Run an analysis
Introduction
Mantle allows you to interact with and derive insights from your data using Jupyter notebooks. These notebooks run in using preconfigured environments that have all the tools that power your discovery preinstalled. Mantle supports tracking of inputs and outputs used in an analysis notebook through a powerful SDK allowing you to understand exactly what data was used to produce the results you are looking at. This guide will walk you through the process of running an analysis within Mantle.
Prerequisites
In order to run an analysis in Mantle, you will need to have at least one analysis environment configured. If you do not have an analysis environment configured, please see the Create an analysis environment guide.
Configuration
There are 3 ways to run an analysis in Mantle:
- From the Analyses page in the Mantle UI
- From an Analysis Environment page in the Mantle UI
- From the Datasets page in the Mantle UI
Running an analysis from the Analyses page
To get started, go to {tenant}.app.mantlebio.com/analyses and click the New Notebook button.
A form will appear with the following fields to fill out:
The name of the notebook. Use a descriptive name that will help you identify the notebook later.
The analysis environment that the notebook will run in. Click the dropdown and select the preconfigured notebook environment you would like to use. Select an environment that has the tools you need to run your analysis.
Once you have completed the form, click Create. It will take a few minutes for the notebook to be created and launched. Once the notebook is launched, you will be able to interact with it as you would any other Jupyter notebook. You can run code, write markdown, and save your work as needed.
Running an analysis from an Analysis Environment page
To get started, go to {tenant}.app.mantlebio.com/analyses#environments.
Click on the analysis environment you would like to use to run your analysis. Note that the environment must have an ACTIVE status in order to be used to run an analysis.
From the Analysis Environment page for the selected environment, click the New Notebook button in the top right hand corner.
A form will appear with the following fields to fill out:
The name of the notebook. Use a descriptive name that will help you identify the notebook later.
Once you have completed the form, click Create. It will take a few minutes for the notebook to be created and launched. Once the notebook is launched, you will be able to interact with it as you would any other Jupyter notebook. You can run code, write markdown, and save your work as needed.
Running an analysis from the Datasets page
To get started, go to {tenant}.app.mantlebio.com/datasets.
Select the datasets you would like to use as input to the analysis. You can select multiple datasets to use as inputs to the analysis.
Once you have selected the datasets you would like to use as input, click the New Notebook button in the panel at the top of the datasets table.
A form will appear with the following fields to fill out:
The name of the notebook. Use a descriptive name that will help you identify the notebook later.
The analysis environment that the notebook will run in. Click the dropdown and select the preconfigured notebook environment you would like to use. Select an environment that has the tools you need to run your analysis.
The key that will be used to reference the dataset in the notebook. This key will be used to access the dataset in the notebook. This field is required for each dataset you select as input.
Once you have completed the form, click Create. It will take a few minutes for the notebook to be created and launched. Once the notebook is launched, you will be able to interact with it as you would any other Jupyter notebook. You can run code, write markdown, and save your work as needed.
Shutting down
When you are finished with your analysis, you can shut down the notebook by navigating to the analysis at {tenant}.app.mantlebio.com/analyses/{analysis_unique_id} and clicking the Shutdown button. This will stop the notebook, but will save the state of your notebook so you can always view your results in Mantle later.