Data management in Medicinal Chemistry workflow

computational-chemistry-med-chem-data/data-management-in-medicinal-chemistry-workflow

Author(s)
Julia Jakiela
Version
1
Last updated
Jan 8, 2024
License
CC-BY-4.0
Tags

Features
Tutorial
Data management in Medicinal Chemistry
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00038
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\nBenzenesulfonyl chloride"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nEthylamine"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Compound conversion"];
  0 -->|output| 2;
  aff8fa4f-c254-4f05-9560-52bad6c7e04a["Output\nBenzenesulfonyl chloride SDF"];
  2 --> aff8fa4f-c254-4f05-9560-52bad6c7e04a;
  style aff8fa4f-c254-4f05-9560-52bad6c7e04a stroke:#2c3143,stroke-width:4px;
  3["Search ChEMBL database"];
  0 -->|output| 3;
  044d2c08-92ed-45c9-9868-ee802998d92c["Output\nSubstructures from ChEMBL database"];
  3 --> 044d2c08-92ed-45c9-9868-ee802998d92c;
  style 044d2c08-92ed-45c9-9868-ee802998d92c stroke:#2c3143,stroke-width:4px;
  4["Search ChEMBL database"];
  0 -->|output| 4;
  99274b60-732d-4276-969f-ccc3673a872a["Output\nLipinski substructures from ChEMBL database"];
  4 --> 99274b60-732d-4276-969f-ccc3673a872a;
  style 99274b60-732d-4276-969f-ccc3673a872a stroke:#2c3143,stroke-width:4px;
  5["Compound conversion"];
  1 -->|output| 5;
  77ad7b99-5761-46a3-b9a6-1dd3d8e2baac["Output\nEthylamine SDF"];
  5 --> 77ad7b99-5761-46a3-b9a6-1dd3d8e2baac;
  style 77ad7b99-5761-46a3-b9a6-1dd3d8e2baac stroke:#2c3143,stroke-width:4px;
  6["Reaction maker"];
  2 -->|outfile| 6;
  5 -->|outfile| 6;
  f9d1d7fd-e854-469b-a464-6811998e058e["Output\nReaction product"];
  6 --> f9d1d7fd-e854-469b-a464-6811998e058e;
  style f9d1d7fd-e854-469b-a464-6811998e058e stroke:#2c3143,stroke-width:4px;
  b0bd7ed2-a80b-44ce-994b-999e1d472281["Output\nReaction maker logfile"];
  6 --> b0bd7ed2-a80b-44ce-994b-999e1d472281;
  style b0bd7ed2-a80b-44ce-994b-999e1d472281 stroke:#2c3143,stroke-width:4px;
  7["Visualisation"];
  6 -->|outfile| 7;
  fc618f3f-6aa5-4970-841d-56f4eabf47b7["Output\nVisualisation of reaction product"];
  7 --> fc618f3f-6aa5-4970-841d-56f4eabf47b7;
  style fc618f3f-6aa5-4970-841d-56f4eabf47b7 stroke:#2c3143,stroke-width:4px;
  8["Drug-likeness"];
  6 -->|outfile| 8;
  7ad8c184-e10d-4fce-a402-3e79da6e09ac["Output\nDrug-likeness of product molecule"];
  8 --> 7ad8c184-e10d-4fce-a402-3e79da6e09ac;
  style 7ad8c184-e10d-4fce-a402-3e79da6e09ac stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Benzenesulfonyl chloride
Input dataset Ethylamine

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 Compound conversion
toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4 Search ChEMBL database
toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4 Search ChEMBL database
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 Compound conversion
toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_rxn_maker/ctb_im_rxn_maker/1.1.4+galaxy0 Reaction maker
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy0 Visualisation
toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0 Drug-likeness

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_rxn_maker/ctb_im_rxn_maker/1.1.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0 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 76375aa18 2024-01-01 19:56:34 workflow tests

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/med-chem-data/workflows/Data-management-in-Medicinal-Chemistry-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