GMOD: System Architecture

1
GMOD System Architecture Integration

• May 2003
• Lincoln Stein, CSHL

2
Issues

• User installation integration
• Documentation
• Directory structure
• Configuration files
• Developer extensibility maintainability
• How do the modules interact?

3
User installation integration

• Packaging
• Dependencies, updates, versions
• README HOWTO files
• Site-specific vs common configuration
• Predictable directory structure
• User support
• Bug tracking feature requests

4
How do the Modules Interact?
?
Query
?
?
?
Edit
?
?
Curate
Visualize
5
Fully Integrated MOD Application
6
Vertical Toolkit
Genome Module
Stock Center Module
Literature Module
7
Federated Toolkit
Curate
Edit
Visualize
Query
Genome Db
Stock Center Db
Literature Db
8
How do we Federate?URL Link Integration
URL Space
http//mydb/lit.cgi
http//mydb/genome.cgi
http//mydb/stock.cgi
Genome Module
Stock Center Module
Literature Module
9
How do we Federate?Common Data Model API
Visualize
Query
Curate
Edit
Common Schema/API
10
How do we Federate?Adaptors
Visualize
Query
Curate
Edit
Red Adaptor
Tan Adaptor
11
How do we Federate?Xchange Format
Visualize
Query
Curate
Edit
BeigeML
12
How do we Federate?Service Architecture
Visualize
Query
Curate
Edit
Get Beige Service
Put Beige Service