|
1 | 1 | { |
2 | 2 | "containers": { |
3 | 3 | "jupyterhub-base": { |
4 | | - "latest": "2026-02-16" |
| 4 | + "latest": "2026-02-16", |
| 5 | + "name": "CCPBioSim Base Image", |
| 6 | + "category": "infrastructure", |
| 7 | + "shortdesc": "CCPBioSim JupyterHub base container for use in other training workshops.", |
| 8 | + "longdesc": "" |
5 | 9 | }, |
6 | 10 | "structure-validation-uglymol": { |
7 | | - "latest": "2026-02-16" |
| 11 | + "latest": "2026-02-16", |
| 12 | + "name": "Uglymol Image", |
| 13 | + "category": "infrastructure", |
| 14 | + "shortdesc": "Uglymol container for hosted deployment as part of the structure validation workshop.", |
| 15 | + "longdesc": "" |
8 | 16 | }, |
9 | 17 | "structure-validation-workshop": { |
10 | | - "latest": "2026-02-16" |
| 18 | + "latest": "2026-02-16", |
| 19 | + "name": "An Introduction to Structure Validation", |
| 20 | + "category": "setup", |
| 21 | + "shortdesc": "This course will introduce methods to deduce that starting structures for preparing simulations represent high quality starting points.", |
| 22 | + "longdesc": "" |
11 | 23 | }, |
12 | 24 | "basic-statistics-workshop": { |
13 | | - "latest": "2026-02-16" |
| 25 | + "latest": "2026-02-16", |
| 26 | + "name": "Introducing Basic Statistics", |
| 27 | + "category": "analysis", |
| 28 | + "shortdesc": "This course illustrates how basic statistical concepts can be applied to the analysis of biomolecular simlation data", |
| 29 | + "longdesc": "" |
14 | 30 | }, |
15 | 31 | "aiida-lysozyme-workshop": { |
16 | | - "latest": "2026-02-16" |
| 32 | + "latest": "2026-02-16", |
| 33 | + "name": "aiida-gromacs - Lysozyme MD simulation tutorial", |
| 34 | + "category": "setup", |
| 35 | + "shortdesc": "Data provenance tools demonstrated with Justin Lemkul's lysozyme in water simulation tutorial.", |
| 36 | + "longdesc": "" |
17 | 37 | }, |
18 | 38 | "basic-analysis-workshop": { |
19 | | - "latest": "2026-02-16" |
| 39 | + "latest": "2026-02-16", |
| 40 | + "name": "Introducing Basic Analysis", |
| 41 | + "category": "analysis", |
| 42 | + "shortdesc": "In this course we will explore some of the issues in simulation preparation and analysis that can trip up the unwary, and how to avoid them.", |
| 43 | + "longdesc": "" |
20 | 44 | }, |
21 | 45 | "equilibration-workshop": { |
22 | | - "latest": "2026-02-16" |
| 46 | + "latest": "2026-02-16", |
| 47 | + "name": "An Introduction to Equilibration", |
| 48 | + "category": "setup", |
| 49 | + "shortdesc": "This course looks at one of the most common methods for assessing equilibration: the calculation of RMSDs. It may be a common approach, but is it a good one? Maybe not.", |
| 50 | + "longdesc": "" |
23 | 51 | }, |
24 | 52 | "ubiquitin-analysis-workshop": { |
25 | | - "latest": "2026-02-16" |
| 53 | + "latest": "2026-02-16", |
| 54 | + "name": "Introduction to Analysis of Ubiquitin", |
| 55 | + "category": "analysis", |
| 56 | + "shortdesc": "This course illustrates the application of a number of Python-based tools to the analysis of the results from a short (1 nanosecond) simulation of ubiquitin, investigating the question, how similar is the MD trajectory to the crystal and NMR structures?", |
| 57 | + "longdesc": "" |
26 | 58 | }, |
27 | 59 | "clustering-workshop": { |
28 | | - "latest": "2026-02-16" |
| 60 | + "latest": "2026-02-16", |
| 61 | + "name": "An Introduction to Clustering", |
| 62 | + "category": "analysis", |
| 63 | + "shortdesc": "This course illustrates the application of a variety of clustering methods to an MD trajectory, comparing their performance.", |
| 64 | + "longdesc": "" |
29 | 65 | }, |
30 | 66 | "aiida-gpcr-workshop": { |
31 | | - "latest": "2026-02-16" |
| 67 | + "latest": "2026-02-16", |
| 68 | + "name": "aiida-gromacs - GPCR MD simulation tutorial", |
| 69 | + "category": "advanced", |
| 70 | + "shortdesc": "An advanced demonstration showing advanced GPCR workflow with full data provenance collection.", |
| 71 | + "longdesc": "" |
32 | 72 | }, |
33 | 73 | "pca-workshop": { |
34 | | - "latest": "2026-02-16" |
| 74 | + "latest": "2026-02-16", |
| 75 | + "name": "An Introduction to Principle Component Analysis", |
| 76 | + "category": "analysis", |
| 77 | + "shortdesc": "The aim of this course is to illustrate methods we can use to assess convergence and sampling in MD trajectories.", |
| 78 | + "longdesc": "" |
35 | 79 | }, |
36 | 80 | "python-workshop": { |
37 | | - "latest": "2026-02-16" |
| 81 | + "latest": "2026-02-16", |
| 82 | + "name": "An Introduction to Python Programming", |
| 83 | + "category": "coding", |
| 84 | + "shortdesc": "This course will introduce more intermediate features of Python that are useful for biomolecular modellers.", |
| 85 | + "longdesc": "" |
38 | 86 | }, |
39 | 87 | "pdb2pqr-workshop": { |
40 | | - "latest": "2026-02-16" |
| 88 | + "latest": "2026-02-16", |
| 89 | + "name": "An Introduction to PDB2PQR", |
| 90 | + "category": "setup", |
| 91 | + "shortdesc": "This short course illustrates the application of pdb2pqr to the analysis of the tautomeric and ionization states of residues in the structure of the cysteine protease cruzein (PDB code 2oz2) - the results may not be what you would have expected!", |
| 92 | + "longdesc": "" |
41 | 93 | }, |
42 | 94 | "docking-workflow": { |
43 | | - "latest": "2026-02-16" |
| 95 | + "latest": "2026-02-16", |
| 96 | + "name": "Introducing Docking Workflows", |
| 97 | + "category": "advanced", |
| 98 | + "shortdesc": "This course introduces docking tools and workflows.", |
| 99 | + "longdesc": "" |
44 | 100 | }, |
45 | 101 | "qmmm-workshop": { |
46 | | - "latest": "2026-02-16" |
| 102 | + "latest": "2026-02-16", |
| 103 | + "name": "Introducing QM/MM", |
| 104 | + "category": "advanced", |
| 105 | + "shortdesc": "The course will introduce non-specialists to the use of combined quantum mechanics/molecular mechanics (QM/MM) methods for modelling enzyme-catalysed reaction mechanisms.", |
| 106 | + "longdesc": "" |
47 | 107 | }, |
48 | 108 | "mm-gbsa-workshop": { |
49 | | - "latest": "2026-02-16" |
| 109 | + "latest": "2026-02-16", |
| 110 | + "name": "Analysing with MM-GBSA", |
| 111 | + "category": "analysis", |
| 112 | + "shortdesc": "This course walks through the process of perfprming a basic MM-GBSA analysis of a molecular dynamics simulation of a protein-ligand complex to estimate the ligand binding free energy.", |
| 113 | + "longdesc": "" |
50 | 114 | }, |
51 | 115 | "protein-ml-workshop": { |
52 | | - "latest": "2026-02-16" |
| 116 | + "latest": "2026-02-16", |
| 117 | + "name": "Protein Analysis with Machine Learning", |
| 118 | + "category": "analysis", |
| 119 | + "shortdesc": "This course introduces the application of Machine Learning methods (specifically, PCA and clustering) to the analysis of protein simulation data.", |
| 120 | + "longdesc": "" |
53 | 121 | }, |
54 | 122 | "protein-analysis-workshop": { |
55 | | - "latest": "2026-02-16" |
| 123 | + "latest": "2026-02-16", |
| 124 | + "name": "Introduction to the Analysis of Proteins", |
| 125 | + "category": "analysis", |
| 126 | + "shortdesc": "This course introduces the application of MDTraj to the analysis of protein simulation data.", |
| 127 | + "longdesc": "" |
56 | 128 | }, |
57 | 129 | "protein-preparation-workshop": { |
58 | | - "latest": "2026-02-16" |
| 130 | + "latest": "2026-02-16", |
| 131 | + "name": "Preparing Proteins for Simulation", |
| 132 | + "category": "setup", |
| 133 | + "shortdesc": "This course walks through the process of preparing a simple protein system for molecular dynamics simulation using Ambertools.", |
| 134 | + "longdesc": "" |
59 | 135 | }, |
60 | 136 | "dna-workshop": { |
61 | | - "latest": "2026-02-16" |
| 137 | + "latest": "2026-02-16", |
| 138 | + "name": "Running DNA Simulations", |
| 139 | + "category": "simulation", |
| 140 | + "shortdesc": "This course introduces tools for running simulations on DNA systems.", |
| 141 | + "longdesc": "" |
62 | 142 | }, |
63 | 143 | "protein-simulation-workshop": { |
64 | | - "latest": "2026-02-16" |
| 144 | + "latest": "2026-02-16", |
| 145 | + "name": "Running MD Simulations", |
| 146 | + "category": "simulation", |
| 147 | + "shortdesc": "This workshop demonstrates two approaches to running MD simulations on a simple protein system.", |
| 148 | + "longdesc": "" |
65 | 149 | }, |
66 | 150 | "coarse-graining-workshop": { |
67 | | - "latest": "2026-02-16" |
| 151 | + "latest": "2026-02-16", |
| 152 | + "name": "Introducing Coarse-Graining", |
| 153 | + "category": "advanced", |
| 154 | + "shortdesc": "This workshop introduces tools for setup and running coarse-grain simulations.", |
| 155 | + "longdesc": "" |
68 | 156 | }, |
69 | 157 | "openff-workshop": { |
70 | | - "latest": "2026-02-16" |
| 158 | + "latest": "2026-02-16", |
| 159 | + "name": "Introducing OpenForceField Tools", |
| 160 | + "category": "advanced", |
| 161 | + "shortdesc": "This workshop introduces the openforcefield tooling.", |
| 162 | + "longdesc": "" |
71 | 163 | } |
72 | 164 | } |
73 | 165 | } |
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