Data management in Medicinal Chemistry workflow 1.0
Visit source
Download RO-Crate
Run on GalaxyWorkflow includes data import, format conversion and some basic medicinal chemistry analyses.
Associated Tutorial
This workflows is part of the tutorial Data management in Medicinal Chemistry, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Julia Jakiela
Tutorial Author(s): Julia Jakiela, Katarzyna Kamieniecka, Krzysztof Poterlowicz
Tutorial Contributor(s): Helena Rasche, Simon Bray, Khaled Jum'ah
Grants(s): DASH UK
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Benzenesulfonyl chloride | #main/Benzenesulfonyl chloride | First input molecule |
|
| Ethylamine | #main/Ethylamine | Second input molecule |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Compound conversion | toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 |
| 3 | Search ChEMBL database | toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4 |
| 4 | Search ChEMBL database | toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4 |
| 5 | Compound conversion | toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 |
| 6 | Reaction maker | toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_rxn_maker/ctb_im_rxn_maker/1.1.4+galaxy0 |
| 7 | Visualisation | toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy0 |
| 8 | Drug-likeness | toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Benzenesulfonyl chloride SDF | #main/Benzenesulfonyl chloride SDF | n/a |
|
| Drug-likeness of product molecule | #main/Drug-likeness of product molecule | n/a |
|
| Ethylamine SDF | #main/Ethylamine SDF | n/a |
|
| Lipinski substructures from ChEMBL database | #main/Lipinski substructures from ChEMBL database | n/a |
|
| Reaction maker logfile | #main/Reaction maker logfile | n/a |
|
| Reaction product | #main/Reaction product | n/a |
|
| Substructures from ChEMBL database | #main/Substructures from ChEMBL database | n/a |
|
| Visualisation of reaction product | #main/Visualisation of reaction product | n/a |
|
Version History
master
Creators and Submitter
Views: 1305 Downloads: 185 Runs: 0
Created: 2nd Jun 2025 at 11:02
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
