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a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows
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README.md

Viroverse

Viroverse is a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows. Developed in-house for twelve years, it serves as the principal data store for HIV sequencing experiments conducted in the Mullins Lab. Viroverse currently houses tens of thousands of viral nucleotide sequences, together with comprehensive metadata about their creation including PCR protocols, gel images, subject clinical data, and more. Learn more about Viroverse at https://viroverse.washington.edu.

The initial public release of Viroverse has many rough edges and very little documentation. If you’re interested in using Viroverse in production after trying it out in dev mode, please reach out to us so we can engage one-on-one to help you out.

Help us fund Viroverse!

Development of Viroverse has been supported by the US National Institutes of Health grants P01AI057005, R01AI111806, R01AI125026, R21AI122361, R37AI047734, and R21AI087161 to Jim Mullins and P30AI027757 to the University of Washington Center for AIDS Research.

You can help us maintain funding for Viroverse by letting us know when you give Viroverse a try or adopt it for use in your lab. We very much appreciate hearing from you.

Getting Started

The easiest way to run Viroverse in a development environment is to start a local virtual machine using Vagrant and VirtualBox. After installing VirtualBox and Vagrant, running vagrant up in the root of a clone of this repository will start and provision a development VM. This will take quite some time! The provisioning script will install dependencies, create a database, and if all goes well, create a user account named after your username on the host system. To run the development server, log in to the VM with vagrant ssh, enter the /home/vagrant/viroverse directory, and run REMOTE_USER=username ./vv plackup, replacing username with your desktop login name. The application should start and its web interface should be available by browsing to http://192.168.0.2:5000 from your desktop.

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