galaxy-SynBioCAD is an open access Galaxy workflow environment to design and build different metabolic routes for the production of a compound of interest. Galaxy-SynBioCAD combines the proven efficiency of RetroPath2.0 and automated script generator to drive robotized workstations for vector assembly and strain transformation.

This workflow encodes the top-ranking predicted pathways from the previous workflow into plasmids intended to be expressed in the specified organism. BASIC is used as assembly method.

This workflow encodes the top-ranking predicted pathways from the previous workflow into plasmids intended to be expressed in the specified organism. Assembly methods are Gibson, Golden or Ligation Chain Reaction.

Annotation: Evaluating and ranking a set of pathways based on multiple metrics. Given a set of pathways generated by RetroPath2.0, this workflow informs the user as to the theoretically best performing ones based on the four criteria (target product flux, thermodynamic feasibility, pathway length, and enzyme availability).

Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools

Domestication of new parts and cloning simulation

Add new parts to your sequences before the cloning simulation and interact with the database.

input:

• input: csv file (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.
• JSON parameters file (optional) : The JSON file should contain the the parameters used in workflow tools. If this ...

Cloning simulation workflow for sequences present in DB

Run the GoldenGate cloning simulation for a list of constructs in a CSV file and interact with a database

inputs:

• Assmbly Plan (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.
• JSON parameters file (optional) : The JSON file should contain the the parameters used in workflow ...

Cloning simulation workflow for sequences present in DB

Run the GoldenGate cloning simulation for a list of constructs in a CSV file and interact with a database

steps:

input: csv file (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.

workflow_1 Parameter_Maystro

1. Distribute workflow parameters on the workflow tools
2. Parameters ...

Domestication of new parts before cloning simulation

Add new parts to your sequences before the cloning simulation and interact with the database.

steps:

input: csv file (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.

seq_from_DB

1. Extract the fragments associated with each constraint from the CSV file.
2. Check if all fragments are ...

Generate annotated gb for fragments and add them to DB

Automatically generate annotated GenBank files for your fragments based on your constraints and store them in your database.

steps:

input: GenBank files : If your fragments are not in the database, you can generate GenBank files for each fragment to be used as input for the annotation workflow and then passed to the evaluate_manufacturability tool.

evaluate_manufacturability

1. Set the constraints for the annotations. ...