Genetic Design (BASIC Assembly)

synthetic-biology-basic_assembly_analysis/genetic-design-basic-assembly

Author(s)

Version
1
Last updated
May 12, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
synthetic-biology

Features
Tutorial
Designing plasmids encoding predicted pathways by using the BASIC assembly method
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00231
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\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;

Inputs

Input Label
Input dataset Pathway (SBML)
Input parameter Host taxon ID
Input parameter Enzyme taxon IDs
Input dataset Linkers and user parts
Input dataset DNA-Bot settings

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0 Selenzyme Selenzyme
toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4 BasicDesign BasicDesign
toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0 DNA-Bot DNA-Bot

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0 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
3 ef543ff8f 2022-03-17 13:04:23 add slides, more background and new contributors
2 002bde239 2022-03-01 15:25:05 add tag synthetic biology
1 e01203d3b 2022-02-23 14:57:10 add new tutorial for synthetic biology: basic assembly analysis

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/basic_assembly_analysis/workflows/Genetic_Design_BASIC_Assembly.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