GMOD

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GMOD Project

This page provides an overview of the GMOD project and how it is relevant to this hackathon.

URL GMOD
6 words or less Organism database toolkit, sequence emphasis.
Participants Dave Clements, Sheldon McKay

GMOD Project

The Overview page at the GMOD web site provides an excellent big picture view of the project.

GMOD is primarily two things: software and community.

Software

GMOD is a set of interoperable open-source software components for managing, visualizing and annotating biological, primarily genomic, data.

Some popular components:

GBrowse Genome viewer; GMOD's most popular component.
Apollo
Table Editor
Genome annotation editor and community annotation.
Chado
BioMart
InterMine
database management tools
CMap Comparative map viewer
GBrowse_syn
SynView
Sybil
comparative genomics visualization

Plus many others.

Community

Equally importantly, GMOD is a community of people and organizations using and developing those components to manage, visualize, and annotate their data. GMOD components are used by organizations around the world, both large (FlyBase) and small (ParameciumDB).

This community has:

What GMOD is Not

GMOD is not

  • A hosted service.
    • GMOD users have their own servers and staff
  • A data repository
  • A custom software development shop.

Some Example GMOD Users

This is meant to give you an idea of the spectrum of GMOD users. This section covers FlyBase, ParameciumDB, and the SOL Genomics Network (SGN). We also cover the HapMap Project in a subsequent section.

FlyBase

FlyBase uses and helped create many GMOD Components, including Chado, Apollo, and the GMODTools and XORT database loading and transfer utilities (and many more).

FlyBase is an example of a large GMOD user and contributor, with a significant informatics and curatorial staff.

ParameciumDB

ParameciumDB is both a typical and atypical GMOD user and developer. They are typical because they are a small shop, with only 1 and a half people working full time on the project, and a significant portion of their manual annotation/curation is performed by members of the (small) Paramecium research community. They are atypical in that their website is a complete Paramecium resource, and that it is powered almost entirely by GMOD components.

SOL Genomics Network

The SOL Genomics Network, or SGN, provides yet another example of the continuum of GMOD users. SGN is a web site with a wide variety of information on Solanascese, but they use a blend of custom software, GMOD components and other open source packages. For example, they use GBrowse, Pathway Tools, and Chado, but they only use Chado to store part of their data. A significant portion of their information is stored in a custom schema.

SGN highlights that GMOD components can be used in combination with each other, or independently of each other,

The Typical User

The vast majority of GMOD users run one or two GMOD components. Usually something GBrowse, Apollo, Chado, BioMart or InterMine and then something else. Over time, several users will start with GBrowse and then bring other parts in as needed. These shops typically have one person who works on the software part time, whenever it needs attention.

GMOD is making a concerted effort to make GMOD useful to small shops such as these.

GMOD Requirements

You need

GMOD and this Hackathon

Additional Reading