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	<title>Comments on: Web 2.0 for Biologists&#8211;Are any of the current tools worth using?</title>
	<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/</link>
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	<pubDate>Fri,  4 Jul 2008 04:48:41 +0000</pubDate>
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		<title>By: James Dadd</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-16398</link>
		<dc:creator>James Dadd</dc:creator>
		<pubDate>Wed, 25 Jun 2008 13:05:51 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-16398</guid>
		<description>I have found your article a very important insight into the world of scientific research as a whole and I think some of your points are well constructed.

I would add that one of the reasons for lack of adoption is that social networks promote a feeling of not working they do not promote the feeling of 'I am working'.

I would argue they are work inhibitors not enablers.

Until somebody, perhaps me (Im a web developer for a life science company), understand that for any site aiming to create a community of purpose they need to start with the idea of enabling work not inhibit. Only create tools which allow the scientist to get their job done quicker.</description>
		<content:encoded><![CDATA[<p>I have found your article a very important insight into the world of scientific research as a whole and I think some of your points are well constructed.</p>
<p>I would add that one of the reasons for lack of adoption is that social networks promote a feeling of not working they do not promote the feeling of &#8216;I am working&#8217;.</p>
<p>I would argue they are work inhibitors not enablers.</p>
<p>Until somebody, perhaps me (Im a web developer for a life science company), understand that for any site aiming to create a community of purpose they need to start with the idea of enabling work not inhibit. Only create tools which allow the scientist to get their job done quicker.</p>
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		<title>By: Sebastian Gonzalez</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-16343</link>
		<dc:creator>Sebastian Gonzalez</dc:creator>
		<pubDate>Wed, 28 May 2008 00:24:23 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-16343</guid>
		<description>I read your post like two months ago, and then I googled for wikipaper, I wanted to see if there was any tool to writes papers online and in a wiki manner. There is not, as far as I know.

In our group (http://www.cec.uchile.cl/cinetica/ a very good example of web 1.0) we use SVN for write the papers and maintain the code and I think that a wiki interface for this would make the work even faster and easier. So after talking with my boss, we are hiring a CS student to install us a wiki server with latex support and forums (he's not convinced in blogging yet). 

I would be really grateful if you or somebody can give ideas on the tools that one can need for a site that want to make scientific research with web 2.0.

regards.</description>
		<content:encoded><![CDATA[<p>I read your post like two months ago, and then I googled for wikipaper, I wanted to see if there was any tool to writes papers online and in a wiki manner. There is not, as far as I know.</p>
<p>In our group (http://www.cec.uchile.cl/cinetica/ a very good example of web 1.0) we use SVN for write the papers and maintain the code and I think that a wiki interface for this would make the work even faster and easier. So after talking with my boss, we are hiring a CS student to install us a wiki server with latex support and forums (he&#8217;s not convinced in blogging yet). </p>
<p>I would be really grateful if you or somebody can give ideas on the tools that one can need for a site that want to make scientific research with web 2.0.</p>
<p>regards.</p>
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		<title>By: Discussing Science 2.0 &#171; A Man With A Ph.D.</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15810</link>
		<dc:creator>Discussing Science 2.0 &#171; A Man With A Ph.D.</dc:creator>
		<pubDate>Sun, 06 Apr 2008 00:29:07 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15810</guid>
		<description>[...] Science&#160;2.0 April 6, 2008 &#8212; Richard    by geishaboy500 Web 2.0 for Biologists&#38;#8211;Are any of the current tools worth using?: [Via Bench [...]</description>
		<content:encoded><![CDATA[<p>[&#8230;] Science&nbsp;2.0 April 6, 2008 &#8212; Richard    by geishaboy500 Web 2.0 for Biologists&#38;#8211;Are any of the current tools worth using?: [Via Bench [&#8230;]</p>
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		<title>By: Richard Gayle</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15809</link>
		<dc:creator>Richard Gayle</dc:creator>
		<pubDate>Sat, 05 Apr 2008 23:29:06 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15809</guid>
		<description>David identifies something very important - scientists are different. It is no wonder that successful Web 2.0 approaches will be different. I have tried to use these technologies for my research and have discussed them with others.

I found a slightly different answer than David did. I talked with biological researchers in academia, those in industry and those working at non-profit research institutions. 

What I found was that the level of multi-disciplinary collaboration had a huge effect on the likelihood of being responsive to Web 2.0 approaches. These types of research were usually seen at companies and at the research institutions, although there are certainly such labs at universities.

These researchers did not suffer as much from too full a plate (as often seen in academia) but from a glut of data that they needed to quickly communicate to the larger group. They were overwhelmed by this and very receptive to approaches that would help them here.

Scientists are not going to use these approaches because they are a good thing to do. They will use them because it makes life easier.

Also, Slideshare is at best a stop gap for scientific presentations. I came across something while perusing the &lt;a href="http://www.educause.edu/content.asp?SECTION_ID=328" rel="nofollow"&gt;EDUCAUSE online conference&lt;/A&gt;. It includes &lt;a href="https://admin.acrobat.com/_a729300474/p79061869/" rel="nofollow"&gt;both slides and voice. &lt;/A&gt; Probably a little to proprietary for many but you get the idea.</description>
		<content:encoded><![CDATA[<p>David identifies something very important - scientists are different. It is no wonder that successful Web 2.0 approaches will be different. I have tried to use these technologies for my research and have discussed them with others.</p>
<p>I found a slightly different answer than David did. I talked with biological researchers in academia, those in industry and those working at non-profit research institutions. </p>
<p>What I found was that the level of multi-disciplinary collaboration had a huge effect on the likelihood of being responsive to Web 2.0 approaches. These types of research were usually seen at companies and at the research institutions, although there are certainly such labs at universities.</p>
<p>These researchers did not suffer as much from too full a plate (as often seen in academia) but from a glut of data that they needed to quickly communicate to the larger group. They were overwhelmed by this and very receptive to approaches that would help them here.</p>
<p>Scientists are not going to use these approaches because they are a good thing to do. They will use them because it makes life easier.</p>
<p>Also, Slideshare is at best a stop gap for scientific presentations. I came across something while perusing the <a href="http://www.educause.edu/content.asp?SECTION_ID=328" rel="nofollow">EDUCAUSE online conference</a>. It includes <a href="https://admin.acrobat.com/_a729300474/p79061869/" rel="nofollow">both slides and voice. </a> Probably a little to proprietary for many but you get the idea.</p>
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		<title>By: David Crotty</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15807</link>
		<dc:creator>David Crotty</dc:creator>
		<pubDate>Fri, 04 Apr 2008 17:19:30 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15807</guid>
		<description>Wililam--

Thanks, as always for the comments.  I think what you're getting at is similar to the views expressed in this article:
http://www.economist.com/business/displaystory.cfm?story_id=10880936
These tools are going to work a lot better when they're built in to our everyday communication methods, rather than requiring you to continuously check a horde of sites to see if there's been any action.  You're right that Connotea is easy to use once you get it going, it's that initial barrier that's tough to overcome if you've got an enormous pile of references already established.  I think it's great if you're just starting out, a way to stay organized from the get-go.  

And glad to see I'm not the only one who doesn't really care that much for the embedded slideshows.  I would much rather read at my own pace and be able to come back later and pick up where I left off than be forced to plod along with someone else.</description>
		<content:encoded><![CDATA[<p>Wililam&#8211;</p>
<p>Thanks, as always for the comments.  I think what you&#8217;re getting at is similar to the views expressed in this article:<br />
<a href="http://www.economist.com/business/displaystory.cfm?story_id=10880936" rel="nofollow">http://www.economist.com/business/displaystory.cfm?story_id=10880936</a><br />
These tools are going to work a lot better when they&#8217;re built in to our everyday communication methods, rather than requiring you to continuously check a horde of sites to see if there&#8217;s been any action.  You&#8217;re right that Connotea is easy to use once you get it going, it&#8217;s that initial barrier that&#8217;s tough to overcome if you&#8217;ve got an enormous pile of references already established.  I think it&#8217;s great if you&#8217;re just starting out, a way to stay organized from the get-go.  </p>
<p>And glad to see I&#8217;m not the only one who doesn&#8217;t really care that much for the embedded slideshows.  I would much rather read at my own pace and be able to come back later and pick up where I left off than be forced to plod along with someone else.</p>
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		<title>By: mr. gunn</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15806</link>
		<dc:creator>mr. gunn</dc:creator>
		<pubDate>Fri, 04 Apr 2008 16:24:06 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15806</guid>
		<description>Reading between the lines here, I think you've uncovered one of the missing links.  It's not just about discovery and organization, but about attention management.  

Connotea does a good job of helping you organize things with minimal effort, and once you get it going, it's pretty good for discovery, too, but what if it could send you an email when someone bookmarks a paper you don't have in your library that contains 3 of your most common tags?

What if you got an email when someone responded to your comment or question on a paper?  I know from personal experience that emailing manuscript authors or even calling doesn't always get a prompt response, but at least with a comment thread you increase the chances that *someone* will answer your question.  I've tried out a couple services that watch sites on which you've left comments  and keep you informed of the ensuing discussions by aggregating the comment threads, but so far I haven't had much luck.  Postgenomic does a pretty good job of aggregating the blog commentary on papers, if it's written as a post, but it can't pick up the comments attached to the articles yet.  &lt;a href="http://scintilla.nature.com/conversations" rel="nofollow"&gt;Scintilla's hidden "conversations" feature&lt;/a&gt; is pretty good too.

So what the current tools are missing is a way to bring things you wanted to know about to your attention without you having to remember to check on it, and to facilitate more timely interaction that is currently realized by the current techniques such as emailing.   The article author can subscribe to a feed of comments on a paper, and commenters can too, so this is a problem that has a solution, but it's just not a easy, streamlined one.

About the slide presentation - I like the way you've done it here.  Others evangelize embedded video and slideshows and such, but to me they're like Youtube URLs.  You never know if it's going to be worth it until you click, and there's no easy way to give things a quick once-over.  Yeah, it can be more engaging, but please let's save that for things which can only be show in that format, like time-lapse imaging and not just slides from your talk which would be better off converted to jpg with commentary.  By all means, upload it to &lt;a href="http://precedings.nature.com" rel="nofollow"&gt;Precedings&lt;/a&gt;, but don't change the way you've got it here.  I read faster than you talk.</description>
		<content:encoded><![CDATA[<p>Reading between the lines here, I think you&#8217;ve uncovered one of the missing links.  It&#8217;s not just about discovery and organization, but about attention management.  </p>
<p>Connotea does a good job of helping you organize things with minimal effort, and once you get it going, it&#8217;s pretty good for discovery, too, but what if it could send you an email when someone bookmarks a paper you don&#8217;t have in your library that contains 3 of your most common tags?</p>
<p>What if you got an email when someone responded to your comment or question on a paper?  I know from personal experience that emailing manuscript authors or even calling doesn&#8217;t always get a prompt response, but at least with a comment thread you increase the chances that *someone* will answer your question.  I&#8217;ve tried out a couple services that watch sites on which you&#8217;ve left comments  and keep you informed of the ensuing discussions by aggregating the comment threads, but so far I haven&#8217;t had much luck.  Postgenomic does a pretty good job of aggregating the blog commentary on papers, if it&#8217;s written as a post, but it can&#8217;t pick up the comments attached to the articles yet.  <a href="http://scintilla.nature.com/conversations" rel="nofollow">Scintilla&#8217;s hidden &#8220;conversations&#8221; feature</a> is pretty good too.</p>
<p>So what the current tools are missing is a way to bring things you wanted to know about to your attention without you having to remember to check on it, and to facilitate more timely interaction that is currently realized by the current techniques such as emailing.   The article author can subscribe to a feed of comments on a paper, and commenters can too, so this is a problem that has a solution, but it&#8217;s just not a easy, streamlined one.</p>
<p>About the slide presentation - I like the way you&#8217;ve done it here.  Others evangelize embedded video and slideshows and such, but to me they&#8217;re like Youtube URLs.  You never know if it&#8217;s going to be worth it until you click, and there&#8217;s no easy way to give things a quick once-over.  Yeah, it can be more engaging, but please let&#8217;s save that for things which can only be show in that format, like time-lapse imaging and not just slides from your talk which would be better off converted to jpg with commentary.  By all means, upload it to <a href="http://precedings.nature.com" rel="nofollow">Precedings</a>, but don&#8217;t change the way you&#8217;ve got it here.  I read faster than you talk.</p>
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		<title>By: David Crotty</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15805</link>
		<dc:creator>David Crotty</dc:creator>
		<pubDate>Fri, 04 Apr 2008 14:03:42 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15805</guid>
		<description>Shafee--thanks, and thanks for the link, I'll start digging in.

Daniel--as I said, the question of blogging is an open one.  There are obvious benefits.  But those making the important career decisions, tenure, hiring committees, etc., may not share the same opinion.  I'd also argue that actually doing research is  more important than any conversation.  Being a prolific writer doesn't do you any good if it's all unrelated to any original results you've uncovered.  Yes, communication and interaction is important, but let's not lose sight of the reason these jobs actually exist.</description>
		<content:encoded><![CDATA[<p>Shafee&#8211;thanks, and thanks for the link, I&#8217;ll start digging in.</p>
<p>Daniel&#8211;as I said, the question of blogging is an open one.  There are obvious benefits.  But those making the important career decisions, tenure, hiring committees, etc., may not share the same opinion.  I&#8217;d also argue that actually doing research is  more important than any conversation.  Being a prolific writer doesn&#8217;t do you any good if it&#8217;s all unrelated to any original results you&#8217;ve uncovered.  Yes, communication and interaction is important, but let&#8217;s not lose sight of the reason these jobs actually exist.</p>
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		<title>By: The negative myths about academic blogging</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15804</link>
		<dc:creator>The negative myths about academic blogging</dc:creator>
		<pubDate>Fri, 04 Apr 2008 12:46:45 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15804</guid>
		<description>[...] David Crottyand Stephen [...]</description>
		<content:encoded><![CDATA[<p>[&#8230;] David Crottyand Stephen [&#8230;]</p>
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		<title>By: Daniel Lemire</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15803</link>
		<dc:creator>Daniel Lemire</dc:creator>
		<pubDate>Fri, 04 Apr 2008 12:24:02 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15803</guid>
		<description>Not blogging will not make you a more prolific writer. Blogging will get you in the habit of writing daily. That's good for tenure.

Blogging and Web 2.0 is a conversation. If you don't have time for this conversation, and it is very much a central part of your job as a researcher, maybe you are spending too much time on the phone or in meetings?</description>
		<content:encoded><![CDATA[<p>Not blogging will not make you a more prolific writer. Blogging will get you in the habit of writing daily. That&#8217;s good for tenure.</p>
<p>Blogging and Web 2.0 is a conversation. If you don&#8217;t have time for this conversation, and it is very much a central part of your job as a researcher, maybe you are spending too much time on the phone or in meetings?</p>
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		<title>By: Yehoshafat Shafee Give'on</title>
		<link>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15802</link>
		<dc:creator>Yehoshafat Shafee Give'on</dc:creator>
		<pubDate>Fri, 04 Apr 2008 11:59:55 +0000</pubDate>
		<guid>http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/#comment-15802</guid>
		<description>You are so right. It is about time that the cultures of potential users will be heard. It is about time that methods of "occupation analysis" to reveal the data types needed will be developed and applied. 

I have not finished yet reading your article, but I already sent it to my students (of applied informatics in education) and to my colleagues. If you will have some time to peep into www.shafee.com you will see that a similar problem exists also in the field of education and since 1985 I have been trying to express similar ideas.. Well. as you said, it is a problem of cultures.

All the best and better luck..

Shafee</description>
		<content:encoded><![CDATA[<p>You are so right. It is about time that the cultures of potential users will be heard. It is about time that methods of &#8220;occupation analysis&#8221; to reveal the data types needed will be developed and applied. </p>
<p>I have not finished yet reading your article, but I already sent it to my students (of applied informatics in education) and to my colleagues. If you will have some time to peep into <a href="http://www.shafee.com" rel="nofollow">http://www.shafee.com</a> you will see that a similar problem exists also in the field of education and since 1985 I have been trying to express similar ideas.. Well. as you said, it is a problem of cultures.</p>
<p>All the best and better luck..</p>
<p>Shafee</p>
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