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welcome.html
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<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link rel="stylesheet" href="style/base.css" type="text/css" />
</head>
<body>
<div class="document">
<!--
<div class="donemessagelarge">
<strong>The Language Application Grid</strong>
<hr>
<p>Welcome to the LAPPS Galaxy instance running at <a href="http://www.cs.brandeis.edu/" target="_blank">Brandeis University</a>.</p>
<p>Through this Galaxy instance you can:</p>
<ol>
<li>Fetch documents from the MASC 3.0.0 or Gigaword sample sources.</li>
<li>Create processing pipelines with tools from:
<ol>
<li>GATE</li>
<li>Apache OpenNLP</li>
<li>Stanford NLP</li>
</ol>
</li>
</ol>
<p>Contacts:<a href="http://jamespusto.com/" target="_blank">James Pustejovsky</a> ([email protected])</p>
</div>
-->
<div class="jumbotron">
<div class="container">
<!--
<h1>The Language Application Grid</h1>
<hr/>
-->
<img src="lapps-logo.png" alt="Language Application Grid"/>
<p>Welcome to the LAPPS Galaxy instance running at Vassar College in Poughkeepsie, New York.</p>
<p>Through this Galaxy instance you can:</p>
<ol>
<li>Fetch documents from the MASC 3.0.0 or Gigaword sample sources.</li>
<li>Create processing pipelines with tools from:
<ol>
<li>GATE</li>
<li>Apache OpenNLP</li>
<li>Stanford NLP</li>
</ol>
</li>
</ol>
</div>
</div>
-->
<div class="jumbotron">
<div class="container">
<h1>The Language Application Grid</h1>
<hr/>
<p>Welcome to the LAPPS Galaxy instance running at Vassar College in Poughkeepsie, New York.</p>
<p>Through this Galaxy instance you can:</p>
<ol>
<li>Fetch documents from the MASC 3.0.0 or Gigaword sample sources.</li>
<li>Create processing pipelines with tools from:
<ol>
<li>GATE</li>
<li>Apache OpenNLP</li>
<li>Stanford NLP</li>
</ol>
</li>
</ol>
</div>
</div>
<div class="panel panel-primary">
<div class="panel-heading">
<h1 class="panel-title">Simple Tutorial</h1>
<p>If you have a good understanding of how Galaxy works you can run the
following tools in order:</p>
<ol>
<li>Get data -> MASC</li>
<li>From the GATE menu ->
<ol>
<li>Tokenizer</li>
<li>Sentence Splitter</li>
<li>Part of speech tagger</li>
</ol>
</li>
<li>From the History panel select ->
<ol>
<li>Edit attributes</li>
<li>Convert Format (there is only one converter, so just run it)</li>
</ol>
</li>
<li>Tools -> Word Count</li>
<li>Expand the output select the <em>Visualize</em> icon and then <em>Charts<em></li>
<li>Click the <tt>Add Data</tt> and select <tt>Column: 1</tt>, <tt>Column: 2</tt>,
and <tt>Column: 3</tt> respectively.</li>
<li>Click the <tt>Draw</tt> button to marvel at the simple word count histogram ;-)</li>
</ol>
</div>
</div>
<div class="panel panel-warning">
<div class="panel-heading">
<h1 class="panel-title">Caveats</h1>
</div>
<div class="panel-body">
<p>While Galaxy ensures that the inputs to a processing tool use
the correct file format (GATE tools require GATE/XML, the other tools
require LIF) it does not currently ensure the document contains the required
annotation types. For example; part of speech taggers typically require
the input document to contain <tt>Token</tt> annotations.</p>
<p>Converters exist to convert between GATE/XML and LIF, however these
converters must be inserted manually into a workflow at the proper places,
say between the GATE Tokenizer and the Stanford POSTagger.</p>
</div>
</div>
<br/>
<hr/>
<a target="_blank" class="reference" href="http://galaxyproject.org/">Galaxy</a> is an open, web-based platform for data intensive biomedical research. The <a target="_blank" class="reference" href="http://wiki.galaxyproject.org/GalaxyTeam">Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>, and the <a target="_blank" class="reference" href="http://www.biology.emory.edu/">Biology</a> and <a target="_blank" class="reference" href="http://www.mathcs.emory.edu/">Mathematics and Computer Science</a> departments at <a target="_blank" class="reference" href="http://www.emory.edu/">Emory University</a>. The <a target="_blank" class="reference" href="http://galaxyproject.org/">Galaxy Project</a> is supported in part by <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>, <a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>, and <a target="_blank" class="reference" href="http://www.emory.edu/">Emory University</a>.</p>
</div>
</body>
</html>