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EC552-HW-1

Authors

Drew Gross and Marlee Feltham

Description

Genetic circuit design program for modifying custom Eco1C1G1T1.UCF.json and Eco1C1G1T1.input.json files

Instructions

1. Install python 3.10 and pip

2. Install Docker

docker pull cidarlab/cello-dnacompiler:latest

3. Cello file structure

git clone https://github.com/CIDARLAB/homework1-template

├── input
│   ├── and.v
│   ├── Eco1C1G1T1.input.json
│   ├── Eco1C1G1T1.output.json
│   ├── Eco1C1G1T1.UCF.json
│   ├── nand.v
│   ├── options.csv
│   ├── struct.v
│   └── xor.v
├── main.py
├── output
└── README.md

Suggested Reading

  1. Vaidyanathan, P., Der, B. S., Bhatia, S., Roehner, N., Silva, R., Voigt, C. A., & Densmore, D. (2015). A Framework for Genetic Logic Synthesis. Proceedings of the IEEE, 103(11), 2196-2207. (This Paper should help understand the basic framework, terms and definitions of Logic Synthesis applied for Genetic circuits. Specifically, Sections 1,2,3 as well as Fig 2 will be helpful)
  2. Yaman, F., Bhatia, S., Adler, A., Densmore, D., & Beal, J. (2012). Automated selection of synthetic biology parts for genetic regulatory networks. ACS synthetic biology, 1(8), 332-344. (The Results section as well as Fig 5 will be useful)
  3. Stanton, B. C., Nielsen, A. A., Tamsir, A., Clancy, K., Peterson, T., & Voigt, C. A. (2014). Genomic mining of prokaryotic repressors for orthogonal logic gates. Nature chemical biology, 10(2), 99-105.