Revision as of 20:29, 15 August 2013 by Scott (Talk | contribs)

Jump to: navigation, search

GMOD Coordinator, software development manager at The Ontario Institute for Cancer Research.

Scott graduated from The Ohio State University in 1990 with a B. S. in Chemical Engineering and continued on to the University of California in San Diego for graduate school, where he studied improvements to monoclonal antibody production in industrial processes through cell culture and cell cycle modifications. Upon earning his Ph. D. in Chemical Engineering, he began work in the software industry, working for MSI/Accelrys, Pangea Systems/DoubleTwist, and Athersys, until finally coming to rest at Cold Spring Harbor Laboratory in Lincoln Stein's lab. He is the coordinator and a lead developer of the GMOD project, focusing mainly on core schema and tool development, but is also a developer for GBrowse as well as in the BioPerl project. Scott also teaches programming, web development and database design courses at the University of Phoenix. Scott is a happy husband and father of thirteen year old boy-girl twins.

Scott can be reached at his email address: or Skype to username scottcain.

100 5955 1.jpg

The GMOD Project

A talk to be given at the Ohio Collaborative Conference on Bioinformatics (OCCBIO), Miami University, Oxford, Ohio, July 9, 2007

Abstract: The Generic Model Organism Database (GMOD) project is a program to develop generic, reusable software components for building organism databases. The resulting collection of software tools can be used for creating and managing both small laboratory database of genome annotations and large web-accessible community database. GMOD tools are in use at FlyBase, WormBase, SGD, BeeBase and many other large and small community databases. I will introduce several of the GMOD components and discuss several options for configuring and using the software.


[1] [2] [3] [4] [5] [6] [7]

  1. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18570664
  2. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:17142227
  3. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:11329013
  4. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:10099273
  5. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:9093553
  6. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:9093554
  7. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:9041112

Support letter templates

Generic intro paragraph

The GMOD project has two related aims: to provide open source and interoperable visualization, annotation and data management software for use with genomics data, and to foster the growth of a community of developers and users who ask diverse questions but share common problems. The project does this in multiple ways: they provide venues for in person interaction, including GMOD community meetings, workshops at conferences and courses, as well as avenues for online interaction, including software repositories, mailing lists, standards and a wiki-powered web site. Their continued work is important for the future of genomics-driven biology research.

Took a summer school course

The GMOD projects has provided many courses to reach out to the community and get new users. I took one of the "summer school" courses WHEN, WHERE which covered several topics, including Chado, GBrowse, Galaxy, Apollo, Intermine, BioMart, WebApollo. The course brought together experts in each of the software projects (typically the lead developer) to teach and it provided an excellent opportunity both to learn about the software and to interact with both the developers and the other students who were also grappling with their own massive data influxes.

More about your personal experience with the course...

Related project

The GMOD project aims to promote communication between software communities and interoperability between software. They provide several venues for communicating: community meetings, workshops, mailing lists, and a wiki-powered website. They also provide some standards for software interoperability. These are important to us because ....