Analysis using MDAnalysis

computational-chemistry-analysis-md-simulations/advanced-workflow

Author(s)
Chris Barnett
Version
1
Last updated
Mar 7, 2022
License
MIT
Tags
computational-chemistry

Features
Tutorial
Analysis of molecular dynamics simulations
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00029
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nDCD input"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nPDB input"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["RDF Analysis"];
  0 -->|output| 2;
  1 -->|output| 2;
  ab90456f-d7ae-4fb1-ba2f-978a59791acc["Output\nRDF Analysis plot"];
  2 --> ab90456f-d7ae-4fb1-ba2f-978a59791acc;
  style ab90456f-d7ae-4fb1-ba2f-978a59791acc stroke:#2c3143,stroke-width:4px;
  1ee2fe4a-0e50-4a4f-828e-3b60d75120e7["Output\nRDF Analysis raw data"];
  2 --> 1ee2fe4a-0e50-4a4f-828e-3b60d75120e7;
  style 1ee2fe4a-0e50-4a4f-828e-3b60d75120e7 stroke:#2c3143,stroke-width:4px;
  3["Cosine Content"];
  0 -->|output| 3;
  1 -->|output| 3;
  5ca6c423-961b-4a55-a821-794a0d311e41["Output\nCosine Content raw data"];
  3 --> 5ca6c423-961b-4a55-a821-794a0d311e41;
  style 5ca6c423-961b-4a55-a821-794a0d311e41 stroke:#2c3143,stroke-width:4px;
  7854cbf9-187f-4117-b494-73a5a404d06f["Output\nCosine Content plot"];
  3 --> 7854cbf9-187f-4117-b494-73a5a404d06f;
  style 7854cbf9-187f-4117-b494-73a5a404d06f stroke:#2c3143,stroke-width:4px;
  4["Ramachandran Plots"];
  0 -->|output| 4;
  1 -->|output| 4;
  aa7afa97-8be6-4e6b-ad2c-5715f3c10362["Output\nRamachandran Plot"];
  4 --> aa7afa97-8be6-4e6b-ad2c-5715f3c10362;
  style aa7afa97-8be6-4e6b-ad2c-5715f3c10362 stroke:#2c3143,stroke-width:4px;
  178f112a-eb0b-4299-aff5-69efd9ffb52b["Output\nRamachandran Plot raw data"];
  4 --> 178f112a-eb0b-4299-aff5-69efd9ffb52b;
  style 178f112a-eb0b-4299-aff5-69efd9ffb52b stroke:#2c3143,stroke-width:4px;
  5["Distance Analysis"];
  0 -->|output| 5;
  1 -->|output| 5;
  eac670fb-f01e-49cd-a103-828a15149f48["Output\nDistance Analysis raw data"];
  5 --> eac670fb-f01e-49cd-a103-828a15149f48;
  style eac670fb-f01e-49cd-a103-828a15149f48 stroke:#2c3143,stroke-width:4px;
  6605884d-7bfa-4f43-bbc6-2352256d2bc7["Output\nDistance Analysis plot"];
  5 --> 6605884d-7bfa-4f43-bbc6-2352256d2bc7;
  style 6605884d-7bfa-4f43-bbc6-2352256d2bc7 stroke:#2c3143,stroke-width:4px;
  6["Dihedral Analysis"];
  0 -->|output| 6;
  1 -->|output| 6;
  755dbb99-3e3e-425b-a4b2-e375df6e39b4["Output\nDihedral Analysis plot"];
  6 --> 755dbb99-3e3e-425b-a4b2-e375df6e39b4;
  style 755dbb99-3e3e-425b-a4b2-e375df6e39b4 stroke:#2c3143,stroke-width:4px;
  e0234472-cc44-483e-997b-8b0e0719c8d7["Output\nDihedral Analysis raw data"];
  6 --> e0234472-cc44-483e-997b-8b0e0719c8d7;
  style e0234472-cc44-483e-997b-8b0e0719c8d7 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset DCD input
Input dataset PDB input

Outputs

From Output Label
Input dataset DCD input
Input dataset PDB input
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_rdf/mdanalysis_rdf/0.19 RDF Analysis
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.19 Cosine Content
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_ramachandran_plot/mdanalysis_ramachandran_plot/0.1.3 Ramachandran Plots
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_distance/mdanalysis_distance/0.19 Distance Analysis
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_dihedral/mdanalysis_dihedral/0.19 Dihedral Analysis

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.19 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_dihedral/mdanalysis_dihedral/0.19 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_distance/mdanalysis_distance/0.19 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_ramachandran_plot/mdanalysis_ramachandran_plot/0.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_rdf/mdanalysis_rdf/0.19 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 cfb492901 2022-03-04 17:21:35 fix link to advanced mdanalysis workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/advanced_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows