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	<title>Comments on: Scientific Wikis &#8211; Part I</title>
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		<title>By: admin</title>
		<link>http://rosettadesigngroup.com/blog/373/scientific-wikis-part-i/comment-page-1/#comment-4666</link>
		<dc:creator>admin</dc:creator>
		<pubDate>Tue, 12 May 2009 09:07:38 +0000</pubDate>
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		<description>@David
a) Fixed. Thanks.
b) One of the advantages of wikis is that the content&#039;s format/quality is up to the readers as well as the writers. If you set a standard of describing the logic behind each parameter in the experiment - they will follow, this will certainly hold when the benefits of keeping such a format are so clear as in the example you gave.  
c) If you spot such mistakes even if you fear to correct them yourself, there&#039;s usually the option to alert some kind of editor or a &quot;higher power&quot; which will investigate the issue.</description>
		<content:encoded><![CDATA[<p>@David<br />
a) Fixed. Thanks.<br />
b) One of the advantages of wikis is that the content&#8217;s format/quality is up to the readers as well as the writers. If you set a standard of describing the logic behind each parameter in the experiment &#8211; they will follow, this will certainly hold when the benefits of keeping such a format are so clear as in the example you gave.<br />
c) If you spot such mistakes even if you fear to correct them yourself, there&#8217;s usually the option to alert some kind of editor or a &#8220;higher power&#8221; which will investigate the issue.</p>
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		<title>By: David Hall</title>
		<link>http://rosettadesigngroup.com/blog/373/scientific-wikis-part-i/comment-page-1/#comment-4653</link>
		<dc:creator>David Hall</dc:creator>
		<pubDate>Tue, 12 May 2009 01:29:48 +0000</pubDate>
		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=373#comment-4653</guid>
		<description>a) if this article was a wiki, I could correct the spelling in this phrase: &quot;Weather we are thinking&quot;.

b) When I was a wet lab person, I often found myself doing experimental protocols where I was unsure whether steps were based on trial and error or calculation.  For instance, a time for a reaction could be based on knowledge of a half life and wanting to allow for multiple half lives, or someone just choosing a time that seemed sufficient.  If I want to vary the method, knowing how I should approach adjusting the step is very useful.  I hoped that wikis could provide some sort of annotation for the whys of every word of every step of a method.  In 6 months, a protocol could go from Kevin Janes to me through 3 different people, and the person I was talking to had no idea for the why of steps (nor did he seem to care).  Hopefully there are labs out there with some sort of lab wiki that will answer those questions for people.  I know OpenWetWare&#039;s protocols page is supposed to serve a function like this, but most of the protocols there are disappointing.  If you just say &quot;incubate for 20 minutes at 72 C&quot;, I get nothing out of that.  A protocol should train the user in good practices for future protocol development.  And it&#039;s a useful exercise for the developer to have to justify every step (something which becomes much more important when you go to work for a company and are turning a bench protocol into a screening protocol which will be used across tens or hundreds of thousands of molecules).

c) My greatest fear in editing scientific articles in wikipedia is putting in wrong information.  This is true on non-scientific articles as well.  You could say that if I put in something wrong, someone will correct me, but I frequently come across long-standing errors in articles.  Sometimes, I have enough confidence to make a change, sometimes I don&#039;t.  Let&#039;s go through my two of my recent edits on wikipedia as examples:
1) http://en.wikipedia.org/w/index.php?title=Bcl-xL&amp;diff=prev&amp;oldid=285461961  Someone claimed that Bcl-xl stands for &quot;basal cell lymphoma extra large&quot;.  But Bcl-xl is part of the Bcl-2 family of proteins which wikipedia says stands for B-cell lymphoma where the B in B-cell stands for either &quot;bursa of Fabricus&quot; or &quot;bone&quot;.  So, I don&#039;t know where basal could possibly come from, so I changed it.
2) http://en.wikipedia.org/w/index.php?title=Talk:St._Stephen%27s_%26_St._Agnes_School&amp;diff=prev&amp;oldid=234315957  John McCain went to my high school for a little while.  For some reason, my high school&#039;s article lists his graduation date from a different school and I know that date to be wrong.  Based on this, I think his dates of attendance at my school are wrong.  I also think the dates that were listed on McCain&#039;s website were wrong.  I have no idea what&#039;s correct, and I wonder whether anyone will stumble across the article and know the truth.  I actually doubt it.  It&#039;s a long tail that I fear wikis frequently can&#039;t reach.</description>
		<content:encoded><![CDATA[<p>a) if this article was a wiki, I could correct the spelling in this phrase: &#8220;Weather we are thinking&#8221;.</p>
<p>b) When I was a wet lab person, I often found myself doing experimental protocols where I was unsure whether steps were based on trial and error or calculation.  For instance, a time for a reaction could be based on knowledge of a half life and wanting to allow for multiple half lives, or someone just choosing a time that seemed sufficient.  If I want to vary the method, knowing how I should approach adjusting the step is very useful.  I hoped that wikis could provide some sort of annotation for the whys of every word of every step of a method.  In 6 months, a protocol could go from Kevin Janes to me through 3 different people, and the person I was talking to had no idea for the why of steps (nor did he seem to care).  Hopefully there are labs out there with some sort of lab wiki that will answer those questions for people.  I know OpenWetWare&#8217;s protocols page is supposed to serve a function like this, but most of the protocols there are disappointing.  If you just say &#8220;incubate for 20 minutes at 72 C&#8221;, I get nothing out of that.  A protocol should train the user in good practices for future protocol development.  And it&#8217;s a useful exercise for the developer to have to justify every step (something which becomes much more important when you go to work for a company and are turning a bench protocol into a screening protocol which will be used across tens or hundreds of thousands of molecules).</p>
<p>c) My greatest fear in editing scientific articles in wikipedia is putting in wrong information.  This is true on non-scientific articles as well.  You could say that if I put in something wrong, someone will correct me, but I frequently come across long-standing errors in articles.  Sometimes, I have enough confidence to make a change, sometimes I don&#8217;t.  Let&#8217;s go through my two of my recent edits on wikipedia as examples:<br />
1) <a href="http://en.wikipedia.org/w/index.php?title=Bcl-xL&amp;diff=prev&amp;oldid=285461961" rel="nofollow">http://en.wikipedia.org/w/index.php?title=Bcl-xL&amp;diff=prev&amp;oldid=285461961</a>  Someone claimed that Bcl-xl stands for &#8220;basal cell lymphoma extra large&#8221;.  But Bcl-xl is part of the Bcl-2 family of proteins which wikipedia says stands for B-cell lymphoma where the B in B-cell stands for either &#8220;bursa of Fabricus&#8221; or &#8220;bone&#8221;.  So, I don&#8217;t know where basal could possibly come from, so I changed it.<br />
2) <a href="http://en.wikipedia.org/w/index.php?title=Talk:St._Stephen%27s_%26_St._Agnes_School&amp;diff=prev&amp;oldid=234315957" rel="nofollow">http://en.wikipedia.org/w/index.php?title=Talk:St._Stephen%27s_%26_St._Agnes_School&amp;diff=prev&amp;oldid=234315957</a>  John McCain went to my high school for a little while.  For some reason, my high school&#8217;s article lists his graduation date from a different school and I know that date to be wrong.  Based on this, I think his dates of attendance at my school are wrong.  I also think the dates that were listed on McCain&#8217;s website were wrong.  I have no idea what&#8217;s correct, and I wonder whether anyone will stumble across the article and know the truth.  I actually doubt it.  It&#8217;s a long tail that I fear wikis frequently can&#8217;t reach.</p>
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		<title>By: Dan Bolser</title>
		<link>http://rosettadesigngroup.com/blog/373/scientific-wikis-part-i/comment-page-1/#comment-4644</link>
		<dc:creator>Dan Bolser</dc:creator>
		<pubDate>Mon, 11 May 2009 20:27:44 +0000</pubDate>
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		<description>Here is an example of one of the growing number of &#039;annotation wikis&#039; that I mentioned above:

http://www.slideshare.net/nm249/sgn-community-annotation-tutorial


(although its not strictly a wiki).</description>
		<content:encoded><![CDATA[<p>Here is an example of one of the growing number of &#8216;annotation wikis&#8217; that I mentioned above:</p>
<p><a href="http://www.slideshare.net/nm249/sgn-community-annotation-tutorial" rel="nofollow">http://www.slideshare.net/nm249/sgn-community-annotation-tutorial</a></p>
<p>(although its not strictly a wiki).</p>
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