RetroSynthesis

synthetic-biology-retrosynthesis_analysis/retrosynthesis

Author(s)

Version
1
Last updated
Jun 23, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
synthetic-biology

Features
Tutorial
Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00233
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Parameter\nTarget to produce"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["Pick SBML Model"];
  dc7acc73-6d5a-4cbb-a8a2-d10a8bd38914["Output\nPick SBML Model - iML1515"];
  1 --> dc7acc73-6d5a-4cbb-a8a2-d10a8bd38914;
  style dc7acc73-6d5a-4cbb-a8a2-d10a8bd38914 stroke:#2c3143,stroke-width:4px;
  2["RRules Parser"];
  9fc1e94f-34ea-4173-bdb1-3ecbef49efe3["Output\nRRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])"];
  2 --> 9fc1e94f-34ea-4173-bdb1-3ecbef49efe3;
  style 9fc1e94f-34ea-4173-bdb1-3ecbef49efe3 stroke:#2c3143,stroke-width:4px;
  3["Sink from SBML"];
  1 -->|sbml_model| 3;
  4["RetroPath2.0"];
  2 -->|out_rules| 4;
  3 -->|sink| 4;
  0 -->|output| 4;
  5["RP2paths"];
  4 -->|Reaction_Network| 5;
  6["Complete Reactions"];
  4 -->|Reaction_Network| 6;
  5 -->|compounds| 6;
  5 -->|master_pathways| 6;
  3 -->|sink| 6;

Inputs

Input Label
Input parameter Target to produce

Outputs

From Output Label
Input parameter Target to produce
toolshed.g2.bx.psu.edu/repos/tduigou/get_sbml_model/get_sbml_model/0.0.1 Pick SBML Model
toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6 RRules Parser
toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1 Sink from SBML
toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0 RetroPath2.0
toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.5.0 RP2paths
toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.2 Complete Reactions

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/tduigou/get_sbml_model/get_sbml_model/0.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6 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
2 79975abd7 2022-06-09 11:41:52 fix(RetroSynthesis.ga): add annotation and tag attribute
1 da3d162e5 2022-06-09 11:07:29 add new tutorial: RetroSynthesis Analysis

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/retrosynthesis_analysis/workflows/RetroSynthesis.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