Enabling Metagenomics and Genomics: Information required for Metagenomics and Genomic Standards
[Session organized by GSC, the Genomic Standards Consortium ]

Organizers:
Dawn Field, Oxford Centre for Ecology and Hydrology
Frank Oliver Gloeckner, Max Planck Institute for Marine Microbiology
John Wooley, UCSD

SESSION I: Genomic and Metagenomic Metadata

08:30 John Wooley, Setting the stage: mobilizing the metagenomics community

08:45 Iddo Friedberg, CAMERA interest in community standards for the
capture and exchange of metadata: stage setting

09:00 Dawn Field, Overview of the GSC and the Minimum Information
about a (Meta) Genome Sequence" (MIGS/MIMS) specification

09:15 Susanna Sansone, The rapidly growing standards landscape in 'omics

09:45 Guy Cochrane, The views of the INSDC on metadata
capture

10-10:30 COFFEE

SESSION II: Core GSC Projects

10:30 Renzo Kottmann, Implementing MIGS/MIMS: The Genomic Contextual
Data Markup Language (GCDML):

10:45 Peter Dawyndt, StrainInfo and the linkage of organisms, gene
and genomes: the Genomic Rosetta Stone

11:00 Lynette Hirschman, Towards computer assisted markup of data: Habitat-Lite

11:15 George Garrity, Towards a Standards Compliant Literature: the GSC
eJournal

11:30 Owen White, Towards transparency of computational analyses:
a central SOP repository

11:45 QUESTIONS & COMMUNITY COMMENTS

12:00-1:00 LUNCH

SESSION III: Defining the scope of GCDML

01:00 Jeroen Raes, The importance of context for the design and
interpretation of comparative metagenomics studies: the
MINIMESS proposal

01:15 Inigo San Gil, Metadata capture for ecological data: The Ecological Markup Language and a harmonization with GCDML

01:30 Frank Oliver, Gloeckner Extending MIGS/MIMS to the description of ribosomal RNA sequences

01:45 QUESTIONS & COMMUNITY COMMENTS

SESSION IV: Ontologies and the description of Habitat and geolocation

02:00 Norman Morrison, The Environment Ontology
02:15 Lynn Schriml, Towards and open access Gazetter
02:30 James Cole, RDP Survey of habitats descriptors

02:45 QUESTIONS & COMMUNITY COMMENTS

3:00-3:30 COFFEE

SESSION V: Metadata Capture - A Key Step for Advancing Understanding

03:30 Nikos Kyrpides, The Genomes Online Database (GOLD): the value of a
comprehensive metadata collection

03:45 Victor Markowitz, Metadata capture in the IMG/IMGm: getting scientists to contribute

04:00 Lynn Schriml, The Genome Catalogue: A future vision

04:15 QUESTIONS & COMMUNITY COMMENTS

4:30-5:30 Panel Discussion: A community vision

Tuesday, November 4

8:00 On-site Registration at Atkinson Hall, Calit2 at UCSD
8:00 - 9:00 Poster Setup/Breakfast

Challenges in Metagenomics for Bioinformatics and Computational Biology (9:00 - 1:30)

Session Chair: John Wooley, UCSD

9:00 Introduction
9:20 Owen White, Univ. of Maryland
10:00 Adam Godzik, UCSD

10:40 20 min Break

11:00 Daniel Huson, Tübingen University
"MEGAN/MetaSim"

11:40 Nikos Kyrpides, JGI
"Efficient Metagenomics Data Processing: Pitfalls and Solutions"

12:20 Patrick Schloss, U Mass, Amherst
" Challenges in Ecological Metagenomics"

1:00 - 2:00 LUNCH

2:00 - 4:00 Two-hour Parallel Discussion Sessions:
Documenting the Emergence and Opportunities of the Field

Janet Jansson, Lawrence Berkeley National Lab
"Connecting metagenomics and metaproteomics"

Tim Hunkapiller, Discovery Biosciences and Applied Biosystems
"New sequence technologies for metagenomic research"

Eric Allen, UCSD
"The metagenomic voyage: in situ to in silico"

Justin L. Sonnenberg, Stanford Univ.
"Wellness and diseases; Implications of important microbiota"

Patrick Schloss, Univ. Massachusetts, Amherst
"Soil options"

Set of GSC Breakouts (details to follow; including GCDML
And Genome Rosetta Stone)

4:15 Shuttles Pick Up at La Jolla Shores Hotel

5:00 - 8:30 Welcome Reception (at La Jolla Shores Hotel)

5:30 - 5:45 Welcome Talk: Mark Ellisman, UCSD

5:45 - 7:00 Dinner

7:00- 8:00 Congress Keynote: Steve Giovannoni, Oregon State Univ.
"The Evolution of Small Bacterial Genomes in the Ultra-Oligotrophic Ocean"

8:00 On-site Reg./Poster Setup/Breakfast

8:30 - 9:30 Wednesday Morning Talk: Alexandra Z. Worden, MBARI
"The importance of marine picoeukaryotes and the search for lost time"

10 min Break

Session 1: Marine Metagenomics (9:40 - 12:30)
Session Chair: Stephen J. Giovannoni, Oregon State Univ.

9:40 Oded Beja, Technion-Israel Institute of Technology, Haifa, Israel
" Photosystem-I gene cassettes in marine phages"

10:20 Shannon Williamson, JCVI
"Deep-Ocean Metagenomics: Comparative Investigations of Microbes Inhabiting Hydrothermal Vents and the Cold Deep Ocean"

11:00 10 min Break

11:10 Hideto Takami, JAMSTEC
"Metagenomic Analysis of Deep Subsurface Environments"

11:50 Elizabeth A. Dinsdale, SDSU/University of Adelaide, South Australia
"Integrative Marine Metagenomics"

12:30 - 1:30 Lunch (12:50-12:20: Sponsor's demo I: Journal of Visualized Experiments (JoVE) by Moshe Pritsker).

Session 2: New Technologies in Metagenomics (1:30 - 3:30)
Session Chair: Paul Gilna, UCSD

1:30 Julian R Marchesi, Cardiff University
"Analysing the Mobilome using Metagenomics"

2:10 Yuri Gorby, JCVI
"Electromicrobiolgy: Novel approaches for investigating charge transfer and energy transformation in microbial systems"

2:50 Jack Gilbert, Plymouth Marine Laboratory
"Sequencing complex marine microbial metatranscriptomes with pyrosequencing technology"

3:30 10 min Break

3:40 Genome Standards Consortium Report: Dawn Field, Oxford Centre for
Ecology and Hydrology

Selected talks by abstract submission (4:00- 5:00)

4:00 Anjanette Johnston, NIH
"Integrated information system for genomic and metagenomic data analysis at NCBI"

4:20 Robin B. Kodner, University of Washington
"Targeted gene identification from short gene fragments in metagenome and their use in biogeochemical studies"

4:40 Jason Flowers, University of Wisconsin-Madison
"Metabolic Characterization of Candidatus Accumulibacter phosphatis using metaproteomic analysis"

5:00 - 7:00 Poster Session
7:00 - 8:00 Dinner

8:00 - 9:00 Dinner Keynote: Jonathan Eisen, UC, Davis
"A genomic encyclopedia of bacteria and archaea (GEBA) and the search for the dark matter of the biological universe"

8:00 On-site Reg./Breakfast

8:30 - 9:30 Thursday Morning Talk: Peer Bork, EMBL
"Comparative metagenomics"

9:30 10 min Break

Session 3: Host-associated Microbes (9:40- 12:30)
Session Chair: Janet Jansson, Lawrence Berkeley National Lab

9:40 Justin L. Sonnenburg, Stanford Univ.
"Genomic and genetic insight into the gut microbiota function and manipulation"

10:20 Jared Leadbetter, California Institute of Technology
"New Insights Into Lignocellulose Conversion by Termite Gut Microbes"

11:00 10 min Break

11:10 Nathan C. VerBerkmoes, Oak Ridge National Lab
"Chemical Science Division, Oak Ridge National Laboratories"

11:50 Falk Warnecke, DOE Joint Genome Institute, Microbial Ecology Program
"Metagenomic comparison of the microbial hindgut communities in drywood- and grass-feeding termites"

12:10 Gabrielle Veronese, INRA
"Screening of the human intestinal microbiota for the discovery of novel enzymes efficient for plant fiber degradation"

12:30 - 1:30 Lunch (12:50-12:20: Sponsor's demo II: TBA).

Session 4: Emerging Sequence Technologies (1:30 - 2:50)
Session Chair: Nikos Kyrpides, JGI

1:30 Kun Zhang, UCSD
"Single molecule analyses of DNA in environmental microbes"

2:10 Feng Chen, JGI
"New Sequencing Technologies at JGI and Applications in Bioenergy Researches"

2:50 20 min Break, move to break-out rooms

3:10 - 5:10 Parallel Tutorial/ Demo Sessions

Parallel session I:
CAMERA: Kayo Arima, UCSD
RDP-II: James Cole, Michigan State Univ.
MEGAN/MetaSim: Daniel Huson, Tuebingen University

Parallel session II:
IMG, IMG/M: Victor Markowitz, Lawrence Berkeley National Lab
Greenegenes: Todd DeSantis, Lawrence Berkeley National Lab
MicrobesOnline: Paramvir Dehal, Lawrence Berkeley National Lab

Parallel session III:
Megx.net: Ivaylo Kostadinov & Melissa Duhaime, Max Planck Institute for Marine Microbiology in Bremen
ARB & SILVA: Frank Oliver Gloeckner, Max Planck Institute for Marine Microbiology in Bremen
The New Version of the MG-RAST Server: Folker Meyer, Argonne National Laboratory

5:10 20 min Break, move back to Auditorium

5:30 - 6:30 Keynote Speech: Timothy M. Vogel, Université de Lyon
Title: International Soil Metagenome Sequencing Project

6:30 - 7:30 Dinner

7:30-8:30 After Dinner Talk
Thomas Jarvie 454, Inc
"Exploring Next Generation Sequencing Today"

8:30 - 8:45 Overview of Microbiome [HMP] (J. Wooley)
8:45 - 9:25 Diversity Profile of Human Skin Microbiome (E. Grice)

9:25 - 9:45 Break / Coffee

9:45 - 10:25 Human Oral Microbiome (F. Dewhirst)
10:25 - 11:05 Metabonomic Profiling of Gut Microbiome (J. Kinross)
11:05 - 11:20 Comparative/Integrative Considerations/Challenges

11:20 - 12:30 Lunch
(12 and 12:15 - STARCAVE DEMO as option)

12:30 - 1:20 Structural Genomics Overview w Discussion (I. Wilson)
1:20 - 1:40 Protein Target Selection and Charge to Breakouts (A. Godzik)
1:40 Break & then move to Breakout Rooms
2:00 - 3:15 Discussion / Breakouts - How might S Geno and M Geno work
together for getting to Biological Function?

3:15 Break

3:30 Summary of Subgroup Discussions
4:00 Closing Remarks/Considerations (J. Wooley, others)