What is CAMERA?

CAMERA stands for Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis. The aim of this project is to serve the needs of the microbial ecology research community by creating a rich, distinctive data repository and a bioinformatics tools resource that will address many of the unique challenges of metagenomic analysis. The Project is funded by the Gordon and Betty Moore Foundation which awarded a 7-year, $24.5-million research grant to the CAMERA project, beginning in Jan 2006.

To achieve this, CAMERA is developing the cyberinfrastructure necessary to support the data, tools and resources that will be needed to enable the scientific community to use the rapidly growing treasure of metagenomic information. Success in this will accelerate understanding of biology and deliver novel biological solutions to important societal challenges in health care, energy, and the environment.

Marine metagenomics is emerging as a focus for innovation at the interface of marine environmental science and information technology. The pace of development and the power of gene sequencing for biological discovery are increasing rapidly with the application of shotgun sequencing technology to entire microbial communities. Unlike the traditional culture-based sequencing methods, metagenomics arises from a breakthrough sequencing approach to examine the interaction of countless microbial species present at a specific environmental location and offers tremendous potential to understand better the functioning of natural ecosystems. It is enabling scientists to consider each gene in the context of its ecology: the composition of the rest of the community, the environmental conditions in which it is found, and its relationships with other species with which it is found at other times and places.

CAMERA is making accessible raw environmental sequence data, associated metadata, pre-computed search results, and high-performance computational resources. It is based on innovative cyberinfrastructure leveraging emerging concepts in data storage, access, analysis, and synthesis not available in current gene sequence resources.

Initially, CAMERA is making available all the metagenomic data being collected by the J. Craig Venter Institute's "Sorcerer II" Global Ocean Sampling (GOS) expedition, which is sampling microbial communities every 200 miles around the globe, plus 150 new full genome maps of ocean microbes. The initial incarnation of CAMERA includes two other data sets: a large-scale metagenomic survey of marine viral organisms collected from sites around the North American continent by Forest Rohwer and his research team at San Diego State University and a vertical profile of marine microbial communities collected at the Hawaii Ocean Time-Series (HOTS) station ALOHA by Ed DeLong and his research team at MIT.

Figure 1: Fragment Recruitment Viewer displays the results from a BLASTN sequence comparison of an available microbial genome against selected metagenome sequence datasets. The utility of the plot is to examine the biogeography and genomic variation of abundant microbes when a close reference genome is available.	Figure 2: Summary of results from a BLAST search.

This resource will include the metadata associated with collection of the samples: the location, date, and time of collection; the chemical and physical conditions where the sample was taken; and a measure of its living environment, i.e., all the other sequences found in the same sample. CAMERA will grow in value to include new sequences, genes, and gene families, together with their annotations and associated environmental metadata. In addition, a suite of tools is being developed to enable scientists to analyze the data in innovative and more comprehensive ways.

CAMERA brings together leaders in high-throughput DNA sequencing and metagenomic analysis tools on the one hand, and cyberinfrastructure innovations in optically coupled computing, emerging Grid middleware, and user workspaces on the other. The project is led by Calit2 in partnership with the J. Craig Venter Institute, the Center for Earth Observations and Applications and the Scripps Genome Center (both at the Scripps Institution of Oceanography), the San Diego Supercomputer Center and UC Davis.

The project plans software releases, training sessions, and periodic solicitation of feedback to ensure the infrastructure and services evolve to serve the needs of the scientific community. The success of this project will depend heavily on continuous input from the genomics, microbiology, molecular biology, ecology, and related communities about their needs and priorities. We encourage your feedback on the utility of the tools and data sets we make available and how we can improve on them in subsequent releases.

When fully annotated, this resource will form a Marine Microbial Ecology Knowledge Base of federated information relating to genomic sequence and associated metadata to support a fundamental paradigm shift in the way in which the biological and biomedical sciences develop in the 21st century.

By Stephanie Sides