NCBC XMLtology for Tool Integration - iTools

Summary

iTools is an infrastructure for managing (databasing, traversal and comparison) of diverse computational biology resources. There are 3 types of resources within iTools – data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the 7 National Centers for Biomedical Computing (www.NCBCs.org). Specifically, iTools provides an infrastructure for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources, developed by the NCBCs and other initiatives, are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools provides several flexible human and machine interfaces to its resource meta-data repository.

Overarching Goals

The goals of this initiative (NCBC YPR Working Group) is to develop an integrated agile interaface to all NCBC Computational Biology resources. Also, see the NCBC Yellow-Pages and Resourceome Working Group Charter statement.

Background

Technical Specifications

• Specifications
• Test Settings
• XML Schema for tool descriptions
• To Dos (02/16/07)

Machine Interfaces

• SOAP/XML Interface (Simple Object Access Protocol)
• WSDL (Web Services Description Language)
  • Description of the iTools WSDL interface
• iTools RDF (05/05/08)

Human Interfaces

• (Current)V.07:
  • HTML Applet (11/15/07). This human interface uses your Java-enabled browser to render the iTools interface in the Browser GUI an an applet. You need to enable java and configure your security settings to allow browser pop-ups!
  • Web-Start (11/15/07). This is a Sun Java Web-start version of the iTools human interface. Running this interface will download iTools on your computer (completely automated process) and run iTools as a stand-alone application (no installation is necessary).
  • Hyperbolic Interface (03/24/07). This is a light-weight and less functional stand-alone Graph interafece to a static version of the iTools hierarchy (one would only run this version of iTools if there are problems with the other two interfaces above).
• Old V.01: Prototype (11/10/06). This is a very old version of iTools to illustrate our original design.
  • iTools HTML development server
  • Web-Start
  • iTools development Admin
  • iTools Development user accounts
  • iTools Web Services

iTools Database

iTools uses Hibernate to connect and interface with its database. Hibernate relies on an Industry-standard ORM (Object-Relation-Mapping).

Use Itools Now

Usage

This contains the current iTools User's Guide

iTools Summary

This contains a quick Guide to iTools' aims, function, usage and interfaces.