Dissertation/Thesis Abstract

Innovative e-infrastructures in bioinformatics: Applications for the next generation globally distributed collaborative networks
by Wu, Hsin-Hui, Ph.D., Saint Louis University, 2012, 171; 3539643
Abstract (Summary)

Integrating distributed, diverse, and dynamic knowledge in evolutionary biology is a tough mission for all biologists. The emerging efforts in bioinformatics are trying to achieve this goal using computational and informatics approaches. Recently, collaborative networks via Internet are being examined within several large international research projects. Examples in the natural sciences include the internationally based, highly integrated and data intensive Cypriniformes Tree of Life (CToL) and International All Cypriniformes Species Initiative (ACSI II). Both of these collaborative initiatives focus on the diversity, taxonomy, nomenclature and evolutionary (phylogenetic) relationships of fishes in the Order Cypriniformes, the world's most diverse group of freshwater fishes occurring natively in North America, Eurasia, and Africa. In these large biodiversity inventory studies, tracking information necessarily linked to the organism's biological classification and nomenclature, changes in these data, documenting descriptive biodiversity information and exchanging information among participating researchers represent only three of the many large tasks for supporting and promoting the research and providing the public and scientific communities a emerging classification reflecting their relationships and all of the various aspects of their biological evolution. This study expands innovative bioinformatic approaches related to, among other elements, data-model and user-experience design that are developed, incorporated, and applied to taxonomic data management, descriptive biodiversity information management, and practical online collaborative networks to demonstrate new systems that are flexible and scalable. These systems also include social networking elements that are embedded into a novel review process involving community input for quality assurance and education of collective contributions through collaborative networks. This system does rely on community contributions and expertise but is a novel, transparent system that will more rapidly advance any field and expedite the education of the public and other scientific disciplines as to the essence, necessity of work in the above listed and other large-scale initiatives, and a superior, globally distributed mega-data center capable of interfacing with many other similar clouds of information. Lastly, remote data transfer and exchange protocol and universal access protocol are applied in the implemented prototype applications. It will support certain functions that take certain parameters and it will return certain data based on the parameters. By examining this novel concept for handling biodiversity information and related knowledge, and making this smart data-taxon informational and educational linkage transparent to a contributing community, the sum of integrated parts clearly illustrate the system's ability to perform novel, insightful, much needed and critical interoperable functions. This approach can be continually enhanced and accessed for maximum information exchange and accessibility performance, essential qualities for advancing a field and distributing highly integrated information and knowledge. The system is inherently based on transparent community investments and full integration of various types of data and the diverse array of possibly needed databases. Full integration of these will advance or enhance our understanding and continual assessment of biodiversity and related information. These two hierarchically arranged set of contributions and their subsidiary components unequivocally transform a broad and rapidly growing series of disciplines in the natural sciences that are all directly related to a globally threatened biodiversity in a rapidly changing environment.

Indexing (document details)
Advisor: Mayden, Richard L., Scannell, Kevin P.
Commitee: Camilo, Gerardo, Chen, Wei-Jen, Knouft, Jason H., Scannell, Kevin P.
School: Saint Louis University
Department: Integrated and Applied Sciences
School Location: United States -- Missouri
Source: DAI-B 74/02(E), Dissertation Abstracts International
Subjects: Evolution and Development, Systematic, Bioinformatics
Keywords: Biodiversity inventory, Collaborative networks, Data model, Nomenclature, Social networking, Taxonomy
Publication Number: 3539643
ISBN: 9781267640734