GMOD: System Architecture & Integration May 2003 Lincoln Stein, CSHL
Issues § User installation & integration § Documentation § Directory structure § Configuration files § Developer extensibility & maintainability § How do the modules interact?
User installation & integration § Packaging § Dependencies, updates, versions § README & HOWTO files § Site-specific vs common configuration § Predictable directory structure § User support: § Bug tracking & feature requests
How do the Modules Interact? ? ? Curate ? ? ? Edit ? Query ? ? Visualize
Fully Integrated MOD Application
Vertical Toolkit Genome Module Stock Center Module Literature Module
Federated Toolkit Curate Edit Visualize Literature Db Stock Center Db Query Genome Db
How do we Federate? URL Link Integration URL Space http: //mydb/genome. cgi Genome Module http: //mydb/stock. cgi Stock Center Module http: //mydb/lit. cgi Literature Module
How do we Federate? Common Data Model & API Edit Curate Visualize Common Schema/API Query
How do we Federate? Adaptors Edit Curate Red Adaptor Visualize Query Tan Adaptor
How do we Federate? Xchange Format Edit Curate Visualize Beige. ML Query
How do we Federate? Service Architecture Edit Curate Get Beige Service Visualize Put Beige Service Query