ProteoParc_Colab

A Colab Implementation of PalaeoParc by Guillermo Carrillo Martín

Overview

ProteoParc in Colab is a Jupyter notebook designed to facilitate the analysis of ancient proteins using Google Colab. This notebook provides a streamlined and accessible environment for performing proteomics research, particularly focusing on the analysis of proteins extracted from archaeological samples. The notebook includes scripts and a user-friendly button interface to simplify the workflow.

Features

• Cloud-based Analysis: Utilise the power of Google Colab to run your analyses without the need for local computational resources.
• Comprehensive Pipeline: Includes steps for data preprocessing, protein identification, and result visualisation.
• Interactive: The notebook format allows for interactive exploration and manipulation of data.
• User-friendly Interface: Includes buttons and scripts to make the process straightforward and accessible.

Getting Started

Prerequisites

To use this notebook, you will need:

• A Google account to access Google Colab.
• Basic knowledge of proteomics and Jupyter notebooks.

Setting up

1. Create a Directory

   Create a directory called proteoparc in your Colab Notebooks folder. (MyDrive/Colab Notebooks) is generated by Colab in your Google Drive:

   /content/drive/MyDrive/Colab Notebooks/proteoparc
   

2. Open the Notebook in Google Colab

   • Navigate to your Google Drive.
   • Open the ProteoParc_in_Colab.ipynb notebook using Google Colab.

3. Install Required Libraries

   The first few cells of the notebook will install the necessary Python libraries. Simply execute these cells to set up the environment.

Usage

1. Load Your Data

   Upload your proteomics data files to the proteoparc directory in the Google Colab environment as instructed in the notebook.

2. Run the Analysis

   Follow the step-by-step instructions provided in the notebook to run the analysis. The user-friendly button interface allows you to execute different parts of the workflow easily.

3. Interpret the Results

   Use the visualisations and output provided by the notebook to interpret your results.

Contributing

We welcome contributions to this project. If you would like to contribute, please follow these steps:

1. Fork the repository.
2. Create a new branch (git checkout -b feature-branch).
3. Make your changes and commit them (git commit -m 'Add new feature').
4. Push to the branch (git push origin feature-branch).
5. Open a pull request.

License

This project is licensed under the MIT License. See the LICENSE file for more details.

Contact

For any questions or feedback, please contact matthew@palaeome.org.