GMOD Alpha Release 0 002 Scott Cain What

GMOD Alpha Release 0. 002 Scott Cain

What this release has ● Chado schema ● Perl scripts for loading ontologies and GFF 3 ● Version 1. 61 of Gbrowse ● ● Sample data (bastardized version of SGD GFF 3) Reasonably user friendly install via make

What this release does not have ● Tools for loading and dumping chado XML – ● ● ● Which means Apollo doesn't work with this release Really good documentation—but it is getting better! Developer's Guide compliance--`make install` doesn't put anything in GMOD_ROOT Dependence on SQL: : Translator

Short term goals ● ● Get XML loading and dump installing and working cleanly Begin testing of Apollo round-tripping—with the understanding that initially, it may not work perfectly. ● Have `make install` populate GMOD_ROOT ● Stabilize GFF loading protocol ● Incorporate turnkey for browsing

Intermediate term goals ● ● ● Get other applications running on top of chado, like Pub* and CMAP Remove hard coded passwords from Class: : DBI modules (requires help from SQL: : Translator authors) Provide a method for updating ontologies

Long term goals ● World-wide domination

Prerequisites ● Perl (probably 5. 6. 1 or better) ● Postgresql (7. 3 or better) ● Bio. Perl 1. 4 ● Many perl modules, notably Class: : DBI

How the install goes ● perl Makefile. PL ● make load_schema ● make prepdb ● make ontologies ● Make install ● gmod_load_gff 3. pl