README

Overview
--------

Knowledge Driven Variable Selection (KDVS) is an experimental knowledge extraction
system that utilizes statistical learning and novel data and knowledge integration
methodologies.

Licensing
---------

Knowledge Driven Variable Selection (KDVS)
Copyright (C) 2014 KDVS Developers. All rights reserved.

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

Authors
-------

See CONTRIBUTORS for full authors list.

The current maintainer is Grzegorz Zycinski <g.zycinski@gmail.com>.

Installation
------------

KDVS can be tried immediately without prior installation. Refer to 'Quick Start' below.

KDVS can be installed as Python module with the following command:

    python setup.py install

Note that the documentation and examples are not copied.

Documentation
-------------

See doc/_build/html/index.html

Quick Start
-----------

(*) Linux/OSX

Lets assume the KDVS source archive has been unpacked to:

    ~/KDVS2.0

where '~' indicates the home directory of current user.

Lets execute the example experiment GSE7390. See also 'examples/GSE7390/README'
for more information.

For running KDVS experiment, the results must be stored in writable output directory.
Lets create one:
> mkdir ~/KDVS2.0-results

The experiment can be executed with the following command:

> cd ~/KDVS2.0
> python wrapper.py kdvs/bin/experiment.py -c examples/GSE7390/GSE7390_cfg.py -o ~/KDVS2.0-results

After some minutes, if the run was successful and no error has been reported,
the root output directory ('KDVS_output') and log file ('kdvs.log') shall be
present in the output directory:

> ls ~/KDVS2.0-results
kdvs.log  KDVS_output

IMPORTANT NOTE: KDVS does not overwrite output files and directories. Therefore
the log file ('kdvs.log') and root output directory ('KDVS_output') must be
deleted manually each time the experiment is run with the same output directory.