MIMB_cellpainting_tutorial

This repository contains the materials for the MIMB cell painting tutorial, including Jupyter Notebooks, data files, and annotations.

Repository Structure

Data Directory

• Data/Annotations/: Contains various annotation files including:
  • blocklist_features.txt: Text file listing features to be blocked, downloaded here
  • chemical_annotations.csv: CSV file containing chemical annotations, dowloaded here.
  • toxcast_data.csv: The dataset used for estrogen receptor activity prediction, downloaded from Moleculenet.
  • ER_activity_luc_bg1.csv: This activity dataset obtained after processing toxcast_data.csv,is generated when running ToxCast_Tox21_ERa.ipynb

Cell_Profiles Directory

• Data/Cell_Profiles/: Directory containing cell profile data files.
  • part_1.csv -> part_63.csv queried from GigaDB

Output Directory

• Data/Output/: Directory where the output of the Jupyter Notebooks will be stored. This directory is initially non-existing and will be created and generated after running the 1st notebook, it will contain:
  • output_notebook_1.pkl: Output of Part1-Data_Processing.ipynb
  • output_notebook_2.pkl: Output of Part2-Similarity_Analysis.ipynb
  • ER_activity_luc_bg1.csv : Output of ToxCast_Tox21_ERa.ipynb

Notebooks Directory

• Notebooks/: Contains Jupyter Notebooks for different parts of the tutorial:
  • Part1-Data_Processing.ipynb: Notebook for data processing.
  • Part2-Similarity_Analysis.ipynb: Notebook for similarity analysis.
  • Part3-Machine_Learning.ipynb: Notebook for machine learning tasks.
  • ToxCast_Tox21_ERa.ipynb: Notebook to prepare Toxcast data.

Other Files

• README.md: This file, provides an overview of the repository structure and contents.
• LICENSE: License information
• mimb_cellpainting.yml : File listing environment dependencies.
• Setup_manual.pdf : The getting started section detailed for beginners and Windows user.

Getting Started

To run the Jupyter Notebooks locally on your machine, follow these steps:

1. Clone the repository:

   git clone https://github.com/volkamerlab/MIMB_cellpainting_tutorial.git
   cd MIMB_cellpainting_tutorial
   

Setting Up the Environment

For setting up the environment install conda :

1. Install MINICONDA To install and use Conda; miniconda installer, follow the instructions on the official Conda installation page for your operating system.

2. Install pip If you have Python version 3.4 or later, PIP is included by default.
   To check your version refers to Setup_manual.pdf.
   To install pip follow the instructions on the official pip installation page.
   

3. Setting Up the Environment You can now create and activate the environment with the following commands:

conda env create -f mimb_cellpainting.yml
conda activate mimb_cellpainting

Getting started: Lunch Jupyter lab

Start JupyterLab to work with the notebooks.

jupyter-lab

or

jupyter-notebook

You can also open and run, specific notebooks from your terminal as follows; more can be found on the official Jupyter page.

jupyter-notebook ToxCast_Tox21_ERa.ipynb
jupyter execute ToxCast_Tox21_ERa.ipynb

Once JupyterLab is running, you can navigate to the Notebooks directory and open the relevant notebooks to start working with the tutorial. For more insight on Jupyter please refer to the last section of the Setup_manual.pdf.