DNA Foundry
OverviewSpace: Paris Biofoundry
SEEK ID: https://workflowhub.eu/projects/355
Public web page: https://parisbiofoundry.org/the-asu-biofoundry/
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team created: 26th Jun 2025
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Related items
Teams: DNA Foundry, Cell Free, galaxy-SynBioCAD
Organizations: Sorbonne Université, INRAe
Teams: DNA Foundry, Cell Free, galaxy-SynBioCAD
Web page: https://parisbiofoundry.org/
ROR ID: https://ror.org/02en5vm52
Department: Not specified
Country: 
France
City: Paris
Web page: https://www.sorbonne-universite.fr
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
- Distribute workflow parameters on the workflow tools
- 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
- Extract the fragments associated with each constraint from the CSV file.
- 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
- Set the constraints for the annotations. ...
