Working with Flow Data

Understanding the Folder Structure

Your notebook environment has two main folders:

`flow-data/` (Read-only)

Contains data files you've marked as importable from Flow
All files are read-only to preserve data integrity

`notebooks/` (Read-write)

Your personal workspace
Create notebooks, scripts, and output files here
All content persists between sessions

Adding Data from Flow

To make your Flow data available in notebooks:

From the Data page:
- Navigate to the Data page in Flow
- Select the files you want to analyze
- Click the "Add to notebooks" button in the top-right corner
From individual file pages:
- Open any file's detail page
- Click the "Add to notebooks" button
Restart your notebook server (Required!):
- In Jupyter, go to File → Hub Control Panel
- Click "Stop My Server"
- Click "Start My Server"
- Your files will now appear in the flow-data/ folder

File Naming Convention

You'll notice that files in flow-data/ have numbers appended to their names (e.g., sample_data_12345.fastq). This ensures unique filenames even when multiple files share the same name across different projects.

Why the numbers? The appended number is the file's unique ID in Flow. This approach:

Prevents naming conflicts
Ensures consistency - a file will always have the same name in your notebooks
Makes it easy to trace files back to Flow

Removing Data from Notebooks

To remove files and free up space:

Use the "Remove from notebooks" button on the Data page or file detail page
Restart your notebook server for changes to take effect