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.

flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  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;
	

flowchart TD
  0["ℹ️ Input Parameter\nPDB code e.g. 6hhr"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Parameter\nLigand name e.g. AG5E"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  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

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: