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Old 07-20-2012, 04:41 PM
Steffen Moeller
 
Default Bug#682242: ITP: python-biom -- observation contingency tables for biological samples

Package: wnpp
Severity: wishlist
Owner: Steffen Moeller <steffen_moeller@gmx.de>

* Package name : python-biom
Version : 1.0.0
* URL : http://biom-format.org/
* License : GPL
Programming Lang: Python
Description : observation contingency tables for biological sampleS

The BIOM file format (canonically pronounced biome) is designed
to be a general-use format for representing biological sample by
observation contingency tables. BIOM is a recognized standard for
the Earth Microbiome Project and is a Genomics Standards Consortium
candidate project.
.
The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this
format is to represent OTU tables: the observations in this case are
OTUs and the matrix contains counts corresponding to the number of
times each OTU is observed in each sample. With respect to metagenome
data, this format would be used to represent metagenome tables: the
observations in this case might correspond to SEED subsystems, and
the matrix would contain counts corresponding to the number of times
each subsystem is observed in each metagenome. Similarly, with respect
to genome data, 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 each subsystem
is observed in each genome.
.
There are two components to the BIOM project: first is definition
of the BIOM format, and second is development of support objects in
multiple programming languages to support the use of BIOM in diverse
bioinformatics applications. The version of the BIOM file format is
independent of the version of the biom-format software.

The binary package is python-biom, while the source package currently runs as
biom-format, just like the web page.

The packaging is made available via the Debian Med subversion repository at


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