User:Scott

From GMOD

GMOD Coordinator, software development manager at Cold Spring Harbor Laboratory.

Bio:

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 the release manager and developer for GBrowse as well as a developer 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 eight year old boy-girl twins.

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

Georgia Tech Seminar

Title: The GMOD Project and Community Annotation

Abstract: Scott will introduce the Generic Model Organism Database (GMOD) project, both its philosophy and the practical results. With open source software projects covering genomics topics like database storage, visualization, feature editing and literature curation, the GMOD project tries to be many things to many people. Then Scott will discuss work tying together several GMOD projects (Chado, Apollo, ModWare, and GBrowse) along with the popular open source wiki engine, MediaWiki, to create a reusable community annotation system.

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]}

1. ↑ O'Connor BD et al. (2008) GMODWeb: a web framework for the Generic Model Organism Database. Genome Biol 9: R102 PubMed
2. ↑ Arnaiz O et al. (2007) ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res 35: D439-44 PubMed
3. ↑ Harrington JJ et al. (2001) Creation of genome-wide protein expression libraries using random activation of gene expression. Nat Biotechnol 19: 440-5 PubMed
4. ↑ Cain SJ & Chau PC (1998) Transition probability cell cycle model with product formation. Biotechnol Bioeng 58: 387-99 PubMed
5. ↑ Cain SJ & Chau PC (1997) Transition probability cell cycle model. Part I--Balanced growth. J Theor Biol 185: 55-67 PubMed
6. ↑ Cain SJ & Chau PC (1997) Transition probability cell cycle model. Part II--Non-balanced growth. J Theor Biol 185: 69-79 PubMed
7. ↑ Cain SJ & Chau PC (1997) A transition probability cell cycle model simulation of bivariate DNA/bromodeoxyuridine distributions. Cytometry 27: 239-49 PubMed