ccpbiosim.github.io/workshop.json at main · CCPBioSim/ccpbiosim.github.io · GitHub

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{
  "containers": {
    "jupyterhub-base": {
      "latest": "2026-03-02",
      "name": "CCPBioSim Base Image",
      "category": "infrastructure",
      "shortdesc": "CCPBioSim JupyterHub base container for use in other training workshops.",
      "longdesc": ""
    },
    "structure-validation-uglymol": {
      "latest": "2026-03-02",
      "name": "Uglymol Image",
      "category": "infrastructure",
      "shortdesc": "Uglymol container for hosted deployment as part of the structure validation workshop.",
      "longdesc": ""
    },
    "structure-validation-workshop": {
      "latest": "2026-03-02",
      "name": "An Introduction to Structure Validation",
      "category": "setup",
      "shortdesc": "This course will introduce methods to deduce that starting structures for preparing simulations represent high quality starting points.",
      "longdesc": ""
    },
    "basic-statistics-workshop": {
      "latest": "2026-03-02",
      "name": "Introducing Basic Statistics",
      "category": "analysis",
      "shortdesc": "This course illustrates how basic statistical concepts can be applied to the analysis of biomolecular simlation data",
      "longdesc": ""
    },
    "aiida-lysozyme-workshop": {
      "latest": "2026-03-02",
      "name": "aiida-gromacs - Lysozyme MD simulation tutorial",
      "category": "setup",
      "shortdesc": "Data provenance tools demonstrated with Justin Lemkul's lysozyme in water simulation tutorial.",
      "longdesc": ""
    },
    "basic-analysis-workshop": {
      "latest": "2026-03-02",
      "name": "Introducing Basic Analysis",
      "category": "analysis",
      "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.",
      "longdesc": ""
    },
    "equilibration-workshop": {
      "latest": "2026-03-02",
      "name": "An Introduction to Equilibration",
      "category": "setup",
      "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.",
      "longdesc": ""
    },
    "ubiquitin-analysis-workshop": {
      "latest": "2026-03-02",
      "name": "Introduction to Analysis of Ubiquitin",
      "category": "analysis",
      "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?",
      "longdesc": ""
    },
    "clustering-workshop": {
      "latest": "2026-03-02",
      "name": "An Introduction to Clustering",
      "category": "analysis",
      "shortdesc": "This course illustrates the application of a variety of clustering methods to an MD trajectory, comparing their performance.",
      "longdesc": ""
    },
    "aiida-gpcr-workshop": {
      "latest": "2026-03-02",
      "name": "aiida-gromacs - GPCR MD simulation tutorial",
      "category": "advanced",
      "shortdesc": "An advanced demonstration showing advanced GPCR workflow with full data provenance collection.",
      "longdesc": ""
    },
    "pca-workshop": {
      "latest": "2026-03-02",
      "name": "An Introduction to Principle Component Analysis",
      "category": "analysis",
      "shortdesc": "The aim of this course is to illustrate methods we can use to assess convergence and sampling in MD trajectories.",
      "longdesc": ""
    },
    "python-workshop": {
      "latest": "2026-03-02",
      "name": "An Introduction to Python Programming",
      "category": "coding",
      "shortdesc": "This course will introduce more intermediate features of Python that are useful for biomolecular modellers.",
      "longdesc": ""
    },
    "pdb2pqr-workshop": {
      "latest": "2026-03-02",
      "name": "An Introduction to PDB2PQR",
      "category": "setup",
      "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!",
      "longdesc": ""
    },
    "docking-workflow": {
      "latest": "2026-03-02",
      "name": "Introducing Docking Workflows",
      "category": "advanced",
      "shortdesc": "This course introduces docking tools and workflows.",
      "longdesc": ""
    },
    "qmmm-workshop": {
      "latest": "2026-03-02",
      "name": "Introducing QM/MM",
      "category": "advanced",
      "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.",
      "longdesc": ""
    },
    "mm-gbsa-workshop": {
      "latest": "2026-03-02",
      "name": "Analysing with MM-GBSA",
      "category": "analysis",
      "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.",
      "longdesc": ""
    },
    "protein-ml-workshop": {
      "latest": "2026-03-02",
      "name": "Protein Analysis with Machine Learning",
      "category": "analysis",
      "shortdesc": "This course introduces the application of Machine Learning methods (specifically, PCA and clustering) to the analysis of protein simulation data.",
      "longdesc": ""
    },
    "protein-analysis-workshop": {
      "latest": "2026-03-02",
      "name": "Introduction to the Analysis of Proteins",
      "category": "analysis",
      "shortdesc": "This course introduces the application of MDTraj to the analysis of protein simulation data.",
      "longdesc": ""
    },
    "protein-preparation-workshop": {
      "latest": "2026-03-02",
      "name": "Preparing Proteins for Simulation",
      "category": "setup",
      "shortdesc": "This course walks through the process of preparing a simple protein system for molecular dynamics simulation using Ambertools.",
      "longdesc": ""
    },
    "dna-workshop": {
      "latest": "2026-03-02",
      "name": "Running DNA Simulations",
      "category": "simulation",
      "shortdesc": "This course introduces tools for running simulations on DNA systems.",
      "longdesc": ""
    },
    "protein-simulation-workshop": {
      "latest": "2026-03-02",
      "name": "Running MD Simulations",
      "category": "simulation",
      "shortdesc": "This workshop demonstrates two approaches to running MD simulations on a simple protein system.",
      "longdesc": ""
    },
    "coarse-graining-workshop": {
      "latest": "2026-03-02",
      "name": "Introducing Coarse-Graining",
      "category": "advanced",
      "shortdesc": "This workshop introduces tools for setup and running coarse-grain simulations.",
      "longdesc": ""
    },
    "openff-workshop": {
      "latest": "2026-03-02",
      "name": "Introducing OpenForceField Tools",
      "category": "advanced",
      "shortdesc": "This workshop introduces the openforcefield tooling.",
      "longdesc": ""
    }
  }
}