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A Project Centric Approach For Cyberinfrastructure In Bioinformatics

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Conference

2007 Annual Conference & Exposition

Location

Honolulu, Hawaii

Publication Date

June 24, 2007

Start Date

June 24, 2007

End Date

June 27, 2007

ISSN

2153-5965

Conference Session

Bioengineering laboratories: Bringing research into the classroom

Tagged Division

Biomedical

Page Count

7

Page Numbers

12.100.1 - 12.100.7

Permanent URL

https://peer.asee.org/2155

Download Count

38

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Paper Authors

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Daphne Rainey Virginia Bioinformatics Institute

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Bruce Mutter Bluefield State College

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Lionel Craddock Bluefield State College

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Susan Faulkner Virginia Bioinformatics Institute

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Frank Hart Bluefield State College

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Martha Eborall Bluefield State College

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Lewis Foster Bluefield State College

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Stephen Cammer Virginia Bioinformatics Institute

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Betsy Tretola Virginia Tech

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Bruno Sobral Virginia Bioinformatics Institute

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Oswald Crasta Virginia Bioinformatics Institute

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Abstract
NOTE: The first page of text has been automatically extracted and included below in lieu of an abstract

Abstract Rapid advances in scientific engineering and computer technologies have facilitated the generation of a vast amount of research data. The integration of knowledge from various fields such as computer science, mathematics, chemistry, and biology has resulted in a vast opportunity for creating new research environments based upon cyberinfrastructure (CI). We describe here two projects that were carried out to train the current scientists as well as future workforce to harness the full power of CI for discovery, learning, and innovation across and within all areas of science and engineering. First, the Training Education Advancement and Mentoring (CI-TEAM) demonstration project focused on preparing the future scientific workforce through development and implementation of an interdisciplinary bioinformatics course. Central to the course is a project-centric teaching paradigm to engage students. In this project, the faculty and their students at Bluefield State College (BSC) were introduced to the concepts of CI. The course modules were further modified by BSC to fit the students’ and training objectives. We report here the first implementation and assessment of the CI course using BSC’s Center for Applied Research and Technology (CART) Course Management Service (CMS). The second project was carried out to involve current scientists through similar project-centric approach using the concepts of CI. The Bioinformatics and Genomics Research Core (BGRC) at VBI, as part of the Mid-Atalantic Regional Center of Excellence (MARCE) provided training and support to over hundred researchers working in the area of emerging infectious diseases to enable them in generation, storage, analysis and/or interpretation of ‘omic data. The effective interaction has enhanced discovery of new knowledge as well as feedback for infrastructure development.

1 Introduction

Advances in computational technology are changing the way research is conducted in all aspects of science. Rapid advances in scientific engineering and computer technologies have facilitated the generation of a vast amount of research data. For example, the number of nucleotide sequences in public databases doubles every six months. The integration of knowledge from various fields such as computer science, mathematics, chemistry, and biology has resulted in a vast opportunity for creating new research environments based upon CI (Atkins et al., 20031). In part, this is accomplished by providing effective and efficient platforms that empower scientists and engineers to conduct multi-disciplinary team research.

Bioinformatics is one area where several CI concepts have been successfully implemented through the development of enabling hardware, software, algorithms, and collaborative research support. One of the major challenges facing the post-genomic era is the integration of diverse data sets (Stein, 20032). As described by Kanehisa and Bork (2003) 3, the main goal of bioinformatics during the 1990s was to create primary databases of genes and proteins. Currently, the focus is on extending the databases for quantitative data from transcriptomes and proteomes and providing interoperability among multiple disciplines. The main goal of bioinformatics in the future will be to create a knowledgebase—and the tool set to use the knowledgebase—to advance discovery by implementing the concepts of CI through the integration of various databases, algorithms, and scientific disciplines4,5.

Rainey, D., & Mutter, B., & Craddock, L., & Faulkner, S., & Hart, F., & Eborall, M., & Foster, L., & Cammer, S., & Tretola, B., & Sobral, B., & Crasta, O. (2007, June), A Project Centric Approach For Cyberinfrastructure In Bioinformatics Paper presented at 2007 Annual Conference & Exposition, Honolulu, Hawaii. https://peer.asee.org/2155

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