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 is a hands-on exercise to (a) setup a DNA + ligand simulation in explicit solvent; (b) run molecular dynamics using AMBER MD engine and (c) Visualise the trajectory using a viewer.

The workshop illustrates:

1. The use of jupyter-notebook (https://jupyter.org/)
2. The use of Python HTMD (https://software.acellera.com/docs/latest/htmd/index.html)
3. The use of Amber simulation (www.ambermd.org) and Ambertools
4. The use of nglviewer (www.nglviewer.org)
5. The use of Python MDtraj module (www.mdtraj.org)

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/dna-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/dna-workshop:latest

Workshop Content Authors:

• Shozeb Haider

Please direct all questions and feedback to Shozeb Haider