User:Scott

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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: sco...@scottcain.net or Skype to username scottcain.

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Thursday, January 16

Time Topic Presenter(s) Presentation
9:15 Introductions Scott Cain
9:30 The State of GMOD Scott Cain PDF
10:15 Coffee break
10:30 Google Summer of Code: what it is and why you should participate Amelia Ireland Slides
11:00 Keynote: A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes Andrew Su Slides
12:00 Lunch
1:15 JBrowse and WebApollo Robert Buels PDF
1:45 Migrating from GBrowse to JBrowse Richard Hayes PDF
2:15 Crowdsourcing genomics with Ash dieback Dan MacLean and Martin Page PDF
2:45 Coffee break
3:30
4:00
4:30
5:00 Dinner (on your own)

Friday, January 17

Time Topic Presenter(s) Links
9:15 Galaxy Update Dave Clements slides, Web site
9:45 Tripal Lacey Sanderson PPT
10:15 ABrowse Kong Lei PPTX
10:45 Coffee break
11:00 Epigenome Browser Xin Zhou PDF
11:30 Genome synteny viewer for customized data - extending GSV to multiple genome pairs Qunfeng Dong PDF
12:00 Lunch
1:00 GMOD's Future: Meetings and Focus, a discussion Scott Cain
1:15 Lightning talks, including an MGI update, an introduction to the interaction Chado module, and PolyBrowse
MGI Update Joel Richardson PPTX
Chado Interaction Module Andy Schroeder PDF
Using Images from Journals @ Xenbase Jeff Bowes
PolyBrowse Regina Cer PDF
bioDBnet & Flexible Database Integrator Uma Mudunuri PDF
OpossumBase Chris Childers
Google Summer of Code Robin Haw
Community Building, Outreach and Support Dave Clements
(+ Robin Haw)
PDF

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.


Publications

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

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Support letter templates

The Generic Model Organism Database project is applying for a community resources for genomics grant from the NIH to continue the work that GMOD does, with a focus on JBrowse and Chado development, and GMOD coordination (standards, meetings, and courses).

We need to demonstrate that we support the community and have the support of the community, and we would like to demonstrate that by submitting many letters of support from users. We would be very grateful if you could take a couple of minutes to write such a letter; it should include information about how you use or plan to use GMOD software. There are some template paragraphs below for inspiration.

The letters should be on institutional letterhead, signed, and then scanned to a PDF. Please contact the GMOD helpdesk or email Scott directly if you're willing to write a letter or if you need any help.

The deadline for getting the letters of support is September 3.

This grant would help to secure the future of important parts of the GMOD project, so we would be very grateful for your help!


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 ....