Jupyter Notebooks Overview

Flow provides an integrated Jupyter notebook environment where you can perform interactive data analysis with your Flow data. This powerful feature gives you a personal workspace to explore, analyze, and visualize your biological data using Python and popular data science libraries.

What are Flow Jupyter Notebooks?

Flow Jupyter Notebooks are personal, interactive computing environments integrated directly into the Flow platform. They provide:

Direct access to your Flow data - Work with your sequencing files and analysis results without downloading
Persistent workspace - Your notebooks persist between sessions
Pre-configured environment - Common bioinformatics and data science libraries ready to use
Secure isolation - Each user has their own isolated notebook server

Common Use Cases

Exploratory data analysis of sequencing results
Custom visualizations beyond Flow's built-in reports
Statistical analysis and hypothesis testing
Integration with external datasets
Development of custom analysis workflows
Quality control and data validation

Key Features

Personal Workspace

Each user gets their own isolated Jupyter environment with:

Persistent storage for notebooks and files
Pre-installed scientific Python packages
Ability to install additional packages as needed

Direct Data Access

Access your Flow data without downloading
Files appear in a read-only flow-data/ folder
Seamless integration with Flow's data management

Full Jupyter Functionality

Create and run Python notebooks
Install custom packages with pip
Export notebooks in various formats
Use markdown for documentation

Getting Help

Explore the following sections to learn more about using Jupyter notebooks in Flow:

Getting Started - Access your notebook environment and create your first notebook
Working with Flow Data - Learn how to access and work with your Flow data
Managing Your Notebooks - Organize your work and install packages
Best Practices - Tips for efficient and effective notebook usage
FAQs - Answers to common questions
Troubleshooting - Solutions to common issues

Next Steps

Ready to start analyzing your data? Head to the Getting Started guide to access your notebook environment and create your first analysis.