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DeepCell Datasets

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Getting Started

DeepCell Datasets is a serverless applicatioin that allows authenticated users to access published datasets. This is aided by using lerna as well as the serverless framework. lerna enables us to easily control all of the services from the root directory, while serverless allows us to deploy and manage AWS infrastructure through .yml configuration files.

Make sure serverless is installed by running npm install -g serverless@2.

Deployment

lerna is used to manage and deploy both the frontend and the application services with a simple yarn or npm command:

yarn deploy:dev
# yarn deploy:prod

Architecture

The application implements a microservice architecture made up of the following components:

  • frontend: a static webpage that is the primary interface of the application.
  • AWS Congito: An AWS service that handles all user authentication. Users that have confirmed their email address are authenticated to download data in a protected S3 bucket. The authentication React components have been overridden in frontend/src/auth to provide the application with a cohesive style.
  • send-email: an AWS Lambda service that can send email to admins on behalf of new users.
  • validate-email-domain: a deprecated service that whitelists certain domains for account creation. This is used as a pre-signup hook for AWS Cognito.

How to update with new data

Data is saved in a protected S3 bucket, but to enable users to view and download these datasets, the details must be saved in frontend/src/datasets/AllDatasets.tsx.

This is a simple JSON object that has the following fields:

Name Description
title The name of the dataset.
objectKey The path to the dataset inside the S3 bucket.
thumbnail The path to the thumbnail example, which must be saved in frontend/public/images.
imagingPlatform The imaging platform that created the dataset.
samples The type of image data.
description A brief description of the data.

Copyright

Copyright © 2016-2021 The Van Valen Lab at the California Institute of Technology (Caltech), with support from the Paul Allen Family Foundation, Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. All rights reserved.

License

This software is licensed under a modified APACHE2.

License

See LICENSE for full details.

Trademarks

All other trademarks referenced herein are the property of their respective owners.

Credits

Van Valen Lab, Caltech