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49   <p>The Osprai API is the set of public functions and classes contained in the <tt class="docutils literal"><span class="pre">osprai_one</span></tt> module.
50   The API provides an interface to the software from a python command line, such as <a class="reference external" href="http://ipython.scipy.org/moin/">IPython</a>.
51   In the future, web or desktop graphical user interfaces could be written using this API to assist SPR users with common data anaylsis procedures.</p>
52 + <p>To use Osprai, set your Python path environment variable to the location where it is installed.
53 + This can be done from the shell (bash example):</p>
54 + <div class="highlight-python"><pre>$ export PYTHONPATH=/home/user/osprai/trunk
55 + $ ipython</pre>
56 + </div>
57 + <p>Alternatively, the path can be set from inside the Python interpreter (IPython example):</p>
58 + <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">sys</span>
59 + <span class="gp">&gt;&gt;&gt; </span><span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">&#39;/home/user/osprai/trunk&#39;</span><span class="p">)</span>
60 + <span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">osprai_one</span> <span class="kn">as</span> <span class="nn">osp</span>
61 + <span class="gp">&gt;&gt;&gt; </span><span class="n">help</span> <span class="n">osp</span>
62 + </pre></div>
63 + </div>
64   </div>
65 < <div class="section" id="module-mdl_module">
66 < <h1>The Python Source Code<a class="headerlink" href="#module-mdl_module" title="Permalink to this headline">¶</a></h1>
65 > <div class="section" id="module-fit_module">
66 > <h1>The Python Source Code<a class="headerlink" href="#module-fit_module" title="Permalink to this headline">¶</a></h1>
67   <div class="section" id="ba-class">
68   <h2>ba_class<a class="headerlink" href="#ba-class" title="Permalink to this headline">¶</a></h2>
69   <p>Biosensor Array class for storing SPRI data.
# Line 264 | Line 276
276   <col class="field-body" />
277   <tbody valign="top">
278   <tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
279 < <li><em>baDot</em> (ba_class) &#8211; Object containing the data.</li>
279 > <li><em>baDot</em> (BiosensorArray) &#8211; Object containing the data.</li>
280   <li><em>title</em> (str) &#8211; Title to place above the graph.</li>
281   </ul>
282   </td>
# Line 285 | Line 297
297   <col class="field-body" />
298   <tbody valign="top">
299   <tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
300 < <li><em>baDot</em> (ba_class) &#8211; Object containing the dotted-line data.</li>
301 < <li><em>baLine</em> (ba_class) &#8211; Object containing the continuous-line data.</li>
300 > <li><em>baDot</em> (BiosensorArray) &#8211; Object containing the dotted-line data.</li>
301 > <li><em>baLine</em> (BiosensorArray) &#8211; Object containing the continuous-line data.</li>
302   <li><em>title</em> (str) &#8211; Title to place above the graph.</li>
303   </ul>
304   </td>
# Line 307 | Line 319
319   <col class="field-body" />
320   <tbody valign="top">
321   <tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
322 < <li><em>baLine</em> (ba_class) &#8211; Object containing the data.</li>
322 > <li><em>baLine</em> (BiosensorArray) &#8211; Object containing the data.</li>
323   <li><em>title</em> (str) &#8211; Title to place above the graph.</li>
324   </ul>
325   </td>
# Line 329 | Line 341
341   <col class="field-body" />
342   <tbody valign="top">
343   <tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
344 < <li><em>ba0</em> (ba_class) &#8211; Object containing the data.</li>
344 > <li><em>ba0</em> (BiosensorArray) &#8211; Object containing the data.</li>
345   <li><em>t1</em> (float) &#8211; Timepoint before binding, first axis.</li>
346   <li><em>t2</em> (float) &#8211; Timepoint after binding, first axis.</li>
347   <li><em>t3</em> (float) &#8211; Timepoint before binding, second axis.</li>
# Line 353 | Line 365
365   Other routines provide background subtraction and data rearrangement.</p>
366   <p>Examples:</p>
367   <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">cal_module</span> <span class="kn">as</span> <span class="nn">cal</span>
368 < <span class="gp">&gt;&gt;&gt; </span><span class="n">io_module</span> <span class="k">as</span> <span class="n">io</span>
368 > <span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">io_module</span> <span class="kn">as</span> <span class="nn">io</span>
369   <span class="gp">&gt;&gt;&gt; </span><span class="n">baC</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">readsprit</span><span class="p">(</span><span class="s">&quot;calibrationdata.txt&quot;</span><span class="p">)</span>
370   <span class="gp">&gt;&gt;&gt; </span><span class="n">ba1</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">readsprit</span><span class="p">(</span><span class="s">&quot;spritdata.txt&quot;</span><span class="p">)</span>
371   <span class="gp">&gt;&gt;&gt; </span><span class="n">ba2</span> <span class="o">=</span> <span class="n">cal</span><span class="o">.</span><span class="n">calibrate</span><span class="p">(</span><span class="n">ba1</span><span class="p">,</span> <span class="n">baCal</span><span class="p">,</span> <span class="n">t1</span><span class="p">,</span> <span class="n">t2</span><span class="p">,</span> <span class="n">n1</span><span class="p">,</span> <span class="n">n2</span><span class="p">)</span>
# Line 648 | Line 660
660   </div>
661   <div class="section" id="mdl-module">
662   <h2>mdl_module<a class="headerlink" href="#mdl-module" title="Permalink to this headline">¶</a></h2>
663 < <p><strong>Example model functions module for SPRI data.</strong>
663 > <p><em>Example model functions module for SPRI data.</em>
664   Just a few simple, common interaction models will go here.
665   In the future, each new model will go in its own module/file.
666 < Each model is a function taking three parameters</p>
667 < <blockquote>
668 < <ol class="arabic simple">
669 < <li><em>time</em>    An array of time values, usually in seconds.</li>
670 < <li><em>data</em>    An array of initial SPR signal values.</li>
671 < <li><em>params</em>  A dictionary of dictionaries.</li>
672 < </ol>
673 < </blockquote>
666 > Each model is a function taking three parameters.</p>
667 > <dl class="docutils">
668 > <dt><strong>Parameters:</strong></dt>
669 > <dd><ul class="first last simple">
670 > <li><em>time</em> (numpy array) &#8211; Time points, usually in seconds.</li>
671 > <li><em>data</em> (numpy array) &#8211; Initial SPR signal values.</li>
672 > <li><em>params</em> (dictionary of dictionaries) &#8211; Model parameter description.</li>
673 > </ul>
674 > </dd>
675 > </dl>
676 > <p><strong>Returns:</strong> numpy array of calculated SPR signal values.</p>
677   <p>The dictionary keys are the names of model parameters
678   (e.g. &#8216;rmax&#8217; for maximal response, or &#8216;kon&#8217; for kinetic on-rate).
679   Each model parameter is described by a subdictionary containing four entries.</p>
680   <blockquote>
681 < <ol class="arabic simple">
682 < <li><em>&#8216;value&#8217;</em>  The current value of the parameter.</li>
683 < <li><em>&#8216;min&#8217;</em>    The minimum allowable value.</li>
684 < <li><em>&#8216;max&#8217;</em>    The maximum allowable value.</li>
685 < <li><em>&#8216;fixed&#8217;</em>  Either &#8216;float&#8217;, &#8216;fixed&#8217;, or a reference to another ROI.</li>
686 < </ol>
681 > <ul class="simple">
682 > <li><tt class="docutils literal"><span class="pre">'value'</span></tt>  The current value of the parameter.</li>
683 > <li><tt class="docutils literal"><span class="pre">'min'</span></tt>    The minimum allowable value.</li>
684 > <li><tt class="docutils literal"><span class="pre">'max'</span></tt>    The maximum allowable value.</li>
685 > <li><tt class="docutils literal"><span class="pre">'fixed'</span></tt>  Either &#8216;float&#8217;, &#8216;fixed&#8217;, or a reference to another ROI.</li>
686 > </ul>
687   </blockquote>
688 < <p>The <em>min</em>, <em>max</em>, and <em>fixed</em> keys are used during automatic curve-fitting.
688 > <p>The <tt class="docutils literal"><span class="pre">min</span></tt>, <tt class="docutils literal"><span class="pre">max</span></tt>, and <tt class="docutils literal"><span class="pre">fixed</span></tt> keys are used during automatic curve-fitting.
689   A fixed parameter is not allowed to change, while a float parameter is adjusted
690   until the least-squares algorithm has minimized the sum-squared error.
691   The <em>fixed</em> parameter may also be an integer, in which case it is fixed to
# Line 684 | Line 699
699   <span class="gp">&gt;&gt;&gt; </span><span class="n">times</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">100</span><span class="p">)</span>
700   <span class="gp">&gt;&gt;&gt; </span><span class="n">data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">100</span><span class="p">)</span>
701   <span class="gp">&gt;&gt;&gt; </span>
702 < <span class="gp">&gt;&gt;&gt; </span><span class="n">params1</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">rate</span><span class="o">=</span><span class="nb">dict</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="nb">min</span><span class="o">=-</span><span class="mf">100.0</span><span class="p">,</span> <span class="nb">max</span><span class="o">=</span><span class="mf">100.0</span><span class="p">,</span> <span class="n">fixed</span><span class="o">=</span><span class="bp">True</span><span class="p">))</span>
702 > <span class="gp">&gt;&gt;&gt; </span><span class="n">param1</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">rate</span><span class="o">=</span><span class="nb">dict</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="nb">min</span><span class="o">=-</span><span class="mf">100.0</span><span class="p">,</span> <span class="nb">max</span><span class="o">=</span><span class="mf">100.0</span><span class="p">,</span> <span class="n">fixed</span><span class="o">=</span><span class="bp">True</span><span class="p">))</span>
703   <span class="gp">&gt;&gt;&gt; </span><span class="n">data1</span> <span class="o">=</span> <span class="n">drift</span><span class="p">(</span><span class="n">time</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">param1</span><span class="p">)</span>
704   <span class="gp">&gt;&gt;&gt; </span>
705   <span class="gp">&gt;&gt;&gt; </span><span class="n">param2</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;t1&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s">&#39;value&#39;</span><span class="p">:</span><span class="mf">30.0</span><span class="p">,</span> <span class="s">&#39;min&#39;</span><span class="p">:</span><span class="mf">30.0</span><span class="p">,</span> <span class="s">&#39;max&#39;</span><span class="p">:</span><span class="mf">30.0</span><span class="p">,</span> <span class="s">&#39;fixed&#39;</span><span class="p">:</span><span class="bp">True</span><span class="p">}</span> <span class="p">}</span>
# Line 703 | Line 718
718   <dd><p>This function simply models a constant signal drift in units/second.
719   It requires numpy arrays of times and starting data values,
720   It only requires one parameter in the params list.</p>
721 < <p>params[&#8216;rate&#8217;][&#8216;value&#8217;]</p>
707 < <table class="docutils field-list" frame="void" rules="none">
708 < <col class="field-name" />
709 < <col class="field-body" />
710 < <tbody valign="top">
711 < <tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
712 < <li><em>time</em> (numpy array) &#8211; Time points.</li>
713 < <li><em>data</em> (numpy array) &#8211; SPR signal values.</li>
714 < <li><em>params</em> (dictionary of dictionaries) &#8211; Binding model parameter description.</li>
715 < </ul>
716 < </td>
717 < </tr>
718 < <tr class="field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">numpy array</p>
719 < </td>
720 < </tr>
721 < </tbody>
722 < </table>
721 > <p><tt class="docutils literal"><span class="pre">params['rate']['value']</span></tt></p>
722   </dd></dl>
723  
724   <dl class="function">
725   <dt id="mdl_module.simple1to1">
726   <tt class="descclassname">mdl_module.</tt><tt class="descname">simple1to1</tt><big>(</big><em>time</em>, <em>data</em>, <em>params</em><big>)</big><a class="headerlink" href="#mdl_module.simple1to1" title="Permalink to this definition">¶</a></dt>
727 < <dd><p>This function simply models a 1:1 interaction.</p>
727 > <dd><p>This function simply models a 1:1 interaction.
728 > The model parameters are described in the table below.</p>
729   <p>Model:</p>
730   <div class="highlight-python"><pre>[A] + [L] --kon--&gt; [AL]
731   [A] + [L] &lt;-koff-- [AL]</pre>
# Line 784 | Line 784
784   <dl class="function">
785   <dt id="mdl_module.simple1to1_mtl">
786   <tt class="descclassname">mdl_module.</tt><tt class="descname">simple1to1_mtl</tt><big>(</big><em>time</em>, <em>data</em>, <em>params</em><big>)</big><a class="headerlink" href="#mdl_module.simple1to1_mtl" title="Permalink to this definition">¶</a></dt>
787 < <dd><p>This function simply models a 1:1 interaction with mass transport limitation.</p>
787 > <dd><p>This function simply models a 1:1 interaction with mass transport limitation.
788 > The model parameters are described in the table below.</p>
789   <p>Model:</p>
790   <div class="highlight-python"><pre>[Abulk]  --km-&gt;  [Asurf] + [L]  --kon--&gt;  [AL]
791   [Abulk]  &lt;-km--  [Asurf] + [L]  &lt;-koff--  [AL]</pre>
# Line 844 | Line 845
845   </dd></dl>
846  
847   </div>
848 + <div class="section" id="fit-module">
849 + <h2>fit_module<a class="headerlink" href="#fit-module" title="Permalink to this headline">¶</a></h2>
850 + <p><em>Curve-fitting module for SPRI data.</em>
851 + These routines are based on the Levenberg-Marquart Algorithm (LMA) from SciPy.
852 + This module provides several extended features that make it
853 + particularly powerful for the analysis of high-throughput SPRI data.</p>
854 + <blockquote>
855 + <ul class="simple">
856 + <li>Constrained parameters.
857 + <em>Invalid results such as negative kinetic rates can be avoided.</em></li>
858 + <li>Simultaneous fitting of multiple curves.
859 + <em>Parameters used in one ROI may be tied to those in other ROIs.</em></li>
860 + <li>Multiple models may be specified.
861 + <em>Different ROIs may exhibit different binding interactions.</em></li>
862 + </ul>
863 + </blockquote>
864 + <p>Users should take advantage of the <tt class="docutils literal"><span class="pre">mclma()</span></tt> function.  
865 + The <tt class="docutils literal"><span class="pre">lma()</span></tt> and <tt class="docutils literal"><span class="pre">clma()</span></tt> functions have been deprecated.</p>
866 + <p>Examples:</p>
867 + <div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">fit_module</span> <span class="kn">as</span> <span class="nn">fit</span>
868 + <span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">mdl_module</span> <span class="kn">as</span> <span class="nn">mdl</span>
869 + <span class="gp">&gt;&gt;&gt; </span><span class="n">ba</span><span class="o">.</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">mdl</span><span class="o">.</span><span class="n">drift</span>
870 + <span class="gp">&gt;&gt;&gt; </span><span class="n">ba</span><span class="o">.</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">mdl</span><span class="o">.</span><span class="n">drift</span>
871 + <span class="gp">&gt;&gt;&gt; </span><span class="n">p1</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;rate&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s">&#39;value&#39;</span><span class="p">:</span><span class="mf">1.0</span><span class="p">,</span> <span class="s">&#39;min&#39;</span><span class="p">:</span><span class="o">-</span><span class="mf">100.0</span><span class="p">,</span> <span class="s">&#39;max&#39;</span><span class="p">:</span><span class="mf">100.0</span><span class="p">,</span> <span class="s">&#39;fixed&#39;</span><span class="p">:</span><span class="s">&#39;float&#39;</span><span class="p">}</span> <span class="p">}</span>
872 + <span class="gp">&gt;&gt;&gt; </span><span class="n">p2</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">rate</span><span class="o">=</span><span class="nb">dict</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="nb">min</span><span class="o">=-</span><span class="mf">100.0</span><span class="p">,</span> <span class="nb">max</span><span class="o">=</span><span class="mf">100.0</span><span class="p">,</span> <span class="n">fixed</span><span class="o">=</span><span class="bp">True</span><span class="p">))</span>
873 + <span class="gp">&gt;&gt;&gt; </span><span class="n">ba</span><span class="o">.</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="n">p1</span>
874 + <span class="gp">&gt;&gt;&gt; </span><span class="n">ba</span><span class="o">.</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="n">p2</span>
875 + <span class="gp">&gt;&gt;&gt; </span><span class="n">i</span> <span class="o">=</span> <span class="n">mclma</span><span class="p">(</span><span class="n">ba</span><span class="o">.</span><span class="n">roi</span><span class="p">)</span>
876 + </pre></div>
877 + </div>
878 + <dl class="function">
879 + <dt id="fit_module.clma">
880 + <tt class="descclassname">fit_module.</tt><tt class="descname">clma</tt><big>(</big><em>roi</em><big>)</big><a class="headerlink" href="#fit_module.clma" title="Permalink to this definition">¶</a></dt>
881 + <dd><p><em>Constrained LMA curve-fitting.  (Deprecated)</em>
882 + Least-squares curve-fitting is performed on the data in the specified ROI.
883 + The ROI must contain SPR data, a model, and initial (guess) parameters.
884 + The roi.params values are modified in place.
885 + The maximum number of iterations is set to 999.</p>
886 + <table class="docutils field-list" frame="void" rules="none">
887 + <col class="field-name" />
888 + <col class="field-body" />
889 + <tbody valign="top">
890 + <tr class="field"><th class="field-name">Parameter:</th><td class="field-body"><em>roi</em> (RegOfInterest) &#8211; ROI containing data, a model, and initial parameter guesses.</td>
891 + </tr>
892 + <tr class="field"><th class="field-name">Returns:</th><td class="field-body">number of iterations completed.</td>
893 + </tr>
894 + </tbody>
895 + </table>
896 + </dd></dl>
897 +
898 + <dl class="function">
899 + <dt id="fit_module.lma">
900 + <tt class="descclassname">fit_module.</tt><tt class="descname">lma</tt><big>(</big><em>roi</em><big>)</big><a class="headerlink" href="#fit_module.lma" title="Permalink to this definition">¶</a></dt>
901 + <dd><p><em>Normal LMA curve-fitting.  (Deprecated)</em>
902 + Least-squares curve-fitting is performed on the data in the specified ROI.
903 + The ROI must contain SPR data, a model, and initial (guess) parameters.
904 + The roi.params values are modified in place.
905 + The maximum number of iterations is set to 500.</p>
906 + <table class="docutils field-list" frame="void" rules="none">
907 + <col class="field-name" />
908 + <col class="field-body" />
909 + <tbody valign="top">
910 + <tr class="field"><th class="field-name">Parameter:</th><td class="field-body"><em>roi</em> (RegOfInterest) &#8211; ROI containing data, a model, and initial parameter guesses.</td>
911 + </tr>
912 + <tr class="field"><th class="field-name">Returns:</th><td class="field-body">number of iterations completed.</td>
913 + </tr>
914 + </tbody>
915 + </table>
916 + </dd></dl>
917 +
918 + <dl class="function">
919 + <dt id="fit_module.mclma">
920 + <tt class="descclassname">fit_module.</tt><tt class="descname">mclma</tt><big>(</big><em>rois</em><big>)</big><a class="headerlink" href="#fit_module.mclma" title="Permalink to this definition">¶</a></dt>
921 + <dd><p><em>Multiple-curve Constrained Levenberg-Marquart Algorithm.</em>
922 + Least-squares curve-fitting is performed on the data in the specified ROIs.
923 + The ROIs must contain SPR data, a model, and initial (guess) parameters.
924 + The roi.params values are modified in place.
925 + The maximum number of iterations is set to 999.</p>
926 + <table class="docutils field-list" frame="void" rules="none">
927 + <col class="field-name" />
928 + <col class="field-body" />
929 + <tbody valign="top">
930 + <tr class="field"><th class="field-name">Parameter:</th><td class="field-body"><em>rois</em> (List of RegOfInterest) &#8211; ROI containing data, a model, and initial parameter guesses.</td>
931 + </tr>
932 + <tr class="field"><th class="field-name">Returns:</th><td class="field-body">number of iterations completed.</td>
933 + </tr>
934 + </tbody>
935 + </table>
936 + </dd></dl>
937 +
938 + </div>
939   </div>
940  
941  
# Line 855 | Line 947
947              <h3><a href="index.html">Table Of Contents</a></h3>
948              <ul>
949   <li><a class="reference external" href="#">The Application Program Interface</a></li>
950 < <li><a class="reference external" href="#module-mdl_module">The Python Source Code</a><ul>
950 > <li><a class="reference external" href="#module-fit_module">The Python Source Code</a><ul>
951   <li><a class="reference external" href="#ba-class">ba_class</a></li>
952   <li><a class="reference external" href="#vu-module">vu_module</a></li>
953   <li><a class="reference external" href="#cal-module">cal_module</a></li>
954   <li><a class="reference external" href="#io-module">io_module</a></li>
955   <li><a class="reference external" href="#mdl-module">mdl_module</a></li>
956 + <li><a class="reference external" href="#fit-module">fit_module</a></li>
957   </ul>
958   </li>
959   </ul>
# Line 902 | Line 995
995          <li class="right" >
996            <a href="tutorial01.html" title="OSPRAI Tutorial 1"
997               >previous</a> |</li>
998 <        <li><a href="index.html">osprai-doc v0.1-110210 documentation</a> &raquo;</li>
998 >        <li><a href="index.html">osprai-doc v0.5-110215 documentation</a> &raquo;</li>
999        </ul>
1000      </div>
1001      <div class="footer">

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