CAMERA Presentation at KNAW ICoMM Colloquium May 2008

C A M E R A A Metagenomics Resource for Microbial Ecology Saul A. Kravitz J. Craig Venter Institute Rockville, Maryland USA KNAW Colloquium May 29, 2008

Goals ,[object Object],[object Object],[object Object]

Presentation Outline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Metagenomic Questions

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Genomics vs Metagenomics

Complexity of Microbial Communities ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Global Ocean Sampling Expedition

Global Ocean Sampling (GOS) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],3/08 3/07 4/04

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],GOS: Sequence Diversity in the Ocean Rusch et al (PLoS 2007)

Comparing of Dominant Ribotypes

Comparison of Total Genomic Content

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],GOS Protein Analysis Yooseph et al (PLoS 2007)

Rubisco homologs Added Protein Family Diversity Yooseph et al (PLoS 2007) New Groups GOS prokaryotes Known eukaryotes Known prokaryotes

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],GOS Viral Analysis (Williamson et al PLoSOne 2008)

Viral acquisition of host genes talC Gene GOS Viral Public Viral GOS Bacterial Public Bacterial Public Euk

Reference Genomes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Motivations for CAMERA

Convention on Biological Diversity ,[object Object],[object Object],[object Object],[object Object],[object Object]

CAMERA – http://camera.calit2.net ,[object Object],[object Object],[object Object],[object Object],[object Object],[email_address]

CAMERA Capabilities ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

CAMRA Compute and Storage Complex at UCSD/Calit2 512 Processors ~5 Teraflops ~ 200 Terabytes Storage Source: Larry Smarr, Calit2

CAMERA Metagenomic Data Volume by Project

CAMERA Users >2000 Registered Since March 2007

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],CAMERA Data Collections

Standardizing Contextual Metadata ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Contextual Metadata Challenges ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

CAMERA Core Metadata by Project ,[object Object],[object Object],[object Object],[object Object],[object Object]

CAMERA 1.3 http://camera.calit2.net

Scalable BLAST with Metadata ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Integration of Metadata and Data

Browsing Large Data Collections: Fragment Recruitment Viewer ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Fragment Recruitment Viewer Sequence Similarity Genomic Position Doug Rusch, JCVI

Sequence Similarity Genomic Position Annotation Geographic Legend

Prochlorococcus marinus str. MIT 9312 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Mate Status Highlights Differences ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Mate Pairs Highlight Variation

View by Sample Filter by mate status

Annotation of Environmental Shotgun Data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Protein Clusters as Gene Finder ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Protein Clusters Advantages and Disadvantages ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Near Future ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Credits ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],http://camera.calit2.net

CAMERA Presentation at KNAW ICoMM Colloquium May 2008

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