This guide walks through how to use Mantle Notebooks to go from data to shareable insight.

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Introduction

Mantle Notebooks provide a workspace for biological data analysis in Python. If you’ve ever used a Jupyter notebook or another .ipynb format code notebook, such as Google Colab, the Mantle Notebook interface should look familiar! We’ve added a few features to simplify interacting with your Mantle Database and transforming your data. Get started with Mantle Notebooks by navigating to the Notebooks tab within Mantle.

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Composing your workflow with cells

Notebooks consist of a series of cells. There are multiple types of cells you can add in a Mantle Notebook, each with their own capabilities:
CapabilityEnables you to…
Code                 
  • Write, edit, and run Python code
  • Results that are returned are displayed as the cell’s output
Text
  • Write, format, and display text using Markdown
Data
  • Interact with your Mantle Database
  • Upload new data files and metadata as Mantle data entities
  • Load data entities into the notebook to access their files and properties within the notebook
You can add a new cell by clicking the type of cell you want in the toolbar at the bottom of the notebook.

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Environment configuration

Mantle Notebooks run in the cloud, so you don’t have to worry about occupying your computer’s resources (like storage, RAM, CPUs or GPUs) or installing any software on your own computer. Learn more about the Notebook environment here.

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How to use Mantle Notebooks

1

Start a new notebook

  • Navigate to the Notebooks tab within Mantle and click the New Notebook button.
2

Load data entities from your Mantle Database into your notebook

  • Add a Data cell and select the type of data you are working with.
  • Add a new entity or select the entity you’re interested in.
  • The entity you’ve added or selected is assigned to a Python variable — feel free to change the variable name.
3

If necessary, download files from your data entity

  • Use the Mantle SDK to download any files you need that are contained in your data entities.
4

Analyze your data

5

Share your results

  • Send a link to your colleagues to show them your new insights.

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Templates

Not sure where to start? Want some inspiration? Every Mantle account comes with a few template notebooks preloaded. These are all fully runnable with example data, or you can upload your own data as new entities within the notebook and run the same analysis. Want more? Browse our collection of templates here!