Open Virome

Open Virome Website
Adopt a Virus Program
Geospatial Reporting
RNA Virus QC

Inspiration

COVID-19 has affected everyone. By leveraging freely-available data, we are creating an Earth-scale pathogen surveillance network for the acceleration of future outbreak-response to ultimately mitigate and prevent the next Pandemic.

Introduction

Last year at Hack Zurich's #CodeVsCovid19 a small team started the Serratus project to uncover the hidden viruses in publicly-available DNA/RNA sequencing data. We analyzed over 5.7 million biological samples (which is >20,000,000 gigabytes of data) to increase the total number of known RNA virus species from 15,000 to over 145,000!

For a deep dive into our background, and to learn more about Serratus (and the new coronavirus species we found) check out our Preprint or the Amazon HCLS Conference Talk (18m).

The "Big-Data" gap

Earth's Sequencing

Serratus increased the total known viruses by an order of magnitude, to translate this data into real world applications we initiated "Open Virome", a front-end interface to distill the world's largest biological datasets into a meaningful knowledge.

By combining virus, host-organism, geography, environment and time data in an intuitive web-interface we will instantly connect scientists, physicians, and epidemiologists to the the available data.

Open Virome Interface

We are proud to present Open Virome a front-end interface for the world's largest public collection of RNA viruses. The RNA Virus Meta-analysis web app is a fully containerized pipeline running on AWS Lambda. The output analysis reports are fully self-contained, and provide all raw data to the end user to facilitate discovery.

Each report provides detailed Quality Control metrics of the input compared against a gold-standard set of 15,000 viral barcodes as described by Edgar and Babaian, 2021.

Virus QC Plots

The virus barcode is then cross-referenced through R-embedded SQL queries against databases to create rich reports showing geospatial distributions, temporal distributions, related viruses, and associated host-organisms. The core philosophy of this design is that it is a data-driven and unbiased approach for understanding virus ecology.

Geospatial Distributions

The reports are fully self-contained and interactive. Explore the data now.

Adopt a Virus Program

Every corner of Our Planet is brimming with viruses, they are a natural part of our ecosystem. By adopting a virus you will receive its “palmprint”, a unique barcode for identifying this species. You can characterise your virus’s ecology with our RNA Virus Meta-analysis web app, and even give it a "nickname”. User assigned nicknames will be shown in our analysis tools, they must be unique and are permanent. Sorry, "Virus McVirusFace" is already taken.

Built With

Submitted to

HackZurich 2021

Created by

Worked on the backend by integrating the analyzation-core - written in R - and wrapped it into a Docker container with Python and made it deployable as an AWS Lambda function, so the analysis can be done ad-hoc. This also allows to have a more sustainable solution and reduce costs by just paying per use.

Matthias Gubler
I developed the R-based analysis reports and web-facing design interfaces for OpenVirome.com.

Artem Babaian, PhD
Daring young biologist hanging out in Cambridge, UK
Andris Prokofjevs