This is not an officially supported Google product.
SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions. See our preprint
Tested on python >= 3.7
We recommend installing into a virtual environment to isolate dependencies.
python3 -m venv env
source env/bin/activate
To install:
pip3 install -q -r requirements.txt
To run the unit tests:
bash -c 'for f in *_test.py; do python3 $f || exit 1; done'
See this colab for an example of using a landscape.
All landscapes were constructed using Mogwai. See that repo's example, which shows how to train a new Potts model and how to (optionally) examine contact accuracy after training. All that is required is an alignment in .a3m format, true contacts are not required (e.g. as in this colab).