Workflows

These workflows are associated with Analysis of molecular dynamics simulations

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.

Analysis using MDAnalysis

Chris Barnett

Last updated Mar 4, 2022

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

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;

Simple Analysis

Last updated Oct 3, 2020

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nprotein_mdsimulation_dcd"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nprotein_pdb"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["RMSD Analysis"];
  0 -->|output| 2;
  1 -->|output| 2;
  6de2beaf-f80e-4788-8598-229a1c582757["Output\nrmsd_tabular_output"];
  2 --> 6de2beaf-f80e-4788-8598-229a1c582757;
  style 6de2beaf-f80e-4788-8598-229a1c582757 stroke:#2c3143,stroke-width:4px;
  3["RMSF Analysis"];
  0 -->|output| 3;
  1 -->|output| 3;
  1f2d715d-230a-4ec5-a509-e8ae501e7634["Output\nrmsf_tabular_output"];
  3 --> 1f2d715d-230a-4ec5-a509-e8ae501e7634;
  style 1f2d715d-230a-4ec5-a509-e8ae501e7634 stroke:#2c3143,stroke-width:4px;
  4["PCA"];
  0 -->|output| 4;
  1 -->|output| 4;
  92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5["Output\npca_tabular_output"];
  4 --> 92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5;
  style 92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5 stroke:#2c3143,stroke-width:4px;

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 galaxy-upload 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: