It looks innocuous sitting on the desk, an Oxford Nanopore MinION, but it can produce a huge data of data from a single sequencing run. Since the nanowire works by inferring which base is in the pore by how much it reduces the flow of ions (and hence current) through the pore, the raw data […]
I’m planning to launch a citizen science project, bashthebug.net, in 2017 which has two distinct ways anyone can help combat antibiotic resistance. I’ve revamped and relaunched what will ultimately become the public-facing project website – please have a look. The first strand is closer to the light of day and will help the international Tuberculosis […]
DOCKER is cool. But what is it? From the DOCKER webpage Docker containers wrap up a piece of software in a complete filesystem that contains everything it needs to run: code, runtime, system tools, system libraries – anything you can install on a server. This guarantees that it will always run the same, regardless of […]
If you want to compile GROMACS to run on a GPU Amazon Web Services EC2 instance, please first read these instructions on how to compile GROMACS on an AMI without CUDA. These instructions then explain how to install the CUDA toolkit and compile GROMACS against it. The first few steps are loosely based on these […]
These are some quick instructions on how to build a more recent version of GCC than is provided by the devel-tools package on the Cent OS based Amazon Linux AMI. (currently GCC 4.8.3) You may, for example, wish to use a more recent version to compile GROMACS – that is my interest. If so, then […]
So we have created an Amazon Machine Image (AMI) with GROMACS installed. In this post I will examine the sort of single core performance you can expect and much this is likely to cost compared to other compute options you might have. Benchmark To test the different types of instances you can deploy our GROMACS […]