https://github.com/althonos/moclo

Modular cloning simulation with the MoClo framework in Python
https://github.com/althonos/moclo

bioinformatics biopython moclo modular-cloning plasmids system-biology

Last synced: 5 months ago
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Modular cloning simulation with the MoClo framework in Python

• Host: GitHub
• URL: https://github.com/althonos/moclo
• Owner: althonos
• License: mit
• Created: 2018-06-20T09:48:58.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2022-05-03T14:00:44.000Z (about 3 years ago)
• Last Synced: 2024-12-17T02:40:37.916Z (6 months ago)
• Topics: bioinformatics, biopython, moclo, modular-cloning, plasmids, system-biology
• Language: Python
• Homepage: http://moclo.rtfd.io
• Size: 1.8 MB
• Stars: 12
• Watchers: 6
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: COPYING

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README

        
# `moclo` [![Stars](https://img.shields.io/github/stars/althonos/moclo.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/moclo/stargazers)

*A Python implementation of the [MoClo](https://www.addgene.org/cloning/moclo/) system logic.*

[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=3600&style=flat-square)](https://github.com/althonos/moclo)

[![Build](https://img.shields.io/github/workflow/status/althonos/moclo/Test?style=flat-square&maxAge=3600)](https://github.com/althonos/moclo/actions)

[![Docs](https://img.shields.io/readthedocs/moclo.svg?maxAge=3600&style=flat-square)](https://moclo.readthedocs.io/)

[![Codecov](https://img.shields.io/codecov/c/github/althonos/moclo/master.svg?style=flat-square&maxAge=600)](https://codecov.io/gh/althonos/moclo)

[![Codacy](https://img.shields.io/codacy/grade/5b29a9c0d91f4e82944a46997bd9a480/master.svg?style=flat-square&maxAge=300)](https://www.codacy.com/app/althonos/moclo)

[![License](https://img.shields.io/pypi/l/moclo.svg?style=flat-square&maxAge=300)](https://choosealicense.com/licenses/mit/)

[![DOI](https://img.shields.io/badge/doi-10.5281%2Fzenodo.1401815-blue.svg?style=flat-square&maxAge=31536000)](https://zenodo.org/badge/latestdoi/138012703)

## 📚 Documentation

The documentation is hosted on [ReadTheDocs](https://moclo.readthedocs.org),

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`](https://github.com/althonos/moclo/tree/master/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`)](https://github.com/althonos/moclo/tree/master/moclo-moclo)

* [Yeast ToolKit and Pichia ToolKit (`moclo-ytk`)](https://github.com/althonos/moclo/tree/master/moclo-ytk)

* [CIDAR Kit (`moclo-cidar`)](https://github.com/althonos/moclo/tree/master/moclo-cidar)

* [EcoFlex Kit (`moclo-ecoflex`)](https://github.com/althonos/moclo/tree/master/moclo-ecoflex)

Once installed, kits are available in the `moclo.kits` namespace module.

[Kit-specific documentation](https://moclo.readthedocs.io/en/latest/#kits) 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

[![Docker Build Status](https://img.shields.io/docker/build/althonos/moclo.svg?style=flat-square&maxAge=3600)](https://hub.docker.com/r/althonos/moclo/builds/) [![Docker Pulls](https://img.shields.io/docker/pulls/althonos/moclo.svg?style=flat-square&maxAge=3600)](https://hub.docker.com/r/althonos/moclo/)

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:

```console

docker run --rm -it -p 8888:8888 althonos/moclo

```

and visit [https://localhost:8888/](https://localhost:8888/) to start interacting

with the notebook.

## ⚖️ License

This project is licensed under the [MIT License](http://choosealicense.com/licenses/mit/).

*This project is in no way affiliated, sponsored, or otherwise endorsed by [Addgene](https://www.addgene.org) or any of the MoClo toolkit creators.

It was developed by [Martin Larralde](https://github.com/althonos/pyhmmer)

during a placement at the [InBio team](https://research.pasteur.fr/en/team/experimental-and-computational-methods-for-modeling-cellular-processes/)

at the Institut Pasteur of Paris during the summer of 2018.*