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Revision: 54
Committed: Wed Feb 16 21:29:02 2011 UTC (9 years, 9 months ago) by clausted
File size: 8335 byte(s)
Log Message:
Added fit_module and mdl_module to sphinx documentation.
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1 clausted 53 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
2     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
3    
4     <html xmlns="http://www.w3.org/1999/xhtml">
5     <head>
6     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
7    
8     <title>Welcome to the OSPRAI documentation! &mdash; osprai-doc v0.1-110210 documentation</title>
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25     <div class="related">
26     <h3>Navigation</h3>
27     <ul>
28     <li class="right" style="margin-right: 10px">
29     <a href="genindex.html" title="General Index"
30     accesskey="I">index</a></li>
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33     accesskey="M">modules</a> |</li>
34     <li><a href="index.html">osprai-doc v0.1-110210 documentation</a> &raquo;</li>
35     </ul>
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37    
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41     <div class="body">
42    
43     <div class="section" id="welcome-to-the-osprai-documentation">
44     <h1>Welcome to the OSPRAI documentation!<a class="headerlink" href="#welcome-to-the-osprai-documentation" title="Permalink to this headline">¶</a></h1>
45     <p>OSPRAI is Open-source SPR Analysis and Integration software.
46     Its aim is to provide a set of command-line tools for processing high-throughput biosensor data.
47     With OSPRAI, you can import and export common formats, annotate sensorgrams,
48     and perform calibration, background subtraction, and curve-fitting.</p>
49     <p>OSPRAI is written in <a class="reference external" href="http://www.python.org">Python</a> so as to run on all popular platforms,
50     including Linux, Windows, and Macintosh.
51     Install Python 2.4 (or newer) and the following libraries:
52     <a class="reference external" href="http://wiki.python.org/moin/TkInter">python-tk</a>,
53     <a class="reference external" href="http://matplotlib.sourceforge.net/">matplotlib</a>, and
54     <a class="reference external" href="www.scipy.org">scipy</a>.
55     Additionally, it is useful to install
56     <a class="reference external" href="http://ipython.scipy.org/moin/">IPython</a>, the interaction Python shell,
57     as well as a good python-aware text editor, such as
58     <a class="reference external" href="http://editra.org/">Editra</a>,
59     <a class="reference external" href="http://www.scintilla.org/SciTE.html">Scite</a>,
60     or <a class="reference external" href="http://projects.gnome.org/gedit/">gedit</a>.</p>
61     <p>OSPRAI is hosted by <a href="#id1"><span class="problematic" id="id2">`Bioinformatics.org &lt;httP://www.bioinformatics.org`_</span></a>
62     and managed using the Subversion version control system.
63     It can be obtained from the <a class="reference external" href="http://www.bioinformatics.org/websvn/listing.php?repname=osprai&amp;path=%2F&amp;sc=0">website</a>
64     or by using a Subversion client such as <a class="reference external" href="http://subversion.apache.org">Svn</a>,
65     <a class="reference external" href="http://www.rabbitvcs.org/">RabbitVCS</a>, or <a class="reference external" href="http://tortoisesvn.tigris.org">TortoiseSVN</a>.
66     Windows users can install all of the necessary prerequisites by installing
67     <a class="reference external" href="http://www.pythonxy.com">PythonXY</a>, while Ubuntu Linux users can find everything they need
68     in the Ubuntu repositories.
69     An example for Ubuntu users follows:</p>
70     <div class="highlight-python"><pre>$ sudo aptitude install python-tk python-matplotlib python-scipy ipython editra
71     $ svn checkout svn://bioinformatics.org/svnroot/osprai</pre>
72     </div>
73     <p>Contents:</p>
74     <ul>
75     <li class="toctree-l1"><a class="reference external" href="tutorial01.html">OSPRAI Tutorial 1</a><ul>
76     <li class="toctree-l2"><a class="reference external" href="tutorial01.html#viewing-data-from-an-spr-file">Viewing data from an SPR file</a></li>
77     <li class="toctree-l2"><a class="reference external" href="tutorial01.html#calibration-and-background-subtraction">Calibration and background subtraction</a></li>
78     <li class="toctree-l2"><a class="reference external" href="tutorial01.html#data-simulation">Data simulation</a></li>
79     <li class="toctree-l2"><a class="reference external" href="tutorial01.html#curve-fitting">Curve-fitting</a></li>
80     <li class="toctree-l2"><a class="reference external" href="tutorial01.html#file-format-conversion">File format conversion</a></li>
81     <li class="toctree-l2"><a class="reference external" href="tutorial01.html#online-help">Online help</a></li>
82     </ul>
83     </li>
84     <li class="toctree-l1"><a class="reference external" href="mainapi.html">The Application Program Interface</a></li>
85 clausted 54 <li class="toctree-l1"><a class="reference external" href="mainapi.html#module-fit_module">The Python Source Code</a><ul>
86 clausted 53 <li class="toctree-l2"><a class="reference external" href="mainapi.html#ba-class">ba_class</a></li>
87     <li class="toctree-l2"><a class="reference external" href="mainapi.html#vu-module">vu_module</a></li>
88     <li class="toctree-l2"><a class="reference external" href="mainapi.html#cal-module">cal_module</a></li>
89     <li class="toctree-l2"><a class="reference external" href="mainapi.html#io-module">io_module</a></li>
90     <li class="toctree-l2"><a class="reference external" href="mainapi.html#mdl-module">mdl_module</a></li>
91 clausted 54 <li class="toctree-l2"><a class="reference external" href="mainapi.html#fit-module">fit_module</a></li>
92 clausted 53 </ul>
93     </li>
94     </ul>
95     <div class="section" id="indices-and-tables">
96     <h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h2>
97     <ul class="simple">
98     <li><a class="reference external" href="genindex.html"><em>Index</em></a></li>
99     <li><a class="reference external" href="modindex.html"><em>Module Index</em></a></li>
100     <li><a class="reference external" href="search.html"><em>Search Page</em></a></li>
101     </ul>
102     </div>
103     </div>
104    
105    
106     </div>
107     </div>
108     </div>
109     <div class="sphinxsidebar">
110     <div class="sphinxsidebarwrapper">
111     <h3><a href="index.html">Table Of Contents</a></h3>
112     <ul>
113     <li><a class="reference external" href="#">Welcome to the OSPRAI documentation!</a><ul>
114     <li><a class="reference external" href="#indices-and-tables">Indices and tables</a></li>
115     </ul>
116     </li>
117     </ul>
118    
119     <h3>This Page</h3>
120     <ul class="this-page-menu">
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149     >modules</a> |</li>
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154     &copy; Copyright 2011, Christopher Lausted.
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