BioLoGI (Biological Logic Gate Inference system) is a computational tool that automates the modeling of logic gate-like interaction in syntheic genetic circuits and human transcriptome.
Install by pip:
pip3 install https://github.com/RandolphLiu/BioLoGI/releases/download/0.1/biologi-0.1-py3-none-any.whlOne of the dependencies, theano may require python development package depending on your platform.
If theano throws an error, try:
# Ubuntu
sudo apt install python3-dev
# CentOS, RHEL or Fedora
sudo dnf install python3-develModeling the 3OC6HSL receiver device, which is a synthetic circuit uses the 3OC6HSL inducible promoter pLux. See iGEM registry: BBa_T9002
After installing BioLoGI:
git clone https://github.com/RandolphLiu/BioLoGI
cd BioLoGI
biologi -c data/BBa_T9002/BBa_T9002_config.jsonThe output will include details of all canditate models and the best model, the dose-response curve and SBOL genetic circuit figure.