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	<title>Comments for Thinking About Bioinformatics</title>
	<atom:link href="http://thinking.bioinformatics.ucla.edu/comments/feed/" rel="self" type="application/rss+xml" />
	<link>http://thinking.bioinformatics.ucla.edu</link>
	<description>Thoughts on Information Evolution, Systems, and Tools</description>
	<pubDate>Sat, 07 Nov 2009 13:48:20 +0000</pubDate>
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		<title>Comment on Organization of Biological Networks Workshop Talk by Daniel Lew</title>
		<link>http://thinking.bioinformatics.ucla.edu/2008/03/09/organization-of-biological-networks-workshop-talk/#comment-6384</link>
		<dc:creator>Daniel Lew</dc:creator>
		<pubDate>Wed, 22 Jul 2009 16:13:58 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2008/03/09/organization-of-biological-networks-workshop-talk/#comment-6384</guid>
		<description>40 million cases, doubling every 10 years is quite a scary thought. Great video and very informative.</description>
		<content:encoded><![CDATA[<p>40 million cases, doubling every 10 years is quite a scary thought. Great video and very informative.</p>
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		<title>Comment on Empirical Information as a metric for Statistical Inference by Ankush Sharma</title>
		<link>http://thinking.bioinformatics.ucla.edu/2008/02/15/empirical-information-as-a-metric-for-statistical-inference/#comment-6254</link>
		<dc:creator>Ankush Sharma</dc:creator>
		<pubDate>Fri, 17 Jul 2009 03:43:39 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2008/02/15/empirical-information-as-a-metric-for-statistical-inference/#comment-6254</guid>
		<description>very nice website and very informative article 

thanks for the information

Regards 

Ankush</description>
		<content:encoded><![CDATA[<p>very nice website and very informative article </p>
<p>thanks for the information</p>
<p>Regards </p>
<p>Ankush</p>
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		<title>Comment on Pygr.Data in A Web Browser! by leec</title>
		<link>http://thinking.bioinformatics.ucla.edu/2007/11/26/pygrdata-in-a-web-browser/#comment-5138</link>
		<dc:creator>leec</dc:creator>
		<pubDate>Sun, 14 Jun 2009 08:13:50 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2007/11/26/pygrdata-in-a-web-browser/#comment-5138</guid>
		<description>Hi Ben,
you can download the code I modified from the following tar.gz package:
http://www.doe-mbi.ucla.edu/~leec/silverlight-python2.4.5-lib.tgz

then just 
tar xzvf silverlight-python2.4.5-lib.tgz
and it will extract a directory called "lib", containing xmlrpclib.py and a few other library files I found I had to add / modify for my purposes.  I did this quite some time ago, so these python files are based on release Python 2.4.5, I think.  I just diffed xmlrpclib.py vs. Python 2.4.5; there are about 40-50 lines of differences where I had to make it use Silverlight functions...  It's been a LONG time since I did this, but my memory is all this was pretty easy to get working at the time.

Hope that's helpful!!

-- Chris Lee</description>
		<content:encoded><![CDATA[<p>Hi Ben,<br />
you can download the code I modified from the following tar.gz package:<br />
<a href="http://www.doe-mbi.ucla.edu/~leec/silverlight-python2.4.5-lib.tgz" rel="nofollow">http://www.doe-mbi.ucla.edu/~leec/silverlight-python2.4.5-lib.tgz</a></p>
<p>then just<br />
tar xzvf silverlight-python2.4.5-lib.tgz<br />
and it will extract a directory called &#8220;lib&#8221;, containing xmlrpclib.py and a few other library files I found I had to add / modify for my purposes.  I did this quite some time ago, so these python files are based on release Python 2.4.5, I think.  I just diffed xmlrpclib.py vs. Python 2.4.5; there are about 40-50 lines of differences where I had to make it use Silverlight functions&#8230;  It&#8217;s been a LONG time since I did this, but my memory is all this was pretty easy to get working at the time.</p>
<p>Hope that&#8217;s helpful!!</p>
<p>&#8211; Chris Lee</p>
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		<title>Comment on Pygr.Data in A Web Browser! by Ben Christenson</title>
		<link>http://thinking.bioinformatics.ucla.edu/2007/11/26/pygrdata-in-a-web-browser/#comment-5027</link>
		<dc:creator>Ben Christenson</dc:creator>
		<pubDate>Tue, 09 Jun 2009 15:16:20 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2007/11/26/pygrdata-in-a-web-browser/#comment-5027</guid>
		<description>I am interested in getting xmlrpclib working inside silverlight.  Where can I find the source code for the project that did this?  Or, do you have instructions on how to do this i.e. what files to include where?</description>
		<content:encoded><![CDATA[<p>I am interested in getting xmlrpclib working inside silverlight.  Where can I find the source code for the project that did this?  Or, do you have instructions on how to do this i.e. what files to include where?</p>
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		<title>Comment on The Feynmanization of Chapter 1 by leec</title>
		<link>http://thinking.bioinformatics.ucla.edu/2008/08/13/the-feynmanization-of-chapter-1/#comment-1064</link>
		<dc:creator>leec</dc:creator>
		<pubDate>Wed, 19 Nov 2008 01:53:37 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2008/08/13/the-feynmanization-of-chapter-1/#comment-1064</guid>
		<description>Thanks, Robert.  The blog was recently moved to a new server and the file attachments don't seem to have come along for the ride.  I have relinked to another copy of the chapter stored on another server.  Hope you enjoy it!

-- Chris Lee</description>
		<content:encoded><![CDATA[<p>Thanks, Robert.  The blog was recently moved to a new server and the file attachments don&#8217;t seem to have come along for the ride.  I have relinked to another copy of the chapter stored on another server.  Hope you enjoy it!</p>
<p>&#8211; Chris Lee</p>
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		<title>Comment on __getattr__ Considered Harmful by Jeanne</title>
		<link>http://thinking.bioinformatics.ucla.edu/2008/08/04/__getattr__-considered-harmful/#comment-959</link>
		<dc:creator>Jeanne</dc:creator>
		<pubDate>Wed, 05 Nov 2008 22:59:19 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2008/08/04/__getattr__-considered-harmful/#comment-959</guid>
		<description>Interestingly, even for accountants :)))))</description>
		<content:encoded><![CDATA[<p>Interestingly, even for accountants :)))))</p>
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		<title>Comment on The Feynmanization of Chapter 1 by Robert Cadena</title>
		<link>http://thinking.bioinformatics.ucla.edu/2008/08/13/the-feynmanization-of-chapter-1/#comment-866</link>
		<dc:creator>Robert Cadena</dc:creator>
		<pubDate>Thu, 30 Oct 2008 07:00:32 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2008/08/13/the-feynmanization-of-chapter-1/#comment-866</guid>
		<description>The link for the new chapter returns a "404 — File not found."  This is the url the link points to:  http://thinking.bioinformatics.ucla.edu/files/2008/08/chapter1.pdf</description>
		<content:encoded><![CDATA[<p>The link for the new chapter returns a &#8220;404 — File not found.&#8221;  This is the url the link points to:  <a href="http://thinking.bioinformatics.ucla.edu/files/2008/08/chapter1.pdf" rel="nofollow">http://thinking.bioinformatics.ucla.edu/files/2008/08/chapter1.pdf</a></p>
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		<title>Comment on The Feynmanization of Chapter 1 by John Baez</title>
		<link>http://thinking.bioinformatics.ucla.edu/2008/08/13/the-feynmanization-of-chapter-1/#comment-161</link>
		<dc:creator>John Baez</dc:creator>
		<pubDate>Wed, 20 Aug 2008 18:28:12 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2008/08/13/the-feynmanization-of-chapter-1/#comment-161</guid>
		<description>Hello again.  I just took a look at your new draft.  It's vastly more appealing than the old one!

I like the dialogues.  You can have a lot of fun with them if you have the same characters appear repeatedly, with their own distinctive personalities - illustrating different cognitive tendencies, or different aspects of your &lt;i&gt;own&lt;/i&gt; thinking.   Done right this sort of thing is very engaging, since we're hard-wired to be fascinated by real people and their conflicts.

It's a real art to bring a taste of "real life" into such dialogues without distracting attention from the points you're trying to make.   Ideally, the characters' personalities can be very &lt;i&gt;helpful&lt;/i&gt; in presenting different points.  For example, it makes sense to have a mathematician named Matt (cute) who is good at rigorous reasoning but a bit naive when it comes to epistemology: he can help out when math is needed, but also serve to illustrate the dangers of certain kinds of naivete.  You could have a frequentist and a Bayesian to carry out two sides of that battle... after all, I think part of your book is about the limitations of "subjective Bayesianism".  Sonya shouldn't be just "a scientist", but some specific &lt;i&gt;kind&lt;/i&gt; of scientist: you may want a number of different kinds: biologists, computer scientists, physicists and so on --- each with their own strengths and weaknesses.  Since you're a Renaissance man, you could use quite a cast of characters.

You write: "Most of us have learned about mathematical logic, theorems and proofs in math class."  Ah, if only that were true!  :-)  It depends who your audience is, I guess.

Using the Monte Hall paradox to introduce Bayes' law is good, but maybe you should start with an easier example, like: "if the probability that you die of cancer given that you smoke is 20%, and the probability that you smoke is 10%, and... then... ?".  In other words, a simple "plug and chug" example, just to illustrate the formula and nail down the concepts in the simplest possible way.

But, you can probably find a real-world example that seems quite striking!  People tend to get mixed up between "the probability that P, given Q" and "the probability that Q, given P", and get shocked when these are drastically different.  Getting over this seems to be crucial to getting good at statistical reasoning.</description>
		<content:encoded><![CDATA[<p>Hello again.  I just took a look at your new draft.  It&#8217;s vastly more appealing than the old one!</p>
<p>I like the dialogues.  You can have a lot of fun with them if you have the same characters appear repeatedly, with their own distinctive personalities - illustrating different cognitive tendencies, or different aspects of your <i>own</i> thinking.   Done right this sort of thing is very engaging, since we&#8217;re hard-wired to be fascinated by real people and their conflicts.</p>
<p>It&#8217;s a real art to bring a taste of &#8220;real life&#8221; into such dialogues without distracting attention from the points you&#8217;re trying to make.   Ideally, the characters&#8217; personalities can be very <i>helpful</i> in presenting different points.  For example, it makes sense to have a mathematician named Matt (cute) who is good at rigorous reasoning but a bit naive when it comes to epistemology: he can help out when math is needed, but also serve to illustrate the dangers of certain kinds of naivete.  You could have a frequentist and a Bayesian to carry out two sides of that battle&#8230; after all, I think part of your book is about the limitations of &#8220;subjective Bayesianism&#8221;.  Sonya shouldn&#8217;t be just &#8220;a scientist&#8221;, but some specific <i>kind</i> of scientist: you may want a number of different kinds: biologists, computer scientists, physicists and so on &#8212; each with their own strengths and weaknesses.  Since you&#8217;re a Renaissance man, you could use quite a cast of characters.</p>
<p>You write: &#8220;Most of us have learned about mathematical logic, theorems and proofs in math class.&#8221;  Ah, if only that were true!  <img src='http://thinking.bioinformatics.ucla.edu/wp-includes/images/smilies/icon_smile.gif' alt=':-)' class='wp-smiley' />  It depends who your audience is, I guess.</p>
<p>Using the Monte Hall paradox to introduce Bayes&#8217; law is good, but maybe you should start with an easier example, like: &#8220;if the probability that you die of cancer given that you smoke is 20%, and the probability that you smoke is 10%, and&#8230; then&#8230; ?&#8221;.  In other words, a simple &#8220;plug and chug&#8221; example, just to illustrate the formula and nail down the concepts in the simplest possible way.</p>
<p>But, you can probably find a real-world example that seems quite striking!  People tend to get mixed up between &#8220;the probability that P, given Q&#8221; and &#8220;the probability that Q, given P&#8221;, and get shocked when these are drastically different.  Getting over this seems to be crucial to getting good at statistical reasoning.</p>
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		<title>Comment on The Feynmanization of Chapter 1 by John Baez</title>
		<link>http://thinking.bioinformatics.ucla.edu/2008/08/13/the-feynmanization-of-chapter-1/#comment-157</link>
		<dc:creator>John Baez</dc:creator>
		<pubDate>Thu, 14 Aug 2008 09:39:34 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2008/08/13/the-feynmanization-of-chapter-1/#comment-157</guid>
		<description>Hi!  I got your email - I'll check out this new draft and make some comments in a while.   I'll have to add this blog to my list of places to visit.

(Lisa and I have been in Paris for most of the summer, but will return to California tomorrow.)

Don't succumb to math envy!  Or if you do, imitate those mathematicians who explain things using words rather than equations.  :-)</description>
		<content:encoded><![CDATA[<p>Hi!  I got your email - I&#8217;ll check out this new draft and make some comments in a while.   I&#8217;ll have to add this blog to my list of places to visit.</p>
<p>(Lisa and I have been in Paris for most of the summer, but will return to California tomorrow.)</p>
<p>Don&#8217;t succumb to math envy!  Or if you do, imitate those mathematicians who explain things using words rather than equations.  <img src='http://thinking.bioinformatics.ucla.edu/wp-includes/images/smilies/icon_smile.gif' alt=':-)' class='wp-smiley' /></p>
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		<title>Comment on A model of clarity: Feynman&#8217;s Lectures by Ameenaaji</title>
		<link>http://thinking.bioinformatics.ucla.edu/2008/07/18/16/#comment-155</link>
		<dc:creator>Ameenaaji</dc:creator>
		<pubDate>Sun, 03 Aug 2008 12:42:29 +0000</pubDate>
		<guid isPermaLink="false">http://thinking.bioinformatics.ucla.edu/2008/07/18/16/#comment-155</guid>
		<description>i need model question paper in bio-informatics and bio-technology from madras university</description>
		<content:encoded><![CDATA[<p>i need model question paper in bio-informatics and bio-technology from madras university</p>
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