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	<title>Frontal Lobe</title>
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	<link>http://www.sandsfish.com/blog</link>
	<description>the mental machinations of sands fish</description>
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		<title>MIT VIVO Ontology Mapping &#8211; Grants and Publications</title>
		<link>http://www.sandsfish.com/blog/?p=24</link>
		<comments>http://www.sandsfish.com/blog/?p=24#comments</comments>
		<pubDate>Thu, 15 Sep 2011 16:41:13 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://www.sandsfish.com/blog/?p=24</guid>
		<description><![CDATA[My colleague Sean Thomas and I are currently working on evaluating the open-source semantic web application VIVO [ http://vivoweb.org/ ] for MIT.  Our latest investigation is how to best model grant data and relate it to other entities in the system, specifically authors and publications. The desire is to have a better grasp on compliance [...]]]></description>
			<content:encoded><![CDATA[<p>My colleague Sean Thomas and I are currently working on evaluating the open-source semantic web application VIVO [ <a href="http://vivoweb.org/" target="_blank">http://vivoweb.org/</a> ] for MIT.  Our latest investigation is how to best model grant data and relate it to other entities in the system, specifically authors and publications.</p>
<p>The desire is to have a better grasp on compliance with <a title="NIH" href="http://www.nih.gov/" target="_blank">NIH</a> (National Institutes of Health) publication requirements, specifically with <a title="PubMed" href="http://www.ncbi.nlm.nih.gov/pubmed/" target="_blank">PubMed</a> and <a title="PubMed Central" href="http://www.ncbi.nlm.nih.gov/pmc/" target="_blank">PubMed Central</a>.</p>
<p>Taking some queues from how the <a title="University of Florida VIVO" href="http://vivo.ufl.edu/" target="_blank">University of Florida</a> and <a title="Cornell VIVO" href="http://vivo.cornell.edu/" target="_blank">Cornell</a> have modeled this type of data, and sketching out our own pseudo-ontological mappings for entities they haven&#8217;t mapped, we&#8217;ve come up with a first draft of how we imagine this will look (below).  I&#8217;m sure this will evolve and I haven&#8217;t double-checked this for accuracy against the <a title="VIVO Core ontology" href="http://vivoweb.org/ontology/core" target="_blank">VIVO Core</a> ontology, but it is at least a start&#8230;</p>
<p>&nbsp;</p>
<p style="text-align: center;"><a href="http://www.sandsfish.com/blog/wp-content/uploads/2011/09/NIH-Grant-Modeling.png"><img class="aligncenter size-full wp-image-26" title="NIH Grant Modeling for MIT VIVO" src="http://www.sandsfish.com/blog/wp-content/uploads/2011/09/NIH-Grant-Modeling.png" alt="NIH Grant Modeling for MIT VIVO" width="615" height="471" /></a></p>
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			<wfw:commentRss>http://www.sandsfish.com/blog/?feed=rss2&#038;p=24</wfw:commentRss>
		<slash:comments>2</slash:comments>
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		<title>UTC Clock Hack for OS/X 10.6</title>
		<link>http://www.sandsfish.com/blog/?p=13</link>
		<comments>http://www.sandsfish.com/blog/?p=13#comments</comments>
		<pubDate>Wed, 26 May 2010 17:12:06 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://www.sandsfish.com/blog/?p=13</guid>
		<description><![CDATA[If you work on open source projects or within distributed work environments, and meetings are scheduled and publicized in UTC, you&#8217;ll find yourself doing the time zone conversion repeatedly. If you run OS/X, you can use the World Clock Widget to keep track easily.  The problem is that the World Clock does not come with [...]]]></description>
			<content:encoded><![CDATA[<p>If you work on open source projects or within distributed work environments, and meetings are scheduled and publicized in UTC, you&#8217;ll find yourself doing the time zone conversion repeatedly.</p>
<p>If you run OS/X, you can use the World Clock Widget to keep track easily.  The problem is that the World Clock does not come with UTC as a default option.  Fortunately, it is easy to add.</p>
<p>I used <a href="http://www.macosxhints.com/article.php?story=20050430193250534" target="_blank">this article</a> to make the modifications, and wasn&#8217;t sure if the method would work on OS/X 10.6, but it didn&#8217;t give me a single issue.  There is some iffy information in the comments of that article, so here is how I proceeded successfully:</p>
<h3>1.)  Crack Open the WorldClock widget</h3>
<p>Applications &amp; widgets in OS/X are not just one file, as they initially appear, but special container objects that hold other files (essentially a special-case folder).</p>
<ul>
<li>Navigate to <strong>/Library/Widgets</strong></li>
<li>Right-click (or command-click) on the <strong>WorldClock.wdgt</strong> file</li>
<li>Click <strong>Show Package Contents</strong></li>
</ul>
<p>This will open a new Finder window displaying the contents of the World Clock widget.</p>
<h3>2.)  Edit the WorldClock.js file</h3>
<p>If you&#8217;re not used to doing these things, this isn&#8217;t as intimidating as it might seem.  (Make a backup copy if you&#8217;re disaster-prone.)</p>
<ul>
<li>Find the line with the text:  &#8220;<strong>var Europe = [</strong>"</li>
<li>Find the bottom of this block of text, terminated by "<strong>];</strong>&#8220;</li>
<li>On the line before this, add &#8220;<strong>{city:&#8217;UTC&#8217;, offsett:0, timezone:&#8217;UTC&#8217;}</strong>&#8220;</li>
<li>Be sure to add a comma to the end of the previous line, since it is no longer the last item.</li>
<li>Save the file.  (You may have to authenticate in order to do this, since it is technically a system file.)</li>
</ul>
<div id="attachment_16" class="wp-caption aligncenter" style="width: 707px"><a href="http://www.sandsfish.com/blog/wp-content/uploads/2010/05/UTC_worldclock1.png"><img class="size-full wp-image-16" title="UTC Worldclock Modification" src="http://www.sandsfish.com/blog/wp-content/uploads/2010/05/UTC_worldclock1.png" alt="" width="697" height="688" /></a><p class="wp-caption-text">Modified &quot;WorldClock.js&quot;</p></div>
<h3>3.)  Edit the localizedStrings.js file</h3>
<p>There is a language localization file for all strings that appear in the widget&#8217;s interface.</p>
<ul>
<li>Find the directory that matches the language you are using (I modified <strong>English.lproj/localizedStrings.js</strong>)</li>
<li>At the bottom of the file, add the line:  &#8220;<strong>localizedCityNames['UTC'] = &#8216;UTC&#8217;;</strong>&#8220;</li>
<li>Save the file.</li>
</ul>
<div id="attachment_18" class="wp-caption aligncenter" style="width: 612px"><a href="http://www.sandsfish.com/blog/wp-content/uploads/2010/05/UTC_locallized1.png"><img class="size-full wp-image-18" title="Modified locallizedStrings.js" src="http://www.sandsfish.com/blog/wp-content/uploads/2010/05/UTC_locallized1.png" alt="" width="602" height="322" /></a><p class="wp-caption-text">Modified localizedStrings.js</p></div>
<h3>4.)  Add the World Clock widget to your Dashboard &amp; Configure</h3>
<p>The widget will have to be initialized with the new changes, so&#8230;</p>
<ul>
<li>If you have an old one, remove it.</li>
<li>Add the widget to your Dashboard again.</li>
<li>Click the &#8220;i&#8221; in the bottom-right corner to configure it.</li>
<li>Choose Country:  <strong>Europe</strong>, City:  <strong>UTC</strong></li>
</ul>
<p>And there you go, a clock reading the UTC time&#8230;</p>
]]></content:encoded>
			<wfw:commentRss>http://www.sandsfish.com/blog/?feed=rss2&#038;p=13</wfw:commentRss>
		<slash:comments>39</slash:comments>
		</item>
		<item>
		<title>How to deploy a Maven Parent POM</title>
		<link>http://www.sandsfish.com/blog/?p=10</link>
		<comments>http://www.sandsfish.com/blog/?p=10#comments</comments>
		<pubDate>Fri, 14 May 2010 18:46:22 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://www.sandsfish.com/blog/?p=10</guid>
		<description><![CDATA[mvn -N deploy Maven help defines the &#8220;-N&#8221; option as: -N,&#8211;non-recursive                     Do not recurse into sub-projects Running this command in the same directory as the Parent POM (pom.xml) will result in just the parent being deployed, avoiding Maven&#8217;s attempt to traverse all sub-projects referenced. (This [...]]]></description>
			<content:encoded><![CDATA[<h3>mvn -N deploy</h3>
<p>Maven help defines the &#8220;-N&#8221; option as:</p>
<p><span style="color: #3366ff;">-N,&#8211;non-recursive                     Do not recurse into sub-projects</span></p>
<p>Running this command in the same directory as the Parent POM (<span style="color: #3366ff;">pom.xml</span>) will result in just the parent being deployed, avoiding Maven&#8217;s attempt to traverse all sub-projects referenced.</p>
<p>(This all presumes that you have the correct prerequisites in place for the deploy phase, such as proper <span style="color: #3366ff;">~/.m2/settings.xml</span> configuration and <span style="color: #3366ff;">&lt;distributionManagement&gt;</span> configuration present in said pom.xml.)</p>
<p>Thanks to Elliot Metsger of the <a title="DSpace" href="http://www.dspace.org">DSpace</a> community for this tip.</p>
]]></content:encoded>
			<wfw:commentRss>http://www.sandsfish.com/blog/?feed=rss2&#038;p=10</wfw:commentRss>
		<slash:comments>25</slash:comments>
		</item>
		<item>
		<title>SIMILE Longwell Command Execution</title>
		<link>http://www.sandsfish.com/blog/?p=5</link>
		<comments>http://www.sandsfish.com/blog/?p=5#comments</comments>
		<pubDate>Fri, 30 Apr 2010 17:12:57 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[longwell]]></category>
		<category><![CDATA[MIT]]></category>
		<category><![CDATA[simile]]></category>

		<guid isPermaLink="false">http://www.sandsfish.com/blog/?p=5</guid>
		<description><![CDATA[Here&#8217;s my high-level analysis of how Longwell commands are executed using HTTP calls.  The most obvious to the end user will be calls triggered by mouse-clicks in the browser, but there are a large amount of these command calls which are made within Longwell itself as somewhat of a local loop-back call that happens after [...]]]></description>
			<content:encoded><![CDATA[<p>Here&#8217;s my high-level analysis of how Longwell commands are executed using HTTP calls.  The most obvious to the end user will be calls triggered by mouse-clicks in the browser, but there are a large amount of these command calls which are made within Longwell itself as somewhat of a local loop-back call that happens after the user triggers something via the UI (e.g. expanding a facet, changing the current view, etc.)</p>
<p style="text-align: center;"><img class="aligncenter size-full wp-image-6" title="longwell_command_diagram" src="http://www.sandsfish.com/blog/wp-content/uploads/2010/04/longwell_command_diagram.png" alt="longwell_command_diagram" width="615" height="471" /></p>
<p>Please comment if you find any errors in the interpretation of the call structure.</p>
]]></content:encoded>
			<wfw:commentRss>http://www.sandsfish.com/blog/?feed=rss2&#038;p=5</wfw:commentRss>
		<slash:comments>21</slash:comments>
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