A Python implementation of the MoClo system logic.
The documentation is hosted on ReadTheDocs, and built against the latest commit of the development repository. It contains a comprehensive API reference as well as examples compiled from Jupyter notebooks at each build.
The base logic is handled by the core moclo
module. It embeds an object model of the MoClo system logic, but does not enforce
any specific sequence structure, and is not usable alone. You must install a kit
(listed below) to be able to validate and compute assemblies.
Additional kits can be installed separately depending on what's needed. The following implementations are available:
- Original MoClo (
moclo-moclo) - Yeast ToolKit and Pichia ToolKit (
moclo-ytk) - CIDAR Kit (
moclo-cidar) - EcoFlex Kit (
moclo-ecoflex)
Once installed, kits are available in the moclo.kits namespace module.
Kit-specific documentation is
available as well.
Kit-specific modules and vectors are distributed with the library files, so that
each library provides the base parts needed to create an assembly. They can be
found in the moclo.registry namespace. See also the documentation of each
moclo.registry submodule for a detail of how sequences were obtained. The
embedded sequences are distributed in GenBank format with the source distributions
of each plugin.
This repository provides a YTK-specific Jupyter notebook as a Docker image, which can be used to generate a protocol for YTK MoClo assembly. Run it locally using the following command:
docker run --rm -it -p 8888:8888 althonos/mocloand visit https://localhost:8888/ to start interacting with the notebook.
This project is licensed under the MIT License.
This project is in no way affiliated, sponsored, or otherwise endorsed by Addgene or any of the MoClo toolkit creators. It was developed by Martin Larralde during a placement at the InBio team at the Institut Pasteur of Paris during the summer of 2018.