Difference between revisions of "User:Scott"

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(Georgia Tech Seminar)
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===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===
 
===The GMOD Project===

Revision as of 15:11, 16 July 2013

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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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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Genome Informatics 2010 machine prep notes

Ubunut 9.10 Server

 sudo apt-get install subversion libgd2-xpm-dev autoconf apache2 libcgi-session-perl libdbd-pg-perl libdigest-md5-file-perl libclass-base-perl libmodule-build-perl inkscape libio-string-perl libstatistics-descriptive-perl libgd-gd2-perl g++ perl-doc libgd-tools postgresql libgd-svg-perl libtemplate-perl libxml-simple-perl liblog-log4perl-perl libparse-recdescent-perl libsql-translator-perl xsltproc
 sudo apt-get install php5 libapache2-mod-php5 php5-xsl php5-gd php-pear php5-pgsql php5-curl php5-memcache
 sudo apt-get install libdbd-sqlite3-perl libproc-processtable-perl libio-all-perl libio-prompt-perl

Installed Java 5 after adding Ubuntu jaunty repos to /etc/apt/sources.list:

 sudo apt-get install sun-java5-jdk

Installed via CPAN:

  • Bio::Graphics::Browser2 (GBrowse version 2.13) (also installed Bio::Graphics, JSON, Data::Stag)
  • Bio::DB::Das::Chado (Chado GBrowse adaptor version 0.30)
  • GO::Parser
  • Module::Load
  • DBIx::DBSchema
  • XML::Parser::PerlSAX



 sudo a2enmod rewrite

Downloaded software in ~/Software:



Downloaded software in ~/Updateable_repos

  • bioperl-live
  • Apollo
  • jbrowse

PostgreSQL prep:

  • create gmod and drupal users
  • open up connections from local host (setting "trust" in pg_hba.conf)
  • create test, chado and drupal databases

Drupal related stuff

  • Added AllowOverride All to /var/www
  • sudo a2enmod rewrite

GBrowse2 stuff:

  • added a simple .htaccess file to override the drupal on in /var/www/gbrowse2. It just contains the line "Options +Indexes"
  • also added index.html to the DirectoryIndex directive in the drupal .htaccess file.

Chado stuff:

  • put environment variables (GMOD_ROOT and CHADO_DB_NAME) in .profile


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 ....