A Community cyberinfrastructure resource for metagenomics research: CAMERA 2.0
Jing Chen, Shulei Sun, Weizhong Li and John C. Wooley
from: Metagenomics: Current Innovations and Future Trends (Edited by: Diana Marco). Caister Academic Press, U.K. (2011)
The sustained deluge of complex experimental data in metagenomics opens extraordinary opportunities for this new science, but also requires an advanced, cyberinfrastructure-based knowledge resource that provides a platform for rigorous analysis of the data sets and in turn, of the microbial communities. In response, we established the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis or CAMERA and recently released a very major extension to this resource, termed CAMERA 2.0. In this chapter, we describe the essential attributes of CAMERA 2.0 and their relationship to expectations of the experimental and computational researchers in metagenomics. An analysis portal provides access to a semantically aware database along with computational infrastructure. Meticulous attention is paid to annotating the sequence data with metadata, the associated contextual information (environmental parameters). Using the standards established by the Genomics Standard Consortium, CAMERA 2.0 enables ready depositing, locating, analyzing, visualizing and sharing data and the use of a range of actual analytical processes or workflows. These workflows, most notably, are user-selected, allowing a flexible approach in which an investigator can set their own requirements for a given sequential analysis. The analytical and computational history is archived, allowing accurate reproducibility, detailed further analysis, and validation read more ...