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

@article{10.1371/journal.pone.0002265, 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.}, author = {Dinov, Ivo D. and Rubin, Daniel and Lorensen, William and Dugan, Jonathan and Ma, Jeff and Murphy, Shawn and Kirschner, Beth and Bug, William and Sherman, Michael and Floratos, Aris and Kennedy, David and Jagadish, H. V. and Schmidt, Jeanette and Athey, Brian and Califano, Andrea and Musen, Mark and Altman, Russ and Kikinis, Ron and Kohane, Isaac and Delp, Scott and Parker, Stott D. and Toga, Arthur W. }, citeulike-article-id = {2853120}, doi = {10.1371/journal.pone.0002265}, journal = {PLoS ONE}, keywords = {bioinformatics, computational-biology, framework, software, tools}, month = {May}, number = {5}, posted-at = {2008-05-31 13:42:35}, priority = {2}, publisher = {Public Library of Science}, title = {iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0002265}, volume = {3}, year = {2008} }

TY - JOUR ID - 10.1371/journal.pone.0002265 L3 - citeulike-article-id:2853120 TI - iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources JF - PLoS ONE VL - 3 IS - 5 PB - Public Library of Science N2 - 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. KW - bioinformatics KW - computational-biology KW - framework KW - software KW - tools AU - Dinov, Ivo AU - Rubin, Daniel AU - Lorensen, William AU - Dugan, Jonathan AU - Ma, Jeff AU - Murphy, Shawn AU - Kirschner, Beth AU - Bug, William AU - Sherman, Michael AU - Floratos, Aris AU - Kennedy, David AU - Jagadish, HV AU - Schmidt, Jeanette AU - Athey, Brian AU - Califano, Andrea AU - Musen, Mark AU - Altman, Russ AU - Kikinis, Ron AU - Kohane, Isaac AU - Delp, Scott AU - Parker, Stott AU - Toga, Arthur PY - 2008/May// UR - http://dx.doi.org/10.1371/journal.pone.0002265 ER -