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<title>Overview — CoCoTools 0.0.1 documentation</title>
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<h1>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h1>
<p>We have designed the <strong>CoCoTools</strong> project as a software library allow users of various interests and technical proficiencies to mine the CoCoMac database in its current form.</p>
<p><strong>CoCoTools</strong> provides:</p>
<blockquote>
<div><ol class="arabic simple">
<li>Tools for querying the <a class="reference external" href="http://cocomac.org">CoCoMac database</a></li>
<li>A processing pipeline that performs operations neccessary for turning query results into connectivity matrices (graphs) suitable for analysis, plotting etc.</li>
<li>Coodinate-free transformation algorithms that allows users to integrate connectivity from across the literature to form large-scale macro-connectomes.</li>
</ol>
</div></blockquote>
<p><strong>CoCoTools</strong> was designed around the following the principles:</p>
<blockquote>
<div><ol class="arabic">
<li><p class="first"><em>To offer users as much control over data processing as they need:</em></p>
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<div><ul class="simple">
<li>a few simple high-level commands supplied with default options will produce results sufficient for most users</li>
<li>yet optional arguments can be supplied to most functions</li>
<li>source code is available and can be modified</li>
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<li><p class="first"><em>To not re-invent the wheel:</em></p>
<blockquote>
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<li>integrates with and borrows functionality from Python standard library allowing users to perform a multitude of functions from well maintained sources (NumPy, matplotlib, etc.)</li>
<li>We utilize the <a class="reference external" href="http://networkx.github.com/">NetworkX</a> software library which provides CoCoTools with an extensive suite of graph theory tools and functions.</li>
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<p>We also have a collection of <a class="reference external" href="https://github.com/cocotools/CoCoTools/tree/master/examples#a-collection-of-notebooks-for-using-cocotools">Interactive Notebook Examples</a>.</p>
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© Copyright 2011, Daniel Bliss, Rob Blumenfeld and Fernando Perez.
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