Synthetic Biology Reusable Optimization Methodology
SBROME (Synthetic Biology Reusable Optimization Methodology) is a tool to design synthetic gene circuits. An abstract user-defined circuit is first transformed and matched against a module database that incorporates circuits that have previously been experimentally characterized. Then the resulting circuit is decomposed to subcircuits that are populated with the set of parts that best approximate the desired function.
- Gcc
make
make install
./main
There are 7 examples in the main.cpp. Edit the file main.cpp for each example, then re-compile and run again.
If you have any questions about PAMDB, please contact Linh Huynh (huynh@ucdavis.edu) or Ilias Tagkopoulos (itagkopoulos@ucdavis.edu).
Huynh, L., Tsoukalas, A., Köppe, M., & Tagkopoulos, I. (2013). SBROME: a scalable optimization and module matching framework for automated biosystems design. ACS synthetic biology, 2(5), 263-273.[link]
See the LICENSE file for license rights and limitations (Apache2.0).
This work was supported by the NSF grant (#0941360 and #1146926).