Skip to content

Update README with workshop and usage information #18

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jimboid merged 1 commit into from
Jan 15, 2026
Merged

Update README with workshop and usage information #18

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
32 changes: 32 additions & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,12 @@
# CCPBioSim Protein Analysis Workshop

[![ci](https://github.com/ccpbiosim/protein-analysis-workshop/actions/workflows/build.yaml/badge.svg?branch=main)](https://github.com/ccpbiosim/protein-analysis-workshop/actions/workflows/build.yaml)
[![latest](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fccpbiosim.github.io%2Fworkshop.json&query=%24.containers.protein-analysis-workshop.latest&labelColor=grey&logo=github&logoColor=white&label=latest&color=purple)](https://github.com/ccpbiosim/protein-analysis-workshop/pkgs/container/protein-analysis-workshop)
[![issues](https://img.shields.io/github/issues/ccpbiosim/protein-analysis-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/protein-analysis-workshop/issues)
[![pr](https://img.shields.io/github/issues-pr/ccpbiosim/protein-analysis-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/protein-analysis-workshop/pulls)

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 introduces the application of MDTraj to the analysis of protein simulation data

It is in two parts:
Expand All @@ -7,3 +16,26 @@ An introduction to the use of MDTraj for the analysis of simulations. The data c

2. EQUILIBRATION
An introduction to a key issue in MD simulation: testing for equilibration, sampling, and convergence. The data here comes from a long simulation of a different protein, chignolin.

## How to Use

This training course is deployed on the [CCPBioSim](www.ccpbiosim.ac.uk) 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/protein-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/protein-analysis-workshop:latest

## Authors

Workshop Content Authors:

- Charlie Laughton

## Contact

Please direct all questions and feedback to [Charlie Laughton](mailto:charles.laughton@nottingham.ac.uk)