This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
This workshop illustrates the application of a number of Python-based tools to the analysis of the results from a short (1 nanosecond) simulation of ubiquitin, investigating the question "how similar is the MD trajectory to the crystal and NMR structures?"
The workshop illustrates:
- The use of the Python MDTraj module (see http://www.mdtraj.org)
- The use of the Python matplotlib module for plotting (see http://www.matplotlib.org)
- The use of the Python MDPlus module for Principal Component Analysis (see http://bitbucket.org/claughton/mdplus)
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/ubiquitin-analysis-workshop:latest
In our containers we are using the JupyterHub default port 8888, so you should forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/ubiquitin-analysis-workshop:latest
Workshop Content Authors:
- Charlie Laughton
Please direct all questions and feedback to Charlie Laughton