Grantee Research Project Results
2006 Progress Report: Development and Application of the DORIAN (Dose-Response Information Analysis) System
EPA Grant Number: R832721C001Subproject: this is subproject number 001 , established and managed by the Center Director under grant R832721
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
Center: New Jersey Research Center for Environmental Bioinformatics and Computational Toxicology
Center Director: Welsh, William J.
Title: Development and Application of the DORIAN (Dose-Response Information Analysis) System
Investigators: Georgopoulos, Panos G. , Tong, Weida
Current Investigators: Georgopoulos, Panos G. , Welsh, William J. , Floudas, Christodoulos , Rabitz, Herschel , Androulakis, Ioannis , Ierapetritou, Marianthi , Tong, Weida
Institution: Rutgers , U.S. Food and Drug Administration
Current Institution: Rutgers , Princeton University , U.S. Food and Drug Administration , University of Medicine and Dentistry of New Jersey
EPA Project Officer: Hahn, Intaek
Project Period: October 1, 2005 through September 30, 2010
Project Period Covered by this Report: October 1, 2005 through September 30, 2006
RFA: Computational Toxicology: Environmental Bioinformatics Research Center (2004) RFA Text | Recipients Lists
Research Category: Computational Toxicology , Human Health , Safer Chemicals
Objective:
The aims of this project have not changed from the original application; original objectives for the report period have been met. However, specific collaborative case studies have been defined during the report period to facilitate testing and evaluating of the accomplishment of these aims.
Progress Summary:
- Developed and deployed the environmental bioinformatics Knowledge Base (ebKB) in a restricted beta version for testing and limited use. The ebKB provides an extensive set of information and modeling resources spanning the source-to-outcome sequence, through a user-oriented interface presenting multiple “views” and search criteria.
- Performed various component-by-component evaluations of ArrayTrack applications to define specific tasks towards the development of ebTrack. Started the design of ebTrack interfaces to the open source database PostgreSQL and Java tools for user interface, analysis, visualization, and W eb-based deployment.
- Performed evaluation of procedures for incorporating biochemical data into the optimization and parameter estimation of the Modeling ENvironment for TOtal Risk studies (MENTOR)-3P components, focusing on Bayesian Tools in conjunction with optimization techniques.
- Developed novel statistical methods for clustering of gene expression data, using multi-level mixture models with simultaneous subset selection.
- Participated in the analysis of gene expression data associated with dibutyl phthalate (DBP) exposures (in collaboration with R832721C002).
- Created a conceptual design for the DOse Response INformation ANalysis system (DORIAN) system to support comprehensive toxicity and risk assessment studies.
Results to Date
- A restricted beta version of the environmental bioinformatics Knowledge Base (ebKB) is deployed and has been demonstrated to collaborators. A public version is expected by the end of the quarter.
- Customized ArrayTrack installations have been completed and a workshop was organized to provide access to the data and tools.
- Case study applications of ArrayTrack were completed with environmentally relevant gene expression data.
- A generalized physiologically based pharmacokinetic (PBPK) modeling system has been applied to study the application of Bayesian techniques for studying exposure reconstruction from biomarker data.
- We developed novel statistical methods for clustering of gene expression data, using multi-level mixture models with simultaneous subset selection.
Future Activities:
- Migration of ArrayTrack from the proprietary Oracle database to open source Postgres database.
- Making the public version of the ebKB available with provisions for soliciting input from collaborators and outside users.
- Continued development of diagnostic tools for sensitivity and stability analysis of mechanistic models and demonstration case studies.
- Refinement and further application of novel statistical methods for data analysis including methods for clustering of gene expression data.
- Definition of specific case studies for comprehensive source-to-outcome modeling and analysis.
Journal Articles on this Report : 1 Displayed | Download in RIS Format
Other subproject views: | All 8 publications | 4 publications in selected types | All 1 journal articles |
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Other center views: | All 330 publications | 132 publications in selected types | All 118 journal articles |
Type | Citation | ||
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|
Georgopoulos PG. A multiscale approach for assessing the interactions of environmental and biological systems in a holistic health risk assessment framework. Water, Air, & Soil Pollution: Focus 2008;8(1):3-21. |
R832721 (2007) R832721 (2008) R832721C001 (2006) R832721C001 (2007) |
Exit Exit |
Supplemental Keywords:
computational toxicology, toxicogenomics, bioinformatics, toxicoinformatics, proteomics, metabonomics, physiomics, cytomics, genomics, transcriptomics, enviroinformatics, cheminformatics, biologically based dose-response modeling, cross-species extrapolation, risk assessment,, Health, Scientific Discipline, ENVIRONMENTAL MANAGEMENT, Geographic Area, State, Risk Assessments, Biochemistry, Environmental Monitoring, Biology, Risk Assessment, ecological risk assessment, computational toxicology, toxicology, environmental risks, biopollution, outreach and training, chemical composition, New Jersey (NJ), human exposure, toxicologic assessment, bioinformatics, biochemical research, human health riskRelevant Websites:
Progress and Final Reports:
Original AbstractMain Center Abstract and Reports:
R832721 New Jersey Research Center for Environmental Bioinformatics and Computational Toxicology Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
R832721C001 Development and Application of the DORIAN (Dose-Response Information Analysis) System
R832721C002 Hepatocyte Metabolism Model for Xenobiotics
R832721C003 Development of Computational Tools for Optimal Identification of Biological Networks
R832721C004 Cheminformatics Tools for Toxicant Characterization
R832721C005 Optimization Tools for In Silico Structural Proteomics
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.
Project Research Results
1 journal articles for this subproject
Main Center: R832721
330 publications for this center
118 journal articles for this center