Metagenomics 2008 Webcasts Now Available for On-Demand Viewing

By Alex Matthews, Tiffany Fox, Erik Jepsen

San Diego, CA, November 20 , 2008 -- Calit2 at UC San Diego recently hosted the Metagenomics 2008 workshop, a week-long opportunity to strengthen collaborations, share data and discuss new trends in metagenomics [read article here ].  Participants included members of Calit2's  Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research (CAMERA) project, as well as other scientists, software developers and infrastructure providers from around the world. Approximately 60 of the plenary presentations are now available for on-demand viewing below. [Windows Media player and broadband connection required; for any trouble viewing the videos,  click here for troubleshooting instructions .]

Jump to: Monday | Tuesday | Wednesday | Thursday | Friday

Monday, 11/3 Enabling Metagenomics and Genomics: Information Required for Metagenomics and Genomic Standards
Genomic and Metagenomic Metadata
John Wooley
Setting the Stage: Mobilizing the Metagenomics Community
John Wooley, UC San Diego; Chair, Metagenomics 2008
Length: 2:49 [video]
Iddo Freidberg
CAMERA and Metadata Standards
Iddo Friedberg, CAMERA-Calit2/UC San Diego
Length: 08:14 [video]
Dawn Field
GSC and the Minimum Information About a (Meta) Genome Sequence (MIGS) Specification
Dawn Field, Oxford Centre for Ecology and Hydrology
Length: 12:27 [video]
Susanna Sansone
The Rapidly Growing Standards Landscape in 'omics
Susanna Sansone, European Bioinformatics Institute
Length: 13:43 [video]
Guy Cochrane
Source Information at INSDC at the Trace Archives
Guy Cochrane, European Bioinformatics Institute
Length: 13:02 [video]
John Wooley - Session 1 Wrap Up
Session 1 Wrap Up
John Wooley, UC San Diego et. al.
Length: 13:36 [video]
CoreGSC Projects
Renzo Kottman
Implementing MIGS/MIMS: The Genomic Contextual Data Markup Language (GCDML)
Renzo Kottman, Max Planck Institute for Marine Microbiology/Genomic Standards Consortium
Length: 21:47 [video]
Dawn Field for Peter Dawyndt
StrainInfo and the Linkage of Organisms, Gene and Genomes: The Genomic Rosetta Stone
Dawn Field, Oxford Centre [for Peter Dawyndt, StrainInfo]
Length: 8:01 [video]
Lynette Hirschman
Towards Computer Assisted Markup of Data: Habitat-Lite
Lynette Hirschman, MITRE Corporation
Length: 21:11 [video]
George Garrity
Towards a Standards Compliant Literature: The GSC eJournal
George Garrity, Michigan State University
Length: 17:07 [video]
Owen White
Towards Transparency of Computational Analyses: Standard Operational Procedures
Owen White, University of Maryland
Length: 24:20 [video
Defining the Scope of GCDML
Jeroen Raes
The Importance of Context for the Design and Interpretation of Comparative Metagenomics Studies: The MINIMESS Proposal
Jeroen Raes, European Molecular Biology Laboratory
Length: 15:56 [video
Ingio San Gill
Metadata Capture for Ecological Data: The Ecological Markup Language and Harmonization with GCDML
Inigo San Gil, University of New Mexico
Length: 16:21 [video
Frank Oliver
Extending MIGS/MIMS for Ribosomal RNA Sequences
Frank Oliver Gloeckner, Jacobs University/Max Planck Institute for Marine Microbiology, Bremen
Length: 28:56 [video]
Ontologies and the Description of Habitat and Geolocation
Norman Morrison
Envo Gaz: The Environment Ontology - Linking Environmental Data
Norman Morrison, University of Manchester
Length: 15:40 [video]
Lynn Schriml
Towards and Open Access Gazetter
Lynn Schriml, University of Maryland School of Medicine
Length: 16:00 [video]
James Cole
RDP Habitat Descriptors Survey
James Cole, Michigan State University
Length: 22:57 [video]
SESSION 5 Metadata Capture: A Key Step for Advancing Understanding
Nikos Kyrpides
The Genomes Online Database (GOLD): The Value of a Comprehensive Metadata Collection
Nikos Kyrpides, DOE Joint Genome Institute
Length: 19:53 [video]
Vistor Markowitz
Metadata Capture in the IMG/IMGm: Getting Scientists to Contribute
Victor Markowitz, Lawrence Berkeley National Lab
Length: 25:12 [video]
Panel Day 1 Metagenomics
Panel Day 1: A Community Vision
Various speakers and affiliations
Length: 1:02:27 [video]

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Tuesday, 11/4  
SESSION 1 Challenges in Metagenomics for Bioinformatics and Computational Biology
Owen White
Rational Approaches of Data Management Across Boodles of Data
Owen White, University of Maryland
Length: 43:09 [video]
Adam Godzik
Studying the Metagenomics Protein Universe: Novelty, Diversity and Divergence
Adam Godzik, Burnham Institute for Medical Research/UC San Diego
Length: 51:40 [video]
Daniel Huson
Computational Aspects of Metagenome Analysis
Daniel Huson, Tuebingen University
Length: 41:19 [video
Nikos Kyrpides
Metagenomic Data Processing: Pitfalls and Solutions
Nikos Kyrpides, DOE Joint Genome Institute/LBL
Length: 42:09 [video]
Patrick Schloss
Challenges in Ecological Metagenomics
Patrick Schloss, University of Massachusetts, Amherst
Length: 36:18 [video]
Two-Hour Parallel Discussion Sessions: Documenting the Emergence and Opportunities of the Field
Justin Sonnenberg
Wellness and Diseases: Implications of Important Microbiota
Justin L. Sonnenberg, Stanford University
Length: 1:00:36 [video
Molecular characterization of the bacterial flora in the lung of healthy, asthmatic and chronic obstructive pulmonary diseased (COPD) subjects
Markus Hilty, Imperial College, London
Length: 18:21 [video]
Metagenomics Discussion Session Wrap Up
Discussion Session Wrap Up
Various speakers and affiliations
Length: 15:00 [video]
Stee Giovannoni
Keynote Dinner Speech: The Evolution of Small Bacterial Genomes in the Ultra-Oligotrophic Ocean
Steve Giovannoni, Oregon State University
Length: 49:58 [video]

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Wednesday, 11/ 5
Alexandra Worden
Morning Talk: The Importance of Marine Picoeukaryotes and the Search for Lost Time
Alexandra Z. Worden, Monterey Bay Aquarium Research Institute (MBARI)
At the speaker's request, this talk will not be webcast until a later date.
SESSION 1 Marine Metagenomics
Oded Beja
Photosystem-I Gene Cassettes in Marine Phages
Oded Beja, Technion-Israel Institute of Technology
Talk Removed by Request of Speaker
Shannon Williamson
Deep-Ocean Metagenomics: Comparative Investigations of Microbes Inhabiting Hydrothermal Vents and the Cold Deep Ocean
Shannon Williamson, J. Craig Venter Institute
Length: 40:06 [video
Hideto Takami
Metagenomic Analysis of Deep Subsurface Environments
Hideto Takami, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Length: 35:13 [video]
Elizabeth Dinsdale
Integrative Marine Metagenomics
Elizabeth A. Dinsdale, SDSU/University of Adelaide, South Australia
Length: 41:08 [video]
SESSION 2 New Technologies in Metagenomics
Julian Marchesi
Analyzing the Mobile Metagenome
Julian R. Marchesi, Cardiff University
Length: 26:58 [video
Yuri Gorby
Electromicrobiology: Novel Approaches for Investigating Charge Transfer and Energy Transformation in Microbial Systems
Yuri Gorby, J. Craig Venter Institute
Length: 35:13 [video
Jack Gilbert
Accessing the Metatransriptome for Complex Marine Microbial Communities
Jack Gilbert, Plymouth Marine Laboratory
Length: 41:20 [video]
Dawn Field
Genomic Standards Consortium Report
Dawn Field, Oxford Centre for Ecology and Hydrology
Length: 21:55 [video]
Anjanette Johnston
Integrated Information System for Genomic and Metagenomic Data Analysis at NCBI
Anjanette Johnston and Bill Klimke, NCBI/NLM/NIH
Length: 16:14 [video]
Robin Kodner
Targeted Gene Identification From Short Gene Fragments in Metagenome and Their Use in Biogeochemical Studies
Robin B. Kodner, University of Washington
Length: 24:03 [video]
Jason Flowers
Metabolic Characterization of Candidatus Accumulibacter Phosphatis Using Metaproteomic Analysis
Jason Flowers, University of Wisconsin-Madison
Length: 20:21 [video]
Jonathan Eisen
Dinner Keynote: A Genomic Encyclopedia of Bacteria and Archaea (GEBA) and the Search for the Dark Matter of the Biological Universe
Jonathan Eisen, UC Davis
Length: 1:03:32 [video]

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Thursday, 11/6
Peer Bork
Morning Talk: Comparative Metagenomics
Peer Bork, European Molecular Biology Laboratory, Heidelberg
Length: 52:11 [video]
SESSION 3 Host-associated Microbes
Justin Sonnenburg
Genomic and Genetic Insight into the Gut Microbiota Function and Manipulation
Justin L. Sonnenburg, Stanford University School of Medicine
Length: 43:08 [video]
Jared Leadbetter
New Insights Into Lignocellulose Conversion by Termite Gut Microbes
Jared Leadbetter, California Institute of Technology
Length: 33:25 [video]
Nathan VerBerkmoes
Metaproteomics as a Key Technology for Characterizing the Human Microbiome
Nathan VerBerkmoes, Oak Ridge National Laboratory
Length: 45:32 [video]
Falk Warnecke
Metagenomic Comparison of the Microbial Hindgut Communities in Drywood- and Grass-Feeding Families
Falk Warnecke, DOE Joint Genome Institute
Length: 19:29 [video]
Gabrielle Veronese
Screening the Human Intestinal Microbiota for the Discovery of Novel Enzymes Specific for Dietary Fiber Degradation
Gabrielle Veronese, Institut National de la Recherche Agronomomique (INRA), Toulouse
[video N/A]
Darryl Leon, TimeLogic/Active Motif
Length: 14:41 [video]
Session 4 Emerging Sequence Technologies
Kun Zhang
Single Molecule Analyses of DNA in Environmental Microbes
Kun Zhang, UC San Diego
Length: 35:38 [video]
Feng Chen
New Sequencing Technologies at JGI and Applications in Bioenergy Researches
Feng Chen, DOE Joint Genome Institute
Length: 37:12 [video]
Timothy M. Vogel
Keynote: Soil Metagenomics
Timothy M. Vogel, Universite de Lyon
[video currently not available]
Thomas Jarvie After-Dinner Talk: Exploring Next Generation Sequencing Today
Thomas Jarvie, 454, Inc./Roche
Length: 37:43 [video]

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 Friday, 11/7
John Wooley
Overview of Human Microbiome Project
John Wooley, UC San Diego
Length: 11:14 [video]
E. Grice
The Skin Microbiome in Health and Disease
Elizabeth Grice, NHGRI / NIH
Length: 39:38 [video]
Human Oral Microbiome
Floyd Dewhirst, The Forsyth Institute/Harvard
Length: 46:03 [video]
J. Kinross
The 'Surgical' Microbiome 
James Kinross, Imperial College, London
Length: 44:15 [video]
I. Wilson
NIH Protein Structure Initiative & Discussion 
Ian Wilson, The Scripps Research Institute
Length: 33:40 [video]
New York-SGX Research Center for Structural Genomics: Brief Report on Collaboration with Gerlt/Raushel P01 Consortium
Stephen Burley, SGX Pharmaceuticals, Inc.
Length: 12:33 [video]
Adam Godzik
Protein Target Selection and Charge to Breakouts
Adam Godzik, Burnham Institute for Medical Research
Length: 16:28 [video]
Metagenomics Discussion
Discussion/Breakouts: How Might S Geno and M Geno Work Together for Getting to Biological Function?
Moderator: John Wooley, Chair, Metagenomics 2008, et. al.
Length: 38:09 [video]

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For more information on the Metagenomics 2008, including news releases, press clips and web articles that detail much of what happened during the workshop and symposium, go to the Metagenomics website at

Related Links

Metagenomics 2008