https://github.com/althonos/moclo
Modular cloning simulation with the MoClo framework in Python
Science Score: 20.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.3%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Modular cloning simulation with the MoClo framework in Python
Basic Info
- Host: GitHub
- Owner: althonos
- License: mit
- Language: Python
- Default Branch: master
- Homepage: http://moclo.rtfd.io
- Size: 1.8 MB
Statistics
- Stars: 12
- Watchers: 5
- Forks: 2
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
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:
console
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.
Owner
- Name: Martin Larralde
- Login: althonos
- Kind: user
- Location: Heidelberg, Germany
- Company: EMBL / LUMC, @zellerlab
- Twitter: althonos
- Repositories: 91
- Profile: https://github.com/althonos
PhD candidate in Bioinformatics, passionate about programming, SIMD-enthusiast, Pythonista, Rustacean. I write poems, and sometimes they are executable.
GitHub Events
Total
Last Year
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Martin Larralde | m****e@e****r | 376 |
| Martin Larralde | m****e@e****e | 23 |
| Martin Larralde | m****e@e****r | 13 |
| dependabot-preview[bot] | 2****] | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 1
- Average time to close issues: 2 days
- Average time to close pull requests: about 2 months
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- fbertaux (1)
Pull Request Authors
- dependabot-preview[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 4
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Total downloads:
- pypi 199 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 6
(may contain duplicates) - Total versions: 30
- Total maintainers: 1
pypi.org: moclo
A Python implementation of the MoClo system logic.
- Homepage: https://github.com/althonos/moclo/
- Documentation: https://moclo.readthedocs.io/en/latest/
- License: MIT
-
Latest release: 0.4.7
published over 4 years ago
Rankings
Maintainers (1)
pypi.org: moclo-ytk
Yeast ToolKit implementation for the base moclo library.
- Homepage: https://github.com/althonos/moclo/tree/master/moclo-ytk
- Documentation: https://moclo.readthedocs.io/en/latest/kits/ytk/index.html
- License: MIT
-
Latest release: 0.4.0
published over 7 years ago
Rankings
Maintainers (1)
pypi.org: moclo-cidar
CIDAR implementation for the base moclo library.
- Homepage: https://github.com/althonos/moclo/tree/master/moclo-cidar
- Documentation: https://moclo.readthedocs.io/en/latest/kits/cidar/index.html
- License: MIT
-
Latest release: 0.4.0
published over 7 years ago
Rankings
Maintainers (1)
pypi.org: moclo-ecoflex
EcoFlex implementation for the base moclo library.
- Homepage: https://github.com/althonos/moclo/tree/master/moclo-ecoflex
- Documentation: https://moclo.readthedocs.io/en/latest/kits/ecoflex/index.html
- License: MIT
-
Latest release: 0.3.1
published over 7 years ago
Rankings
Maintainers (1)
Dependencies
- Pygments *
- codacy-coverage *
- codecov *
- coverage *
- docutils *
- green *
- setuptools *
- twine *
- wheel *
- IPython *
- Sphinx *
- biopython *
- configparser *
- dna_features_viewer *
- fs *
- ipykernel *
- matplotlib *
- nbsphinx *
- property-cached *
- requests *
- semantic-version *
- setuptools >=30.3
- six *
- sphinx-bootstrap-theme *
- typing *
- biopython *
- fs *
- ipywidgets *
- jupyter *
- jupyterlab *
- moclo *
- moclo-ytk *
- pandas *
- qgrid *
- six *
- backports.lzma * test
- contexter * test
- fs * test
- fs.archive * test