Workflows

These workflows are associated with High Throughput Molecular Dynamics and Analysis

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.

Workflow constructed from history 'Hsp90-MDAnalysis'

Last updated Jul 21, 2020

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

flowchart TD
  0["Input dataset"];
  1["Input dataset"];
  2["GROMACS structure configuration"];
  0 -->|output| 2;
  3["MDTraj file converter"];
  1 -->|output| 3;
  4["RMSD Analysis"];
  2 -->|output| 4;
  3 -->|output| 4;
  5["RMSF Analysis"];
  2 -->|output| 5;
  3 -->|output| 5;
  6["PCA"];
  2 -->|output| 6;
  3 -->|output| 6;
  7["Cosine Content"];
  3 -->|output| 7;
  2 -->|output| 7;
  8["PCA visualization"];
  2 -->|output| 8;
  3 -->|output| 8;
  9["Hydrogen Bond Analysis using VMD"];
  3 -->|output| 9;
  2 -->|output| 9;
  10["RMSD Analysis"];
  2 -->|output| 10;
  3 -->|output| 10;

	
MD protein-ligand workflow (from PDB structure)

Last updated Jul 21, 2020

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

flowchart TD
  0["Input parameter"];
  1["Input parameter"];
  2["Get PDB file"];
  0 -->|output| 2;
  3["Search in textfiles"];
  2 -->|output| 3;
  4["Search in textfiles"];
  2 -->|output| 4;
  1 -->|output| 4;
  5["GROMACS initial setup"];
  3 -->|output| 5;
  6["Compound conversion"];
  4 -->|output| 6;
  7["Generate MD topologies for small molecules"];
  6 -->|outfile| 7;
  8["Merge GROMACS topologies"];
  7 -->|gro_output| 8;
  5 -->|output1| 8;
  5 -->|output2| 8;
  7 -->|output| 8;
  9["GROMACS structure configuration"];
  8 -->|complex_gro| 9;
  10["GROMACS solvation and adding ions"];
  8 -->|complex_top| 10;
  9 -->|output| 10;
  11["GROMACS energy minimization"];
  10 -->|output2| 11;
  10 -->|output1| 11;
  12["GROMACS simulation"];
  5 -->|output3| 12;
  10 -->|output2| 12;
  11 -->|output1| 12;
  13["GROMACS simulation"];
  5 -->|output3| 13;
  10 -->|output2| 13;
  12 -->|output1| 13;
  12 -->|output5| 13;
  14["GROMACS simulation"];
  10 -->|output2| 14;
  13 -->|output1| 14;
  13 -->|output5| 14;

	

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: