.. Osprai documentation master file `index.rst`
   created by Christopher Lausted in February 2011.
   Last modified 110203 (yymmdd) CGL.
   Use reStructuredText (reST) and the `.rst` extension.
   See <http://sphinx.pocoo.org/rest.html>.
   To assist viewing differences during version control, try placing a carriage return after every sentence.
   Python source code docstrings also use reST and should be compatible with Epydoc as well.
   This file should at least contain the root `toctree` directive.

####################################
Welcome to the OSPRAI documentation!
####################################

OSPRAI is Open-source SPR Analysis and Integration software.
Its aim is to provide a set of command-line tools for processing high-throughput biosensor data.
With OSPRAI, you can import and export common formats, annotate sensorgrams, 
and perform calibration, background subtraction, and curve-fitting.

OSPRAI is written in Python_ so as to run on all popular platforms, including Linux, Windows, and Macintosh.
Install Python 2.4 (or newer) and the following libraries: python-tk_, matplotlib_, and scipy_.
Additionally, it is useful to install IPython_, the interaction Python shell, 
as well as a good python-aware text editor, such as Editra_, Scite_, or gedit_.

OSPRAI is hosted by Bioinformatics.org_ and managed using the Subversion version control system.
It can be obtained from the website_ or by using a Subversion client such as Svn_, 
RabbitVCS_, or TortoiseSVN_.
Windows users can install all of the necessary prerequisites by installing PythonXY_, 
while Ubuntu Linux users can find everything they need in the Ubuntu repositories.
An example for Ubuntu users follows::

 $ sudo aptitude install python-matplotlib python-scipy python-tk ipython editra
 $ svn checkout svn://bioinformatics.org/svnroot/osprai


Contents:

.. toctree::
   :maxdepth: 2
   
   tutorial01.rst
   mainapi.rst


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`


.. _Python: http://www.python.org
.. _python-tk: http://wiki.python.org/moin/TkInter
.. _matplotlib: http://matplotlib.sourceforge.net/
.. _scipy: http://www.scipy.org
.. _IPython: http://ipython.scipy.org/moin/
.. _Editra: http://editra.org/ 
.. _Scite: http://www.scintilla.org/SciTE.html
.. _gedit: http://projects.gnome.org/gedit/
.. _Bioinformatics.org: http://www.bioinformatics.org
.. _website: http://www.bioinformatics.org/websvn/listing.php?repname=osprai&path=%2F&sc=0
.. _Svn: http://subversion.apache.org
.. _RabbitVCS: http://www.rabbitvcs.org/
.. _TortoiseSVN: http://tortoisesvn.tigris.org
.. _PythonXY: http://www.pythonxy.com