iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

Abstract

The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–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 seven National Centers for Biomedical Computing. iTools provides a system 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 are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.

What are we learning from the cancer genome?

“…A growing number of pathway analysis tools are now becoming available to organize diverse candidate driver aberrations into functional networks. 99–105 Several recent publications document this approach. 7,106,107 They typically either identify pathways curated from the literature that harbour more genomic aberrations than would be expected by chance, or use genomic information to calculate pathway activity scores that take into account the regulatory ‘directionality’ that is known from the curated literature.…”

“…Several large-scale systems biology efforts are now underway to identify and validate regulatory networks that are deregulated by genomic aberrations, and to use this information to guide the development of pathway-targeted therapies. 99,106,108 …”

Hyperbolic Wheel: A Novel Hyperbolic Space Graph Viewer for Hierarchical Information Content

“…Here we rendered the hierarchy of iTools resources [41]. Detailed explanation of this case is included in the section Limitations.…”

Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

“…A good example is iTools 65 (Dinov et al 2008), a system for classification, categorization and integration of different computational biology resources. This system has several functionalities, such as storage, searching, traversal and retrieval of resources and their corresponding metadata description.…”