Metabolomics Standards Workshop
Bethesda Hyatt Hotel
Bethesda, MD
August 1-2, 2005
Abstract
The unique informatics challenge to sharing metabolomics information is being addressed by multiple research groups. This workshop will bring together international groups of biologists, chemists, engineers and bioinformatics experts to discuss the development of informatics standards and shared resources in this emerging field. Metabolomics uses high throughput methods to study metabolism, metabolites and small molecules within cells and tissues. These collective small molecule constituents, or metabolome, along with the proteome and genome, comprise the building blocks of living systems. The metabolome is a dynamic system of chemical reactions and interactions with the building blocks of life. This requires tools to study the chemical properties, or chemoinformatics, of metabolite detection and temporal-spatial dynamics of biochemical pathways and systems biology. The study of metabolomics requires large rates of acquisition, processing, storing, and interchange of metabolic information generated from multiple technologies and experimental model systems. Each of these processes requires descriptions about experimental data, or metadata. Informatics standards will help the process of building a better collective understanding of metabolomes through more effective collaborations among investigators.
Agenda
Monday, August 1, 2005
7:30 a.m. Arrival and Light Refreshments
7:55 a.m. Opening Remarks Arthur Castle, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH)
8:00 a.m. Opening Presentation "Standards for Microarrays: Lessons From the MGED Experience" John Quackenbush, Dana-Farber Cancer Institute
8:45 a.m. Scientific Session I: Technology Overview Several technologies are widely used in metabolomics investigations including mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR). The basic use of these technologies and challenges for identification and quantification of metabolites in biological systems will be reviewed along with emerging new technologies that will contribute to the metabolomics knowledge base.
Speakers: “NMR Spectroscopic Methods for Metabolomics Applications” John Lindon, Imperial College London "Metabolome Annotations by Mass Spectrometry" Oliver Fiehn, University of California, Davis "Profiling Unbound Metabolites with Fluorescent Proteins" Alan Kleinfeld, FFA Sciences
10:30 a.m.
Session II:
Data Acquisition, Processing and Analysis Diverse transformation algorithms are used to derive the identification and quantification of metabolites, fluxes, and metabolomic profiles from raw instrument data. Specific technical aspects of data acquisition, processing and analysis used in metabolomics require informatics support and can be platform dependent. Metadata needed to describe these processes and their effects on interpretation and integration of data for publication will be presented.
Chair: Oliver Fiehn, University of California, Davis Speakers: "High-throughput Extraction and Alignment of Metabolomic Datasets" Lloyd Sumner, The Samuel Roberts Noble Foundation "Identifying and Interpreting Patterns in Metabolomic Data" Truman Bown & Radka Stoyanova, Columbia University
11:45 a.m. Lunch Break (on your own)
12:45 p.m. Panel Discussion on Standards and Informatics Needs for Platforms, Acquisition, Processing, and Analysis Moderator: Arthur Castle, NIDDK, NIH This discussion will address the basic metadata needed to describe instrumentation and processing of raw data to forms that can be used to describe metabolites and metabolic profiles.
2:10 p.m.
Session III: Experimental Designs for Model Systems Several model systems are being used to investigate mechanistic understanding of metabolomes and their temporal-spatial dynamics with regard to biological pathways. Understanding the metadata needed to describe these experiments and intricacies of each model system will provide a foundation for comparing high throughput experimental results. Chair: John Lindon, Imperial College London
Speakers: "Metabolomics Experiments for Yeast Systems Biology" Pedro Mendes, Virginia Tech University "Metabolimics Measurements and Data Integration: How Do We Get There?" Vincent Jo Davisson, Purdue University "Challenges and Developments in GC-EI-MS Based Metabolite Profiling: Enhanced Metabolite Identification and Metabolome Characterization" Joachim Kopka, Max-Planck Institute for Molecular Plant Physiology
4:00 p.m. Break
4:15 p.m.
Session IV: Experimental Design for Preclinical and Clinical Metabolomics Applications Metabolomics has great potential for describing both normal and disease processes in tissues and systems biology. Clinical and preclinical investigation into biomarker discovery, diagnostics, predictive toxicology and understanding of human nutritional and energy balances through interrogation of body fluids and tissues are being conducted with metabolomics approaches. Understanding what metadata information must be captured and conveyed for these uses will be vital to the development of clinical metabolomics approaches to translational medicine.
Chair: Rima Kaddurah-Daouk, Duke University Medical Center/Metabolomics Society Speakers: "The Preclinical Metabonomics Experiment: Meta Data Matter" Don Robertson, Pfizer, Inc. "Accommodating Metabolic Variation in Clinical and Population Based Human Studies" Elaine Holmes, Imperial College London
Tuesday, August 2, 2005
8:00 a.m. Arrival and Light Refreshments
8:30 a.m. Update on Current Activities in Metabolomics Rima Kaddurah-Daouk, Duke University Medical Center/Metabolomics Society
9:00 a.m.
Session IV: Experimental Design for Preclinical and Clinical Metabolomics Applications (continued) "Sample Acquisition and Processing Factors Affecting Multi-Parameter Data Quality" Wayne Matson, ESA, Inc. "Tracer Substrate-Based Metabolomics: Data Handling, Biomarkers, and Patient Stratification" Laszlo Boros, University of California, Los Angeles "NCTR's Center for Metabolomics and ArrayTrack Software for 'Omics' Data Management, Analysis, and Interpretation" Richard Beger, U.S. Food and Drug Administration
10:45 a.m.
Session V: Database Resources, Integration, and Interoperability Metabolomics database resources are being developed by multiple groups. An overview of these resources, their uses, and efforts to allow for integration and interoperability with other resources including chemoinformatics, proteomics, genomics and literature information will be reviewed. Chair: Pedro Mendes, Virginia Polytechnic Institute and State University Speakers: "NCBI Resources for Archival and Analysis of Metabolimics Results" Steve Bryant, National Center for Biotechnology Information (NCBI) "The ArMet Proposal: Development and Integration" Nigel Hardy, University of Wales Aberystwyth
12:00 p.m. Lunch Break (on your own)
1:00 p.m.
Session V: Database Resources, Integration, and Interoperability (Continued) Speakers: "Isotope Assisted Differential Metabolomics and Its Associated NMR" John Markley and Eldon Ulrich, University of Wisconsin-Madison "Metabolomics - The Third Piece of the Omics Puzzle" Susanna-Assunta Sansone, European Bioinformatics Institute "Integration and Interoperability of Cellular Data - the Foundation for Systems Biology" Shankar Subramaniam, University of California, San Diego
2:45 p.m. Discussion: Database Resource Needs and Integration of Current Resources Discussion will address how current government and other public resources can work together to better serve the community; what future resources would be useful; and how information standards can help reach these goals. Moderator: John Whitmarsh, National Institute of General Medical Sciences (NIGMS), NIH
4:15 p.m. Adjourn
Up To Top
Page last updated: May 05, 2008
