[show abstract][hide abstract] ABSTRACT: The NIAID (National Institute for Allergy and Infectious Diseases) Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center (www.proteomicsresource.org) has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1) The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2) The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3) Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and prioritization of ten potential diagnostic targets from Bacillus anthracis. The integrative analysis across data sets from multiple centers can reveal potential functional significance and hidden relationships between pathogen and host proteins, thereby providing a systems approach to basic understanding of pathogenicity and target identification.
PLoS ONE 01/2009; 4(9):e7162-. · 3.73 Impact Factor
[show abstract][hide abstract] 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 theCI 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 emerginginfectious diseases to enable them in generation, storage, analysis and/or interpretationof ‘omic data. The effective interaction has enhanced discovery of new knowledge,as well as feedback for infrastructure development.
[show abstract][hide abstract] ABSTRACT: Abstract It is increasingly difficult for teaching to keep pace with rapid advances in technology, especially at the interface of several disciplines. We describe here the development,and implementation of an interdisciplinary bioinformatics course focused on preparing the future scientific workforce. Central to the course is a project-centric teaching paradigm,to engage students in applying the concepts of cyberinfrastructure through the integration of the disciplines of biology, computer science, mathematics, and statistics in the field of bioinformatics. In this project, Bluefield State College (BSC) professors and their students were introduced to the concepts of cyberinfrastructure (CI) through the application of genomics software toolsand data. The
[show abstract][hide abstract] ABSTRACT: Although the role of cyberinfrastructure in engineering education and research is advancing, the use of the concept and infrastructure are quite limited in the courses for the allied health professionals. CIBRED* (CI-TEAM Implemenrtation for Biological Researchers, Educators, and Developers), an NSF funded project, provides a unique opportunity for these authors to introduce the concept of cyberinfrastructure to non-engineering educators and students by designing, developing, and deploying course materials with a interdisciplinary approach. At present, two courses are being developed for deployment and assessment during Fall of 2009. These interdisciplinary courses are being developed in a modular format integrating scientific and technology information from a variety of disciplines. These modules can be incorporated into existing or newly developed courses. One module is for allied health professionals to learn about cyberinfrastructure for healthcare management. The other module focuses on human migration, which introduces engineering education to the undergraduate students from humanities and social sciences. Project-based learning concepts have been implemented in developing these courses to teach various relevant disciplines. The focus is to teach students from diverse disciplines some essential concepts on computer technology in the context of applying cyberinfrastructure. These courses developed for K13 & K14 levels will be offered in an innovative classroom setting for hands-on experimental learning with a focus on solving scientific problems as a team. These courses will also be deployed for online learning in a virtual classroom. The effectiveness of such an approach, introducing concepts from engineering education to the non-engineering students, will be assessed through formative and summative methods for further development and dissemination.
[show abstract][hide abstract] ABSTRACT: We have developed an interdisciplinary bioinformatics course focused on preparing the future scientific workforce. Central to the course is a project-centric teaching paradigm to engage students in applying the concepts of cyberinfrastructure through the integration of the disciplines of biology, computer science, mathematics, and statistics in the field of bioinformatics. High school and college teachers and their students were introduced to the concepts of cyberinfrastructure (CI) through the incorporation of genomics software tools and data. The cornerstone of the project-centric approach was the development and implementation of educational modules centered on applying a transdisciplinary approach to specific and typical challenges that are faced by current scientists in the area of pathosystems biology (host-pathogen-environment interactions). The course modules were further modified by the institutions deploying the course to tailor to specific needs and objectives and to fit the education level and background of the trainees. We report here the first implementation of the CI course and a summary of our initial observations to aid others in implementating similar courses. Specifically, we discuss some of the materials that were developed, some of the pedagogical considerations important to course implementation and communication requirements needed in the establishment of a "virtual community". Additional information is available at https://ci.vbi.vt.edu/CITEAM .