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IDPredict is a project to identify intrinsically disordered proteins as biomarkers of targeted cancer therapies with the use of network topology and motif identification. We created machine learning models using the Random Forest and XGBoost algorhythms that are able to predict new biomarkers based on biological annotation and topological data.

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Project Setup and Troubleshooting

Introduction

To run the codes in this project, we created a .toml file, so creating virtual environments and installing dependencies is possible with the Poetry Python package. This document outlines the steps taken to set up and troubleshoot Poetry with Python, focusing on resolving issues related to virtual environments and Python version compatibility.

Steps to Set Up and Troubleshoot Poetry

1. Verify Python Installation

Ensure that Python 3.9 is correctly installed and accessible:

C:\Users\YourUsername\AppData\Local\Programs\Python\Python39-32\python.exe --version

This should output Python 3.9.x. If it fails, reinstall Python 3.9.

2. Reconfigure Poetry to Use Python 3.9

  1. Remove Existing Virtual Environment

    poetry env remove python
  2. Set Python Version for Poetry

    poetry env use C:\Users\YourUsername\AppData\Local\Programs\Python\Python39-32\python.exe
  3. Reinstall Dependencies

    If using poetry install is not preferred, skip this step.

3. Manually Create and Manage Virtual Environment (If Needed)

  1. Create Virtual Environment

    C:\Users\YourUsername\AppData\Local\Programs\Python\Python39-32\python.exe -m venv myenv
  2. Activate Virtual Environment

    .\myenv\Scripts\activate
  3. Install Poetry in the Virtual Environment

    pip install poetry
  4. Initialize Poetry

    Navigate to your project directory and run:

    poetry init
  5. Add Dependencies

    Manually add dependencies as needed:

    poetry add <dependency>

4. Run Jupyter Notebook (If Required)

  1. Add Jupyter Notebook

    poetry add jupyter
  2. Run Jupyter Notebook

    poetry run jupyter notebook

5. Troubleshooting Common Issues

  1. Python Executable Issues

    Verify that the correct Python executable is being used and is functional.

  2. Virtual Environment Errors

    Ensure that old or conflicting virtual environments are removed.

  3. Configuration Issues

    Check and reset Poetry’s configuration:

    poetry config --list
    poetry config --unset virtualenvs.prefer-active-python
  4. Permissions Errors

    Run PowerShell or Command Prompt as an Administrator if facing permission issues.

Summary

  • Verify Python Installation.
  • Reconfigure Poetry and Set Python Version.
  • Manually Create and Manage Virtual Environment if needed.
  • Run Jupyter Notebook and troubleshoot common issues.

For further assistance, refer to Poetry and Python documentation or seek help from relevant forums.


Replace YourUsername with your actual Windows username in the file.

About

IDPredict is a project to identify intrinsically disordered proteins as biomarkers of targeted cancer therapies with the use of network topology and motif identification. We created machine learning models using the Random Forest and XGBoost algorhythms that are able to predict new biomarkers based on biological annotation and topological data.

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