From 0eaef1a48890914cc20875dcf25a740934558256 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Thu, 15 Jan 2026 16:04:25 +0000 Subject: [PATCH] Update README with workshop and usage information Added workshop details, usage instructions, and author information. --- README.md | 36 ++++++++++++++++++++++++++++++++++-- 1 file changed, 34 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8c9a36b..2ac93f7 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,13 @@ -Though Python is a very popular and powerful environment for Biomolecular Simulation, -many important and well-established tools require working from the command line in a terminal window. So it's an advantage to be familiar and comfortable with both ways of working. +# CCPBioSim Protein Simulation Workshop + +[![ci](https://github.com/ccpbiosim/protein-simulation-workshop/actions/workflows/build.yaml/badge.svg?branch=main)](https://github.com/ccpbiosim/protein-simulation-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-simulation-workshop.latest&labelColor=grey&logo=github&logoColor=white&label=latest&color=purple)](https://github.com/ccpbiosim/protein-simulation-workshop/pkgs/container/protein-simulation-workshop) +[![issues](https://img.shields.io/github/issues/ccpbiosim/protein-simulation-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/protein-simulation-workshop/issues) +[![pr](https://img.shields.io/github/issues-pr/ccpbiosim/protein-simulation-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/protein-simulation-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. + +Though Python is a very popular and powerful environment for Biomolecular Simulation, many important and well-established tools require working from the command line in a terminal window. So it's an advantage to be familiar and comfortable with both ways of working. This workshop demonstrates two approaches to running MD simulations on a simple protein system: @@ -7,3 +15,27 @@ This workshop demonstrates two approaches to running MD simulations on a simple 2. In Python, via a Jupter Notebook, using OpenMM The focus is on the preliminary simulations that are required to relax and equiliobrate an initially-built system, so that later "production" simulations have the best chance of being stable and reliable. + + +## 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-simulation-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-simulation-workshop:latest + +## Authors + +Workshop Content Authors: + +- Charlie Laughton + +## Contact + +Please direct all questions and feedback to [Charlie Laughton](mailto:charles.laughton@nottingham.ac.uk)