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Revision: 54
Committed: Wed Feb 16 21:29:02 2011 UTC (8 years, 4 months ago) by clausted
File size: 8335 byte(s)
Log Message:
Added fit_module and mdl_module to sphinx documentation.
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8 <title>Welcome to the OSPRAI documentation! &mdash; osprai-doc v0.1-110210 documentation</title>
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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 <li class="toctree-l1"><a class="reference external" href="mainapi.html#module-fit_module">The Python Source Code</a><ul>
86 <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 <li class="toctree-l2"><a class="reference external" href="mainapi.html#fit-module">fit_module</a></li>
92 </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>
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104
105
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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>
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