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A data normalizer and processor for files containing taxon biomass/density data for ecotopes.
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README.rst

BioDen

BioDen is a data transformer for files containing taxon biomass/density data for ecotopes. In general the input file of BioDen includes a list of records that give species name, an abundance measure (biomass and/or density), a sample code, the surface sampled, and the ecotope. This list is transformed to a table in which the rows represent species (names) and the columns represent samples. This output table can serve as the input file for various software applications that conduct species community analyses.

Documentation Status

Requirements

BioDen has the following dependencies:

  • GTK+ (>=3.6)
  • Python (>=2.7)

On Debian (based) systems, the dependencies can be installed from the software repository:

sudo apt-get install python-appdirs python-gobject python-xlrd python-xlwt

More recent versions of some Python packages can be obtained via the Python Package Index:

pip install -r requirements.txt

Windows users can install the PyGObject Windows installer with Gtk3 support. Then use pip as described above to install the remaining dependencies. Note that this step is not needed if you have the Windows installer for BioDen, which comes bundeled with the requirements.

Installation

From the GitHub repository:

git clone https://github.com/figure002/bioden.git
pip install bioden/

Or if you have a source archive file:

pip install bioden-x.x.tar.gz

Windows installers can be obtained from SourceForge.

Documentation

The documentation can be found here:

http://bioden.readthedocs.org/

Alternatively, the same documentation can be built using Sphinx:

$ python setup.py build_sphinx

Then launch build/sphinx/html/index.html in your browser.

Contributing

Please follow the next steps:

  1. Fork the project on github.com.
  2. Create a new branch.
  3. Commit changes to the new branch.
  4. Send a pull request.

First make sure that all dependencies are installed as described above. Then follow the next steps to run and develop BioDen within a virtualenv isolated Python environment:

$ git clone https://github.com/YOUR-USERNAME/bioden.git
$ cd bioden/
$ virtualenv --system-site-packages env
$ source env/bin/activate
(env)$ pip install -r requirements.txt
(env)$ python setup.py develop
(env)$ bioden
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