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As sequencing technology becomes faster and less expensive, there is an increasing need for computing resources and software to process the data it produces. Making use of "cloud computing"--hosting data and/or applications on existing networked computer systems--to give users access to preconfigured, extensible servers is an alternative to building and maintaining large computing infrastructure in-house. The GMOD project has created a community annotation server with a Chado database, GBrowse2, JBrowse, Tripal, and Apollo or WebApollo installed, hosted by Amazon Web Services. Users can clone the GMOD Amazon Machine Image (AMI) and create their own server for storing data and making it accessible to the public. Potential applications of the GMOD AMI range from short term usage, such as during annotation jamborees, to the long term provision of access to genome data and applications to the community.
GMOD.org
Using GMOD to annotate and distribute data in the cloud
http://gmod.org/wiki/Cloud
1Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3
Scott Cain1 and the GMOD Consortium
GMOD is supported by a specific cooperative agreement from the USDA Agricultural Research Service, and by NIH grants co-funded from the National Human Genome Research Institute and the National Institute of General Medical Sciences. GBrowse development is also funded by the Ontario Ministry of Research and Innovation.
Getting Started
Amazon Web Services (AWS)
As a community annotation server, where you don't
have to set up the server.
As an example implementation to guide your own efforts.
As a test bed for software you are developing.
1Mungall CJ, et al. A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics. 2007 Jul 1;23(13):i337-46. PMID: 17646315
2Cantarel BL, et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008 Jan;18(1):188-96. Epub 2007 Nov 19. PMID: 18025269
3Stein LD, et al. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 Oct;12(10):1599-610. PMID: 12368253
4Skinner ME, et al. JBrowse: a next-generation genome browser. Genome Res. 2009 Sep;19(9):1630-8. Epub 2009 Jul 1. PMID: 19570905
5Ficklin SP, et al. Tripal: a construction toolkit for online genome databases. Database (Oxford). 2011 Sep 29;2011:bar044. PMID: 21959868
To get started with GMOD in the Cloud for community annotation, you need raw materials: GFF3 of computational results, such as similarity analyses and gene predictions, as well as the assembled sequence in FASTA format. One choice for generating the computational GFF3 files is MAKER2 (http://www.yandell-lab.org/software/maker.html), a GMOD project that automates several genome annotation tasks.
Amazon Web Service (AWS) is a collection of remote computing resources. GMOD in the Cloud uses EC2, the Elastic Compute Cloud, allowing users to quickly create fully configured and ready-to-use servers. The cost of using EC2 depends on how much you use it, but can be quite competitive with buying and configuring your own server. Amazon also provides a “free tier,” a low-powered server that you can use to test out servers without having to pay.
More information: http://aws.amazon.com/ec2/pricing/
GFF3
FASTA
GMOD in the Cloud AMI
(Amazon Machine Image)
Chado1 is an organism-agnostic database schema for storing a variety of biological data types. It is used by many organism databases across the tree of life.
Chado
Exon-level zoom
JBrowse4 is the next generation GMOD genome browser. It uses primarily client-side rendering to make it very responsive. It also supports SAM and BigWig formatted data and can use data from a Chado database.
Additional Resources
Email: help@gmod.org
Web: http://gmod.org/wiki/Cloud
Demo: http://cloud.gmod.org/
GBrowse3 is GMOD's widely used genome browser. It supports a variety of data formats including GFF3, SAM/BAM, Wiggle, BigWig, DAS and directly reading from Chado. GBrowse2 has several enhancements including support for multiple image renders to improve performance and Google Maps-style side scrolling.
Tripal5 is a Drupal-based web front end for Chado. It supports several Chado data types, including features, stocks, and natural diversity. In allows both browsing and editing the data in the Chado database. The Drupal foundation provides considerable power, including full user and permission support and expansion through community created modules.
WebApollo is a web-browser-based annotation editor for distributed community annotation. WebApollo allows real time interactive editing, so numerous people can work on the same region at the same time and see each other's edits as they happen. WebApollo is based on Jbrowse, with drag and drop feature editing, undo and redo, and supports multiple formats, including running off a Chado database.
Why use GMOD in the Cloud?