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Informations about the package biom-conversion-server

biom-conversion-server

A simple php server that can convert biom version 2 (hdf5) files and data to biom version 1 (json) and vice versa. It simply provides a web and API interface to the convert feature of the official python biom format tool. This project is not part of the official biom project.

Please cite our article at f1000 Research that describes this module:

You can cite the current version of this software repository using the Zenodo Zenodo

Please cite the original biom project in addition to this project as:

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J. Gregory Caporaso.
GigaScience 2012, 1:7. doi:10.1186/2047-217X-1-7

A public instance of the server is running at https://biomcs.iimog.org

Getting started

To run your own conversion server on localhost port 8080 using the docker container execute the following commands:

Now you can visit your conversion server in the browser at http://localhost:8080/ And you can point tools that use the conversion api as a webservice to http://localhost:8080/convert.php (e.g. biojs-io-biom).

Changes

1.0.6 (2018-10-04)

1.0.5 (2018-03-27)

1.0.4 (2017-07-28)

1.0.3 (2017-03-29)

1.0.2 (2016-12-22)

1.0.1 (2016-12-22)

1.0.0 (2016-09-07)

0.4.0 (2016-09-06)

0.3.0 (2016-07-29)

0.2.0 (2016-07-25)

0.1.0 (2016-07-08)

All versions of biom-conversion-server with dependencies

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