althonos/moclo

Modular cloning simulation with the MoClo framework in Python

moclo

A Python implementation of the MoClo system logic.

📚 Documentation

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.

🔩 Base module

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.

🧰 Kits

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.

🗂️ Registries

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.

🗒️ Notebook

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/moclo

and visit https://localhost:8888/ to start interacting with the notebook.

⚖️ License

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.

moclo's Issues

Bio.Alphabet removed from BioPython

assembly.py wants to import IUPAC from Bio.Alphabet, but was removed from Biopython:

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.