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1 | 1 | # CCPBioSim PCA Workshop |
2 | 2 |
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3 | | -[](https://github.com/ccpbiosim/pca-workshop/actions/workflows/build.yaml) |
| 3 | +[](https://github.com/ccpbiosim/pca-workshop/actions/workflows/build.yaml) |
| 4 | +[](https://github.com/ccpbiosim/pca-workshop/pkgs/container/pca-workshop) |
| 5 | +[](https://github.com/CCPBioSim/pca-workshop/issues) |
| 6 | +[](https://github.com/CCPBioSim/pca-workshop/pulls) |
| 7 | + |
| 8 | +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. |
4 | 9 |
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5 | 10 | The aim of the workshop is to illustrate methods we can use to assess convergence and sampling in MD trajectories. You will compare and contrast the most basic and widely-used method to do this - RMSD analysis - with the use of more sophisticated approaches based on Principal Component Analysis (PCA). |
6 | 11 |
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7 | 12 | You will apply the approaches to two common scenarios: firstly the comparison of the dynamics of a protein the presence and absence of a bound ligand, and secondly the evaluation of sampling and convergence in an ensemble of independent, replicate, MD trajectories of a protein. |
8 | 13 |
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9 | | -## Docker |
| 14 | +## How to Use |
| 15 | + |
| 16 | +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. |
10 | 17 |
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11 | | -This container is derived from the CCPBioSim JupyterHub image. This container |
12 | | -adds the necessary software packages and notebook content to form a deployable |
13 | | -course container. The source content for this course can be found at |
14 | | -https://github.com/CCPBioSim/pca-workshop |
| 18 | +Pull the container from our repository:: |
15 | 19 |
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16 | | -## How to Use |
| 20 | + docker pull ghcr.io/ccpbiosim/pca-workshop:latest |
17 | 21 |
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18 | 22 | In our containers we are using the JupyterHub default port 8888, so you should |
19 | 23 | forward this port when deploying locally:: |
20 | 24 |
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21 | 25 | docker run -p 8888:8888 ghcr.io/ccpbiosim/pca-workshop:latest |
22 | 26 |
|
| 27 | +## Authors |
| 28 | + |
| 29 | +Workshop Content Authors: |
| 30 | + |
| 31 | +- Charlie Laughton |
| 32 | + |
23 | 33 | ## Contact |
24 | 34 |
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25 | | -Please direct all comments and enquiries to [Charlie Laughton](mailto:charles.laughton@nottingham.ac.uk) |
| 35 | +Please direct all questions and feedback to [Charlie Laughton](mailto:charles.laughton@nottingham.ac.uk) |
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