#Itools 3 portable#
#Itools 3 software#
#Itools 3 code#

#Itools 3 software#

There are a number of efforts to develop integrated resources that provide a common user-friendly access to variety of tools and software programs for computational biology. Rather it is intentionally designed to be extensible and applicable to broader range of biomedical research.Д¬urrent approaches for software tool classification, categorization and integration The proposed infrastructure is not limited to needs and applications of the NCBCs. We leveraged the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing (NCBC) to design, implement and validate a new schema for classifying, categorizing and integrating different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. There is an increasing need in the bioinformatics community for accurate accounting of data and resources, e.g., the bioinformatics Resourceome effort.

iTools aims to provide an open, yet secure, infrastructure for resource archival, retrieval and traversal communication between tool developers, clinicians, scientists and the general community and to facilitate the interoperability of resources developed by a wide spectrum of investigators and employed in a variety of computational biology studies.

#Itools 3 portable#

We propose a new decentralized, extensible, lightweight, scalable and portable framework ( iTools) to enable resource location, management, evaluation and mediation. The rapid growth, usage specifications, application domain and method diversity of contemporary computational biology resources presents an impediment to finding, comparing and integrating such data and tools.

In this manuscript, we discuss challenges of development, maintenance and dissemination of robust computational biology resources (data, tools and services, see below). Many space, time, function or interaction modeling techniques apply across the vast spectrum of scales from genotypes to phenotypes, from the small scale of microarray imaging for genomics, to the larger in vivo neuroimaging scale. For example, biological imaging and shape representation вЂ“, sequence analysis, regulatory genomics and alternative splicing are critical components of computational biology. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page .Д«ioinformatics is quickly becoming the central core that integrates the many disparate bodies of data, scientific knowledge and computational infrastructure from fields as diverse as genetics, structural biology, medical and animal models of disease, imaging, engineering, etc. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management.

#Itools 3 code#

iTools is an open source project both in terms of the source code development as well as its meta-data content. 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. We propose two ways to browse and display the iTools dynamic collection of resources. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. iTools includes human and machine interfaces to its resource meta-data repository. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. 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. 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. Specifically, iTools stores information about three types of resourcesвЂ“data, software tools and web-services. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources.

There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. The advancement of the computational biology field hinges on progress in three fundamental directions вЂ“ the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize.