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README.md

The Genome Modeling System (GMS)

A paper describing the GMS has been published here: Genome Modeling System: A Knowledge Management Platform for Genomics.

For a brief demonstration of the GMS please start with the: Quick Tour in a Pre-configured Virtual Machine.

More detailed documentation and tutorials are available in the home page: GMS Home

This documentation includes: the Installation Guide, the Location and Description of the HCC1395 Data, the FAQ page, the Guide to Importing your own Data, the Reference Manual for useful Genome Commands, the Beginners Guide to Demonstration analysis, and much more.

Installation of the GMS is possible by many avenues. The following approaches have been tested and have associated tutorials and other documentation: On dedicated hardware, as a preconfigured VirtualBox virtual machine, using Vagrant to create a virtual machine, using Docker, on an Amazon (AWS) EC2 instance, using an OpenStack instance. Refer to the installation types overview for more details.

Some of the tools made available through the GMS can be downloaded individually from Genome Modeling Tools.

The raw data and reference files needed for the GMS tutorial are made available through our FTP and as an Amazon Public Dataset.

Installation of the GMS involves installation of many commonly used bioinformatics tools, a postgres database, other services and use of the following git repositories: genome, UR, gms-webviews, and tgi-workflow. Additional related projects developed at the Genome Institute can be found at github genome and external software packaged for use in the GMS can be found at github genome-vendor.

Quick navigation:

[Install] (https://github.com/genome/gms/wiki/Install) [Docs] (https://github.com/genome/gms/wiki/Docs) [Tutorials] (https://github.com/genome/gms/wiki/Tutorials) [FAQ] (https://github.com/genome/gms/wiki/FAQ)
Step-by-step instructions for installing the sGMS Technical documentation about the internals of the sGMS Tutorials for running different analyses using the sGMS Frequently asked questions about the sGMS
[Home] (https://github.com/genome/gms/wiki/Home) [Install] (https://github.com/genome/gms/wiki/Install) [Docs] (https://github.com/genome/gms/wiki/Docs) [Tutorials] (https://github.com/genome/gms/wiki/Tutorials) [FAQ] (https://github.com/genome/gms/wiki/FAQ)
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