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1 < .. osprai-doc documentation master file, created by
2 <   sphinx-quickstart on Mon Jan 31 23:07:52 2011.
3 <   You can adapt this file completely to your liking, but it should at least
4 <   contain the root `toctree` directive.
1 > .. Osprai documentation master file `index.rst`
2 >   created by Christopher Lausted in February 2011.
3 >   Last modified 110203 (yymmdd) CGL.
4 >   Use reStructuredText (reST) and the `.rst` extension.
5 >   See <http://sphinx.pocoo.org/rest.html>.
6 >   To assist viewing differences during version control, try placing a carriage return after every sentence.
7 >   Python source code docstrings also use reST and should be compatible with Epydoc as well.
8 >   This file should at least contain the root `toctree` directive.
9  
10 + ####################################
11   Welcome to the OSPRAI documentation!
12 < ====================================
8 <
9 < Contents:
10 <
11 < .. toctree::
12 <   :maxdepth: 2
13 <  
14 <   tutorial01.rst
15 <
16 <
17 < Overview
18 < ========
12 > ####################################
13  
14   OSPRAI is Open-source SPR Analysis and Integration software.
15   Its aim is to provide a set of command-line tools for processing high-throughput biosensor data.
16 < With OSPRAI, you can import and export common formats, annotate sensorgrams, and perform calibration, background subtraction, and curvefitting.
23 <
24 <
25 < Software installation
26 < =====================
16 > With OSPRAI, you can import and export common formats, annotate sensorgrams, and perform calibration, background subtraction, and curve-fitting.
17  
18   OSPRAI is written in Python so as to run on all popular platforms, including Linux, Windows, and Macintosh.
19   Install Python 2.4 (or newer) and the following libraries: python-tk, matplotlib, and scipy.
20   Additionally, it is useful to install IPython, the interaction Python shell, as well as a good python-aware text editor, such as Scite or gedit.
21   OSPRAI is hosted by Bioinformatics.org and managed using the Subversion version control system.
22 < It can be obtained from the website or by using a Subversion client such as `Svn <http://subversion.apache.org>`_, `RapidSVN <http://rapidsvn.tigris.org>`_, or `TortoiseSVN <http://tortoisesvn.tigris.org>`_.
23 < Windows users can install all of the necessary prerequisites by installing `PythonXY <http://www.pythonxy.com>`_, while Ubuntu Linux users can find everything they need in the Ubuntu repositories.
22 > It can be obtained from the website or by using a Subversion client such as
23 > `Svn <http://subversion.apache.org>`_, `RapidSVN <http://rapidsvn.tigris.org>`_, or `TortoiseSVN <http://tortoisesvn.tigris.org>`_.
24 > Windows users can install all of the necessary prerequisites by installing
25 > `PythonXY <http://www.pythonxy.com>`_, while Ubuntu Linux users can find everything they need in the Ubuntu repositories.
26   An example for Ubuntu users follows::
27  
28   $ sudo aptitude install python-tk python-matplotlib python-scipy ipython scite
29   $ svn checkout svn://bioinformatics.org/svnroot/osprai
30  
31  
32 < API
41 < ===
42 <
43 < .. automodule:: vu_module
44 <   :members:
32 > Contents:
33  
34 < .. automodule:: io_module
35 <   :members:
34 > .. toctree::
35 >   :maxdepth: 2
36    
37 < .. automodule:: ba_class
38 <   :members:
37 >   tutorial01.rst
38 >   mainapi.rst
39 >
40  
41   Indices and tables
42   ==================

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