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	<title>88 Proof Synth Bio Blog &#187; Software</title>
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	<link>http://88proof.com/synthetic_biology/blog</link>
	<description>Genetically Engineered Organisms, Systems Biology, and Synthetic Biology from an Engineer&#039;s Viewpoint</description>
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		<title>More on Bio-lab Automation &#8211; Software for Controlling FIAlab Devices for Microfluidics</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/407?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/407#comments</comments>
		<pubDate>Sat, 10 Oct 2009 01:06:34 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Technical]]></category>
		<category><![CDATA[automation]]></category>
		<category><![CDATA[hardware]]></category>
		<category><![CDATA[lab equipment]]></category>
		<category><![CDATA[microfluidics]]></category>
		<category><![CDATA[Perl]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=407</guid>
		<description><![CDATA[Perl software to control lab syringe pump and valve device, for biology automation, initial version finished today. Works great.  Next, need to add the network code, it can be controlled remotely and in synchronization with other laboratory devices, including the bio-robot.  This software will be used in the microfluidics project.  The software is also part [...]]]></description>
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		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>Don&#8217;t Always Trust Open Source Software.  Why Trust Open Source Biology?</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/389?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/389#comments</comments>
		<pubDate>Fri, 07 Aug 2009 22:05:36 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bio-Business]]></category>
		<category><![CDATA[Notes]]></category>
		<category><![CDATA[Open Source]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=389</guid>
		<description><![CDATA[The software you are happily using may be.. unnecessarily brittle. Recently I&#8217;ve been developing a little bit of high-level software using open source libraries.  Sometimes it amazes me that open source software works at all.  Here&#8217;s an excerpt from the internals I found in the open source library when I looked at why it might [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/389/feed</wfw:commentRss>
		<slash:comments>7</slash:comments>
		</item>
		<item>
		<title>Perl Bio-Robotics module, Robotics.pm and Robotics::Tecan</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/386?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/386#comments</comments>
		<pubDate>Thu, 30 Jul 2009 23:28:26 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Notes]]></category>
		<category><![CDATA[Technical]]></category>
		<category><![CDATA[automation]]></category>
		<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[lab equipment]]></category>
		<category><![CDATA[Perl]]></category>
		<category><![CDATA[robot]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=386</guid>
		<description><![CDATA[FYI for Bioperl developers:
I am developing a module for communication with biology robotics, as discussed recently on #bioperl, and I invite your comments.  Currently this module talks to a Tecan genesis workstation robot.  Other vendors are Beckman Biomek, Agilent, etc.  No such modules exist anywhere on the &#8216;net with the exception of [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/386/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Software for Biohackers</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/382?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/382#comments</comments>
		<pubDate>Thu, 30 Jul 2009 18:33:39 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Notes]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=382</guid>
		<description><![CDATA[Some open source software collections of biology interest are noted here.  I&#8217;ll update this list as time goes on.  If you would like to have your project listed too, leave a comment with all the fields of the table and I&#8217;ll add your project.  If any of these links do not work, [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/382/feed</wfw:commentRss>
		<slash:comments>8</slash:comments>
		</item>
		<item>
		<title>Low Cost Microcontroller-based Digital Microfluidics using &#8220;Processing&#8221;</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/338?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/338#comments</comments>
		<pubDate>Thu, 02 Jul 2009 03:49:04 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Skunkworks]]></category>
		<category><![CDATA[Technical]]></category>
		<category><![CDATA[hardware]]></category>
		<category><![CDATA[microcontroller]]></category>
		<category><![CDATA[microfluidics]]></category>
		<category><![CDATA[Processing.org]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=338</guid>
		<description><![CDATA[I&#8217;ve now tested the digital microfluidics board via microcontroller. The digital microfluidics board moves a liquid droplet via Electrowetting-on-Dielectric (EWOD).  The microcontroller switches the high voltage via a switching board (pictured below, using Panasonic PhotoMOS chips), which controls the +930VDC output by the HVPS (posted earlier), and runs over USB using no cost Processing.org software.  [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/338/feed</wfw:commentRss>
		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>Playing with the $100K Robots for Biology Automation</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/318?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/318#comments</comments>
		<pubDate>Sat, 27 Jun 2009 03:26:00 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Notes]]></category>
		<category><![CDATA[Technical]]></category>
		<category><![CDATA[automation]]></category>
		<category><![CDATA[Perl]]></category>
		<category><![CDATA[robot]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=318</guid>
		<description><![CDATA[The Tecan Genesis Workstation 200:  It&#8217;s an industrial benchtop robot for liquid handling with multiple arms for tray handling and pipetting.

The robot&#8217;s operations are complex, so an integrated development environment is used to program it (though biologists wouldn&#8217;t call it an integrated development environment; maybe they&#8217;d call it a scripting application?), with custom graphical [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/318/feed</wfw:commentRss>
		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>Analog Data Acquisition from USB Microcontroller using the &#8220;Processing&#8221; Language</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/277?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/277#comments</comments>
		<pubDate>Wed, 25 Mar 2009 06:45:27 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Technical]]></category>
		<category><![CDATA[microcontroller]]></category>
		<category><![CDATA[Processing.org]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=277</guid>
		<description><![CDATA[Building on the previous two mini-projects, I have a mini-graphical data acquisition project now running under the Processing language, getting real-world signals from the USB microcontroller (which is a Microchip PIC on a UBW Board from Sparkfun).  Source code below the screenshot.

The sampling rate runs at the frame rate (maximum unknown, perhaps depends on my [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/277/feed</wfw:commentRss>
		<slash:comments>3</slash:comments>
		</item>
		<item>
		<title>Blinky LED &#8216;Hello World&#8217; using USB Microcontroller in &#8216;Processing&#8217;</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/273?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/273#comments</comments>
		<pubDate>Tue, 24 Mar 2009 21:16:37 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Technical]]></category>
		<category><![CDATA[microcontroller]]></category>
		<category><![CDATA[Processing.org]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=273</guid>
		<description><![CDATA[Every good embedded systems hardware project begins with a blinking LED (or toggling level as seen on the oscilloscope).  In Processing.org language, there&#8217;s the opportunity for both, since the built-in graphics allow for data display as well as the USB microcontroller interface.  (There&#8217;s several Processing projects for Arduino, BTW.)   Source code is below.

The firmware in [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/273/feed</wfw:commentRss>
		<slash:comments>1</slash:comments>
		</item>
		<item>
		<title>Using the Processing.org Language with Microcontrollers</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/270?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/270#comments</comments>
		<pubDate>Mon, 23 Mar 2009 00:32:26 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Technical]]></category>
		<category><![CDATA[microcontroller]]></category>
		<category><![CDATA[Processing.org]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=270</guid>
		<description><![CDATA[Media-technology engineers at MIT have created a computer language and easy-to-use runtime environment called Processing, hosted at processing.org.  I wrote a small code snip for accessing the PIC microcontroller from a USB port, using Processing; it&#8217;s pasted below.

The Processing language and frameworks run on top of Java, so all Processing programs can run on Windows [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/270/feed</wfw:commentRss>
		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>Apple iPhone 3.0 as next generation Biomedical device</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/268?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/268#comments</comments>
		<pubDate>Tue, 17 Mar 2009 23:20:52 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bio-Business]]></category>
		<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Technical]]></category>
		<category><![CDATA[iphone]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=268</guid>
		<description><![CDATA[Apple&#8217;s developer preview today, of iPhone 3.0 software, included the interesting news of support for external accessories, either connected through the physical docking connector or through Bluetooth wireless.

A spokesman from Johnson &#38; Johnson announced an iPhone-blood-pressure-monitor accessory, which provides health biometrics and allows the biometrics to be sent over the iPhone&#8217;s network connection as an [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/268/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Stanford University: Programmable Microfluidics (2007) &#8211; Video</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/260?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/260#comments</comments>
		<pubDate>Mon, 02 Mar 2009 20:42:16 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Educational]]></category>
		<category><![CDATA[microfluidics]]></category>
		<category><![CDATA[Software]]></category>
		<category><![CDATA[video]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=258</guid>
		<description><![CDATA[October 3, 2007 lecture by Bill Thies for the Stanford University Computer Systems Colloquium (EE 380). Bill Thies provides an overview of microfluidic technologies from a computer science perspective, highlight areas in the which computer science researchers can contribute to this field; he will also describe recent work in developing new architectures, programming languages, and [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/260/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Play Fold.it, the &#8220;Tetris-On-Steroids&#8221; game that solves protein folding</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/250?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/250#comments</comments>
		<pubDate>Thu, 29 Jan 2009 22:53:52 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Educational]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=247</guid>
		<description><![CDATA[&#8220;Protein folding&#8221; is what again?
It&#8217;s this: Foldit (curiously, at the web address: &#8220;fold.it&#8221;).  And it&#8217;s fun to play.  Addictive, really.  Check out the picture:

After I had been playing a while, my 8-year old niece came over to my laptop to see what the cute sound-effects were all about.  After a minute of watching, she said:  [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/250/feed</wfw:commentRss>
		<slash:comments>1</slash:comments>
		</item>
		<item>
		<title>In-Depth Review, Part 3 of 5: “Beginning Perl for Bioinformatics” by James Tisdall</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/114?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/114#comments</comments>
		<pubDate>Tue, 04 Nov 2008 03:38:13 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Educational]]></category>
		<category><![CDATA[Technical]]></category>
		<category><![CDATA[Perl]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=114</guid>
		<description><![CDATA[In my previous write-ups of Part 1 and Part 2, I traced the Perl code and examples in the first half of the book, Beginning Perl for Bioinformatics, by James Tisdall, highlighting different approaches to bioinformatics in Perl.  As I mentioned before, Perl provides many different (and often stylistic) methods to solving a software problem.  [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/114/feed</wfw:commentRss>
		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>&#8220;SynBioSS: The Synthetic Biology Modeling Suite&#8221;</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/80?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/80#comments</comments>
		<pubDate>Mon, 20 Oct 2008 11:03:38 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Notes]]></category>
		<category><![CDATA[BioBricks]]></category>
		<category><![CDATA[Modeling]]></category>
		<category><![CDATA[Python]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=80</guid>
		<description><![CDATA[SynBioSS (Synthetic Biology Software Suite) is a suite of software for the modeling and simulation of synthetic genetic constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to multiscale simulation algorithms.  SynBioSS is available under the GNU General Public License.  &#8212; Anthony [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/80/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>In-Depth Review, Part 2 of 5: &#8220;Beginning Perl for Bioinformatics&#8221; by James Tisdall</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/36?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/36#comments</comments>
		<pubDate>Tue, 09 Sep 2008 02:19:13 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Educational]]></category>
		<category><![CDATA[Technical]]></category>
		<category><![CDATA[Perl]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=36</guid>
		<description><![CDATA[My Part 1 of 5 review of the book, Beginning Perl for Bioinformatics, by James Tisdall, left off at Chapter 8, just before Tisdall explains associative arrays, gene expression, FASTA files, genomic databases, and restriction sites.
Tisdall: &#8220;For simplicity, let&#8217;s say you have the names for all the genes in the organism and a number for [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/36/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>In-Depth Review, Part 1 of 5: &#8220;Beginning Perl for Bioinformatics&#8221; by James Tisdall</title>
		<link>http://88proof.com/synthetic_biology/blog/archives/15?utm_source=subscriber&amp;utm_medium=rss&amp;utm_campaign=rss</link>
		<comments>http://88proof.com/synthetic_biology/blog/archives/15#comments</comments>
		<pubDate>Sun, 07 Sep 2008 01:03:54 +0000</pubDate>
		<dc:creator>JonathanCline</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Educational]]></category>
		<category><![CDATA[Technical]]></category>
		<category><![CDATA[Perl]]></category>
		<category><![CDATA[Software]]></category>

		<guid isPermaLink="false">http://88proof.com/synthetic_biology/blog/?p=15</guid>
		<description><![CDATA[As a specialized field, Bioinformatics is rather young.  It can be difficult to find universities which teach bioinformatics.  Bioinformatics can refer to many different types of tasks &#8212; from using programs and data without any computer science knowledge, to implementing database or web software, to writing data conversion programs which modify file formats between database [...]]]></description>
		<wfw:commentRss>http://88proof.com/synthetic_biology/blog/archives/15/feed</wfw:commentRss>
		<slash:comments>1</slash:comments>
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