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.
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
git clone https://github.com/CIDARLAB/goldbar-generator.git
cd goldbar-generator/
Install using pip
pip install pandas
pip install numpy
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.
Can be found in the library folder. This includes the part library, not orthogonal library, and part junction interference library
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.
To see the Design space graph and enumerate designs use Constellation.
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.
Brophy, J., Voigt, C. Principles of genetic circuit design. Nat Methods 11, 508–520 (2014). https://doi.org/10.1038/nmeth.2926
Nicholas Roehner, James Roberts, Andrei Lapets, Dany Gould, Vidya Akavoor, Lucy Qin, D. Benjamin Gordon, Christopher Voigt, and Douglas Densmore. GOLDBAR: A Framework for Combinatorial Biological Design. ACS Synthetic Biology Article ASAP (2024).
DOI: https://pubs.acs.org/doi/full/10.1021/acssynbio.4c00296
The GOLDBAR-Generator was developed by James Roberts at CIDAR LAB under Douglas Densmore.