Workflows

These workflows are associated with Designing plasmids encoding predicted pathways by using the BASIC assembly method

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.

Genetic Design (BASIC Assembly)

Last updated Mar 17, 2022

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

Download Galaxy Workflow.ga Galaxy Main Galaxy Europe Galaxy Australia Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nPathway SBML"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nHost taxon ID"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nEnzyme taxon IDs"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Dataset\nLinkers and user parts"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nDNA-Bot settings"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Selenzyme"];
  2 -->|output| 5;
  1 -->|output| 5;
  0 -->|output| 5;
  54b833fa-ec4f-458a-b085-23211f4e56ca["Output\nUniprot IDs"];
  5 --> 54b833fa-ec4f-458a-b085-23211f4e56ca;
  style 54b833fa-ec4f-458a-b085-23211f4e56ca stroke:#2c3143,stroke-width:4px;
  6["BasicDesign"];
  3 -->|output| 6;
  5 -->|uniprot_ids| 6;
  7["DNA-Bot"];
  4 -->|output| 7;
  6 -->|Constructs| 7;
  6 -->|User parts plate| 7;
  6 -->|Biolegio plate| 7;

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: