Examples of the <i>input</i> and <i>output</i> XML descriptions in the Pipeline, an integrated graphical workflow environment that mediates inter-resource communications.

<p>If resources described in <i>iTools</i> include such data I/O descriptions, external interoperability environments (like the Pipeline) will be able to automatically enable construction and validation of inter-resource computational workflows.</p

Examples of Meta-Resources for Computational Biology.

<p>Summary comparing <i>iTools</i> to other similar meta-resources environments for archival and retrieval of software tools for computational biology.</p

The main two displays of <i>iTools</i> resources provide tabular (left) and graph-based (right) human interfaces to the resource database (http://<i>iTools</i>.ccb.ucla.edu/).

<p>Both of these facilitate comprehensive traversal, comparison and search of resources. There are several other human and machine interfaces to the <i>iTools</i> database which are discussed in the text.</p

A schematic and dynamic integration of <i>iTools</i> resources demonstrating interoperability of multi-disciplinary tools via graphical workflow environments.

<p>The three nodes with dash-boundaries on the <i>left</i> demonstrate schematically the integration of some computational biology tools. The graphical workflow on the <i>right</i> depicts the practical means of using <i>iTools</i> meta-data to construct module descriptions and generate multidisciplinary and heterogeneous data analysis protocols.</p

This figure illustrates the utilization of <i>iTools</i> for search, comparison and integration of bioinformatics tools.

<p>In this example, we demonstrate the use of the Basic Local Alignment Search Tool (BLAST) for comparing gene and protein sequences against other nucleic sequences available in various public databases. The <i>top row</i> shows <i>iTools</i> traversal and search (keyword = blast) using the hyperbolic graphical interface, and tools comparison and investigation of interoperability using the tabular resource view panel. The <i>bottom row</i> shows the design of a simple BLAST analysis workflow using one specific graphical workflow environment (LONI Pipeline). This BLAST analysis protocol depicts the NCBI DB formatting, index generation and filtering using <i>miBLAST</i>, sequence alignment and result textual visualization.</p

Left <i>panel</i> shows the search, traversal and comparison of tools (in this case image alignment and visualization) based on their data input/output specifications.

<p>The <i>right</i> panel illustrates how streaming data through independent tools (via an external graphical workflow environment, e.g., LONI Pipeline) may be facilitated by the types of data I/O parameters stored as iTools resource-specific meta-data.</p

<i>iTools CompBiome </i>– the <i>iTools</i> Computational Biology Resourceome plug-in consists of a decentralized collection of BioSiteMaps (<i>sitemaps</i> of resources for biomedical computing) and a <i>Yahoo!Search</i>-based crawler for discovering new and updating existent BioSiteMaps anywhere on the web.

<p> These updates propagate automatically to <i>iTools</i>' SandBox and are later reviewed by expert users for inclusion in the <i>iTools</i> DB. The distributed nature of the NCBC CompBiome may be utilized by any tool developer, user or librarian to find, compare, integrate and expand the functionality of different resources for biomedical computing. The left and right panels illustrate the XML schema definition for the BioSiteMap.xml files and the results of a <i>manual</i> initiation of the <i>Yahoo!Search</i> using the <i>iTools</i> CompBiome plug-in, respectively. <i>iTools</i> has an automated weekly crawler initiation as well as manual triggering of the crawler.</p