GOLDBAR-Generator

This software tool generates the GOLDBAR (Grammars for cOmbinatoriaL Design and Bio-Assembly Revision) and Categories for Constellation based on known principles of Genetic Circuit Design.

Rules

P - Promoter Road Blocking: Road-blocking promoters must be alone or in front of regular promoters

L - Leaky Terminators: Leaky Terminators can only be at end of circuit

O - Orthogonality: Certain parts can not be in the same circuit

I - Part-junction Interference: Certain parts can not be next to each other

R - Do not Reuse Certain Parts: Certain parts will not be reused in the same sequence

Cloning the REPO

git clone https://github.com/CIDARLAB/goldbar-generator.git
cd goldbar-generator/

Installing Python Packages

Install using pip

pip install pandas
pip install numpy

Using the GOLDBAR Generator

Run

goldbar-generator.py

To Run in Terminal

python goldbar-generator.py

Follow the prompts for which Part Library you would like to use then the number of transcriptional units and rules.

Library/Sample Inputs

Can be found in the library folder. This includes the part library, not orthogonal library, and part junction interference library

Example Output

Can be found in the output folder. This example is based on the libraries in library folder and uses P L O I R rules.

Try Constellation

To see the Design space graph and enumerate designs use Constellation.

Try Knox

To save and perform further graph analysis, use Knox. You can output your design from Constellation as SBOL and import this SBOL file into Knox.

References

Brophy, J., Voigt, C. Principles of genetic circuit design. Nat Methods 11, 508–520 (2014). https://doi.org/10.1038/nmeth.2926

Credits

The GOLDBAR-Generator was developed by James Roberts at CIDAR LAB under Douglas Densmore.