From 4ac1712a0fbc2bebfa28cf3c8e0824d9a499d2a7 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Thu, 15 Jan 2026 16:23:21 +0000 Subject: [PATCH 1/2] Revise README for CCPBioSim Clustering Workshop Updated the README to reflect the new workshop title, added usage instructions, and included author and contact information. --- README.md | 33 +++++++++++++++++++++++++++++++-- 1 file changed, 31 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 54fce83..e9fe14e 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,11 @@ -### Introduction to coarse graining: 2025 CCPBioSim Training Week -Authors: Robert Clark, Iain Peter Shand Smith +# CCPBioSim Clustering Workshop + +[![ci](https://github.com/ccpbiosim/coarse-graining-workshop/actions/workflows/build.yaml/badge.svg?branch=main)](https://github.com/ccpbiosim/coarse-graining-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.coarse-graining-workshop.latest&labelColor=grey&logo=github&logoColor=white&label=latest&color=purple)](https://github.com/ccpbiosim/coarse-graining-workshop/pkgs/container/coarse-graining-workshop) +[![issues](https://img.shields.io/github/issues/ccpbiosim/coarse-graining-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/coarse-graining-workshop/issues) +[![pr](https://img.shields.io/github/issues-pr/ccpbiosim/coarse-graining-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/coarse-graining-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. Here we present a practical introduction to the construction and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit. @@ -21,3 +27,26 @@ We acknowledge the work published by the `Vanni lab` which inspired the topic of Li D., Rocha-Roa C., Schilling M.A., Vanni S.\ https://www.pnas.org/doi/10.1073/pnas.2319476121 +## 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/coarse-graining-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/coarse-graining-workshop:latest + +## Authors + +Workshop Content Authors: + +- Robert Clark +- Iain Peter Shand Smith + +## Contact + +Please direct all questions and feedback to [Robert Clark](mailto:robert.clark@magd.ox.ac.uk) or [Iain Peter Shand Smith](mailto:iain.smith@bioch.ox.ac.uk) From 1a0330071d41510bf4b0303e18c8d4d970523a8c Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Thu, 15 Jan 2026 16:38:23 +0000 Subject: [PATCH 2/2] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e9fe14e..ada11d0 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# CCPBioSim Clustering Workshop +# CCPBioSim Coarse-Graining Workshop [![ci](https://github.com/ccpbiosim/coarse-graining-workshop/actions/workflows/build.yaml/badge.svg?branch=main)](https://github.com/ccpbiosim/coarse-graining-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.coarse-graining-workshop.latest&labelColor=grey&logo=github&logoColor=white&label=latest&color=purple)](https://github.com/ccpbiosim/coarse-graining-workshop/pkgs/container/coarse-graining-workshop)