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Biological Observation Matrix BIOM

Supports sparse and dense matrix representations. BIOM is a format developed to be a general-use format for representing biological sample by observation contingency tables. This project is designed for general use in broad areas of comparative -omics. This format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times where each subsystem is observed in each genome. The BIOM package provides a command line interface and Python API for working with BIOM files.

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Publications

Institution(s)

Biofrontiers Institute, University of Colorado, Boulder, CO, USA; Department of Chemistry & Biochemistry, University of Colorado, Boulder, CO, USA; Second Genome, San Bruno, CA, USA; Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA; Argonne National Laboratory, Argonne, IL, USA; Marine Biological Laboratory, Woods Hole, MA, USA; Howard Hughes Medical Institute, Boulder, CO, USA

Funding source(s)

Supported by Amazon Web Services, the Alfred P. Sloan Foundation, and the Howard Hughes Medical Institute.

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