GNOS Pre-Installation Checklist

Overview

GNOS can be deployed on-premises behind your firewall or in a storage bucket with a third party cloud provider (like Microsoft Azure). Alternately, Annai Systems can host GNOS in our data center, providing a Repository as a Service (RaaS).

Repository as a Service

The RaaS is a hosted, fully managed instance of Annai GNOS.  As a customer, you will retain all ownership of the data and control over who has access to the files.  You are able to provide access to the data to users inside or outside of your organization.

There are no fees for transferring data into or out of the RaaS.

If you or your collaborators need compute or storage resources adjacent to the files you store in the RaaS, we can provide these through our BioCompute Farm offering.

All Deployments

Define Your Metadata Schema

As an administrator, GNOS allows you to define the metadata standards for the files contained in your repository. GNOS will require users to conform to these metadata standards as they upload new files to the system.

Before you begin GNOS installation, decide which metadata fields are relevant for your organization. Examples include organism type, disease names, and reference assembly.

Alternately, our team of bioinformaticians and software engineers can help develop a metadata schema that is right for you. We have extensive experience developing robust genomic metadata standards from our work with the NIH, CG Hub, and the International Cancer Genome Consortium.

Pick Studies

Your GNOS repository can contain a single study, or you can divide it into two or more studies. Each study can have its own metadata schema, and users can be granted access to files on a study-by-study basis. You can always add or remove studies later, but it's a good idea to come up with a list beforehand.

Assign Permissions to Users

Once you have a list of studies, develop a list of users who should have access to GNOS. Remember that permissions are assigned on a study by study basis.

List your user permissions in two CSV files. One CSV should contain a list of all users with download permissions; the other should contain a list of all users with upload permissions. Provide the user's first and last name, their email address, and the study name that they should have access to. If a user has access to more than one study, provide a row for each study. Here's an example.

David Golst, dgolst@duke.edu, melanoma
Robert Hwong, rhwong@princeton.edu, melanoma
Clint Warren, cwarren@texas.edu, pancreatic
Clint Warren, cwarren@texas.edu, neuroblastoma

Designate a Technical Point of Contact

Pick somebody (preferably a member of your IT team) who we can contact with questions about your environment.

Prepare Your Existing Files

We provide a script for migrating your existing files en masse to GNOS, but before you can use it, you need to determine where they reside in your storage media. Determining absolute paths to your existing files will greatly accelerate the data migration process.

Additionally, please ensure that each of your files has a unique name.

Determine Gene Torrent OS Requirements

You will use the Gene Torrent client to upload and download files from the GNOS repository. We currently offer Gene Torrent for the following OSes.

CentOS 6.x

Ubuntu 12.02

Ubuntu 14.04

If you would like clients for another OS, let us know and we will prepare a build for you.

Additional Items for On-Premises Deployments

Acquire Hardware

GNOS has some basic hardware requirements. Please make sure the necessary compute and storage resources are ready before installation starts.

You will also need to install at least one GeneTorrent client to upload files to your new repository. GeneTorrent requirements can be found here

Open Ports

You will need to open several ports for outside collaborators to download files stored in your GNOS repository. These ports are covered in the GNOS system requirements.

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