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Conceptualizing a Genomics Software Institute (GSI)

By Jack A. Gilbert, Charlie Catlett, Narayan Desai, Rob Knight, Owen White, Robert Robbins, Rajesh Sankaran, Susanna-Assunta Sansone, Dawn Field and Folker Meyer

Abstract

Microbial ecology has been enhanced greatly by the ongoing ‘omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI)

Topics: White Papers
Publisher: Michigan State University
OAI identifier: oai:pubmedcentral.nih.gov:3359878
Provided by: PubMed Central

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Citations

  1. (2011). Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol
  2. (2011). Beyond Open Data: Commoning for the collection, curation, management and distribution of bioscience investigations.
  3. (2008). Beyond Server Consolidation. Queue
  4. (2001). Challenges in bioinformatics: infrastructure, models and analytics. Trends Biotechnol
  5. (2012). Defining seasonal marine microbial community dynamics.
  6. (2002). Exploring prokaryotic diversity in the genomic era.
  7. IMG/M: a data management and analysis system for metagenomes.
  8. (2010). ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics
  9. (2010). Meeting report:
  10. (2010). Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci
  11. (2011). Metagenomic mining for microbiologists.
  12. (1998). Prokaryotes: the unseen majority.
  13. Quantitative Insights into Microbial Ecology.
  14. (2010). The case for cloud computing in genome informatics.
  15. (2011). The future of microbial metagenomics (or is ignorance bliss?).
  16. The Genomic Standards Consortium.
  17. The Genomic Standards Consortium. PLoS Biol 2011; 9:e1001088.
  18. (2008). The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.
  19. (2008). The RAST Server: rapid annotations using subsystems technology.
  20. The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation. PLoS ONE 2010; 5:e15545.

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