of Experimental Psychology at the University of Oxford.
Short for “Genbank Mutation Locator”. A simple Python3 package that if you pass it a mutation it will give you the location in the specified genbank file. > gemucator-run.py –mutation rpoB_S450L rpoB_S450L: 761153 t 761154 c 761155 g (H37rV.gbk for M. tuberculosis is loaded by default). Or you can go the other way > gemucator-run.py –location […]
Whenever a paper involving sequencing the genome of bacteria (or other species for that matter), the researcher is obliged to deposit the (usually short reads) in either the European Nucleotide Archive (ENA) and the Short Read Archive (SRA) along with some metadata. Sounds good, but there has been a flaw until recently; whilst one could […]
Setting up my own computing cluster with a batch queuing system and then using it run large numbers of molecular dynamics simulations was one of the more satisfying things I have done professionally. The compute nodes were Apple Xserves from 2008 and 2009. Myself and Ben Hall won the first seven of these nodes from […]