Welcome to Outbreak.network

Outbreak.network local build is an offshoot project from Outbreak.info, which originated in the Su, Wu, and Andersen labs at Scripps Research. The goal of Outbreak.network local build is to allow researchers to use the outbreak.info visualizations for genomic variants to explore SARS-CoV-2 data from customizable data sources.

Using Tornado, and ElasticSearch users can turn their sequnces in to a website and api for original data analysis. The process is dockerized to make it as simple as possible.

You can view the list of current local builds here.

How it Works Overview

1. Sequencing data is pre-proccessed using the tool bjorn.

2. Pre-processed data is ingested into ElasticSearch.

3. Tornado server goes up, allowing API access to data.

4. Outbreak.info local web application builds and the client side goes up.

Each of the boxes in the above figure represent a containerized docker process (except for the ‘Sequencing Data’) that can be run via the project Makefile.

Check out how the Getting Started page for installation.

Note

This project is under active development.

Contents

• Getting Started
  • Overview
  • Installation
    • Clone The Repository
    • Populate the Submodules
  • Formatting Data
  • Modify Parameter Configuration
  • Run a Docker Command
• Docker Commands
• Parameters an Data Formatting
  • Parameters
  • Data Formatting
    • Sequencing Data Formatting
    • Zipcode Data Formatting
• New Features
  • Data Explorer
  • Sequencer Acknowledgements
  • Epidemiology Data Inclusion
  • County Level Choropleth
  • Zipcode Level Choropleth