Biology Python Colabs

Colabs for biology-related Python projects.
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Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
3. Usage Example
4. Roadmap
5. Contributing
6. License
7. Contact
8. Acknowledgments

About The Project

There are many great biology-related Python projects on Github. This repo attempts to use Colab to walk through a selected few as a fun side project.

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Requirement

• Familiarity with Python and Colab

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Getting Started

Each .ipynb file is a standalone project that walks through certain models or tools. Open any .ipynb file and click Open in Colab to start running Python code.

Prerequisites

All prerequisites should be provided or installed in the Colab. Here lists a few common tools in Colab to deal with dependencies.

• pip

  !pip install biopython

• git

  !git clone https://github.com/collvey/Biopython.git

• Set current directory in Colab as target PATH to import from

  import sys
  
  sys.path.insert(0,'/content/')

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Usage Example

Open NCRFpp Walkthrough and click Open in Colab to start running code.

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Roadmap

Projects added:

• NCBI_Entrez_Alignment_Example
• Local_copy_of_training_MRL_CNN
• Sklearn_Regressor_Models
• Testing_Devil625_Codon_Optimization
• Walkthrough_for_jiesutd_NCRFpp
• Testing_human_utr_modeling
• More to add..

See the open issues for a full list of proposed features (and known issues).

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Contributing

Any contributions you make are greatly appreciated.

Steps to contribute:

1. Fork the Project
2. Create Feature Branch (git checkout -b feature/FeatureName)
3. Commit your Changes (git commit -m 'Add some feature')
4. Push to the Branch (git push origin feature/FeatureName)
5. Open a Pull Request

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License

Distributed under the MIT License. See LICENSE.md for more information.

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Contact

Hongcheng Xu - @collvey - hongchengxu123[at]gmail.com

Project Link: https://github.com/collvey/Biopython

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Acknowledgments

• yuzhuoji

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