From e6b256d9e905b90a736d565be1061212a4b3ef18 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Thu, 15 Jan 2026 16:16:58 +0000 Subject: [PATCH 1/2] Revise README for CCPBioSim OpenForcefield Workshop Updated README to reflect new workshop details and resources. --- README.md | 53 +++++++++++++++++++++++++++++++++-------------------- 1 file changed, 33 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 84396c1..62e461d 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,13 @@ -# 2025 CCPBioSim Training Week materials +# CCPBioSim OpenForcefield Workshop -[![CI](https://github.com/openforcefield/ccpbiosim-2025/actions/workflows/ci.yaml/badge.svg)](https://github.com/openforcefield/ccpbiosim-2025/actions/workflows/ci.yaml) +[![ci](https://github.com/ccpbiosim/openff-workshop/actions/workflows/build.yaml/badge.svg?branch=main)](https://github.com/ccpbiosim/openff-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.openff-workshop.latest&labelColor=grey&logo=github&logoColor=white&label=latest&color=purple)](https://github.com/ccpbiosim/openff-workshop/pkgs/container/openff-workshop) +[![issues](https://img.shields.io/github/issues/ccpbiosim/openff-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/openff-workshop/issues) +[![pr](https://img.shields.io/github/issues-pr/ccpbiosim/openff-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/openff-workshop/pulls) -These tutorials were delivered at the 2025 CCPBioSim training week, but are suitable for self-guided learning. +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. -Presenters: - -* Danny Cole -* Finlay Clark - -## Materials +### Materials We recommend you view the materials in the following order: @@ -19,17 +17,8 @@ We recommend you view the materials in the following order: Answers to most exercises are given in the [notebooks_with_solutions directory](notebooks_with_solutions). -## Local installation - -To use these notebooks on your local machine, we recommend using [mamba](https://docs.openforcefield.org/en/latest/install.html#quick-install-guide) to create an environment from the provided YAML file: - -```shell -$ mamba env create --file environment.yaml -$ ... -$ mamba activate openff-env -``` -## More resources +### More resources * Main [OpenFF docs](https://docs.openforcefield.org/en/latest/) * See "Projects" on the left for package-specific documentation @@ -38,8 +27,32 @@ $ mamba activate openff-env * [Discussions](https://github.com/orgs/openforcefield/discussions) - for general usage questions -## Acknowledgements +### Acknowledgements Most of the material for the notebook [Parameterising small molecules with OpenFF](notebooks/small_molecule_parameterisation.ipynb) was adapted from the [2023 CCPBioSim Workshop Open Force Field Sessions](https://github.com/openforcefield/ccpbiosim-2023?) created by Matt Thompson and Jeff Wagner. Most of the material for the notebook [Parameterisation, molecular dynamics, and basic trajectory analysis for a protein-ligand complex](notebooks/protein_ligand_complex_parameterisation_and_md.ipynb) was adapted from the OpenFF [toolkit showcase](https://docs.openforcefield.org/en/latest/examples/openforcefield/openff-toolkit/toolkit_showcase/toolkit_showcase.html) and the [ProLIF Ligand-protein MD tutorial](https://prolif.readthedocs.io/en/latest/notebooks/md-ligand-protein.html#ligand-protein-md). + +## 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/openff-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/openff-workshop:latest + +## Authors + +Workshop Content Authors: + +- Danny Cole +- Finlay Clark + +## Contact + +Please direct all questions and feedback to [Finlay Clark](mailto:charles.laughton@nottingham.ac.uk) From f4502e5e36cb5365d5bf3d9150146e1ecc358785 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Thu, 15 Jan 2026 16:26:01 +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 62e461d..ebacc90 100644 --- a/README.md +++ b/README.md @@ -55,4 +55,4 @@ Workshop Content Authors: ## Contact -Please direct all questions and feedback to [Finlay Clark](mailto:charles.laughton@nottingham.ac.uk) +Please direct all questions and feedback to [Finlay Clark](mailto:finlay.clark@newcastle.ac.uk) or [Danny Cole](mailto:daniel.cole@newcastle.ac.uk)