CELLO-3.0 is a software package for designing genetic circuits based on logic gate designs written in the Verilog format. It includes a core cell-logic synthesis process, plus a web-interface for modifying UCF files. It is still a work in progress, and more features are coming soon. CELLO-3.0 is capable of efficiently handling single and multi-cellular partitioning, gerenating results saved in a local directory on your machine, with optional verbose commandline-outputs.
Currently, you can find two modules for Cello-3.0:
- CELLO-V3-Core (run the Cello genetic circuit design algorithm)
- UCFormatter (modify and visualize UCF files containing genetic part specifications)
You will find the instructions for the UCFormatter in this Repository below:
git clone https://github.com/CIDARLAB/UCFormatter
cd UCFormatter/
You'll need to install Redis on your computer
Ex. On MacOS:
brew install redis
(for other platforms, please check Redis installation guide)
Then, install a few python pacakges
pip install -r req.txt
python UCFormatter.py
Finally, navigate to localhost:8050 to see use UCFormatter running!
If You get the error that port 8050 is already running it means that UCFormatter was not shut down correctly from the last session. You can try to shut it down this way:
redis-cli shutdown
(Ignore if it takes forever, use 'ctrl+c')
lsof -i :8050
This will show you as list of PIDs running on port 8050
kill PID
(use the PIDs that listed from the last step, repeat if needed)
Now, you are able to restart Cello again!
If that doesn't work, just restart your computer, all your cache will be reset this way.
CELLO-3.0 can be used in a variety of ways, depending on your needs:
- As a standalone tool: Use the interactive shell interface to design optimized genetic circuits.
- As a Python package: Import the core CELLO code as a Python library and use it as a component in your own software.
- As a GUI tool (feature coming in the future!)
CELLO-3.0 also includes a proprietary UCF formatter tool (this tool) that can modify or create UCF files through an intuitive graphial user interface. As well as letting you see the DNA sequences for the parts required in the resulting Cello designs on the UCFormatter interface
- Core cell-logic synthesis process from logic circuits.
- Optional verbose command-line outputs
- Visualizes circuit mapping and circuit-flow scores
- Transform design to SBOL format for universtal transport
UCFormatter is an ongoing project, and future work may include:
- Optimizing the UCFormatter user interface
- Completing some of the additional features:
- To save and output modifications to the UCF files
- Make graphical previews that represent the biological parts
- Building an interface to interact with the Cello command-line tool
We welcome contributions from the community! If you'd like to contribute to CELLO-3.0, please follow the guidelines in the CONTRIBUTING.md file.
CELLO-3.0 was developed by Weiqi Ji and other contributors at CIDAR LAB under Douglas Densmore. It was inspired by the original CELLO and Cello-v2 software packages developed by CIDAR LAB.
CELLO-3.0 is released under the MIT license. See the LICENSE file for more information.