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	<title>Comments on: Mendeley: a very short review</title>
	<atom:link href="http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/feed/" rel="self" type="application/rss+xml" />
	<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/</link>
	<description>Bits of science</description>
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	<item>
		<title>By: Paulo Nuin</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1699</link>
		<dc:creator>Paulo Nuin</dc:creator>
		<pubDate>Thu, 30 Apr 2009 14:57:58 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1699</guid>
		<description>Yes, many people are having the same problem you mentioned. It seems that it&#039;s not ready to prime time and I wouldn&#039;t devote a lot of time and effort running it.</description>
		<content:encoded><![CDATA[<p>Yes, many people are having the same problem you mentioned. It seems that it&#8217;s not ready to prime time and I wouldn&#8217;t devote a lot of time and effort running it.</p>
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	<item>
		<title>By: Sakshath</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1698</link>
		<dc:creator>Sakshath</dc:creator>
		<pubDate>Thu, 30 Apr 2009 07:02:36 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1698</guid>
		<description>Hi,
     I installed Mendeley version 0.6.4 just yesterday. I have only added a small set of pdfs but it just does not finish sending all the metadata files online for more than an hour. So, I chose to cancel the process and it is not able to do that as well for a very long time....Yesterday it crashed during a similar operation. 


sakshath</description>
		<content:encoded><![CDATA[<p>Hi,<br />
     I installed Mendeley version 0.6.4 just yesterday. I have only added a small set of pdfs but it just does not finish sending all the metadata files online for more than an hour. So, I chose to cancel the process and it is not able to do that as well for a very long time&#8230;.Yesterday it crashed during a similar operation. </p>
<p>sakshath</p>
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	<item>
		<title>By: Blind.Scientist &#187; Blog Archive &#187; Mendeley: an extremely short review (sort of)</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1685</link>
		<dc:creator>Blind.Scientist &#187; Blog Archive &#187; Mendeley: an extremely short review (sort of)</dc:creator>
		<pubDate>Fri, 03 Apr 2009 19:21:35 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1685</guid>
		<description>[...] to test Mendeley again (Yes, I have some kind of a masochist behaviour for software), and as the last time I tried, I can say I&#8217;m not [...]</description>
		<content:encoded><![CDATA[<p>[...] to test Mendeley again (Yes, I have some kind of a masochist behaviour for software), and as the last time I tried, I can say I&#8217;m not [...]</p>
]]></content:encoded>
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	<item>
		<title>By: Victor</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1683</link>
		<dc:creator>Victor</dc:creator>
		<pubDate>Thu, 02 Apr 2009 19:06:01 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1683</guid>
		<description>Hi Nortexoid,

apologies to you, too, for not meeting your expections! We&#039;re aware of the sore spots you&#039;re pointing out - they are our top priority. Please also keep in mind that Paulo tested our very first public beta version (0.5.7), and the current version is still quite early (beta 0.6.3), so there are major changes with every release. 

Regarding the quality of the metadata extraction: There are great variations between different journals and layouts - many are parsed perfectly, and for some it doesn&#039;t work at all. For the next major release (beta 0.7, due in approx. 6-8 weeks), author &amp; title extraction should be improved significantly across the board; moreover, we&#039;ll make use of the PubMed API to retrieve metadata for most bio/life science papers.

Regarding the crashes: All I can say is we&#039;re very sorry - and all known bugs that lead to crashes (particularly during import) should be fixed in the next release (0.6.4) out early next week. If you should still experience crashes after that release, we&#039;d be very grateful if you could send a bug report so we can trace it down. We do have Windows Vista and XP, Mac OS Tiger and Leopard, and many different Linux distributions running on our office machines, but of course we still can&#039;t cover all possible configurations that lead to problems.

As for performance, we&#039;ve so far focused our efforts on the handling of large libraries - the earliest versions got sluggish if you had more than 100 documents in them. We&#039;ve tested beta 0.6.4 with libraries of more than 5,000 PDF documents (including cited references, that&#039;s more than 100,000 metadata sets), and it&#039;s working well, but it takes about a minute to start. Obviously, our goal for beta 0.7 is to support much larger libraries than that while still starting up much faster.

You were also mentioning the indexing speed. Indeed, if we were just indexing the full-text like Copernic or Google Desktop, we&#039;d be much faster - it&#039;s the metadata and reference recognition (which also involves server interaction) that slows it down. Admittedly, we haven&#039;t had the chance to work on this since Paulo tested it, but we&#039;ll be experimenting with a few ideas for improvements for beta 0.7.

I know this won&#039;t solve your problems with the current release, but perhaps you can give the next ones another shot and see whether things have improved for you! Thanks in any case for trying,

best wishes,
Victor</description>
		<content:encoded><![CDATA[<p>Hi Nortexoid,</p>
<p>apologies to you, too, for not meeting your expections! We&#8217;re aware of the sore spots you&#8217;re pointing out &#8211; they are our top priority. Please also keep in mind that Paulo tested our very first public beta version (0.5.7), and the current version is still quite early (beta 0.6.3), so there are major changes with every release. </p>
<p>Regarding the quality of the metadata extraction: There are great variations between different journals and layouts &#8211; many are parsed perfectly, and for some it doesn&#8217;t work at all. For the next major release (beta 0.7, due in approx. 6-8 weeks), author &amp; title extraction should be improved significantly across the board; moreover, we&#8217;ll make use of the PubMed API to retrieve metadata for most bio/life science papers.</p>
<p>Regarding the crashes: All I can say is we&#8217;re very sorry &#8211; and all known bugs that lead to crashes (particularly during import) should be fixed in the next release (0.6.4) out early next week. If you should still experience crashes after that release, we&#8217;d be very grateful if you could send a bug report so we can trace it down. We do have Windows Vista and XP, Mac OS Tiger and Leopard, and many different Linux distributions running on our office machines, but of course we still can&#8217;t cover all possible configurations that lead to problems.</p>
<p>As for performance, we&#8217;ve so far focused our efforts on the handling of large libraries &#8211; the earliest versions got sluggish if you had more than 100 documents in them. We&#8217;ve tested beta 0.6.4 with libraries of more than 5,000 PDF documents (including cited references, that&#8217;s more than 100,000 metadata sets), and it&#8217;s working well, but it takes about a minute to start. Obviously, our goal for beta 0.7 is to support much larger libraries than that while still starting up much faster.</p>
<p>You were also mentioning the indexing speed. Indeed, if we were just indexing the full-text like Copernic or Google Desktop, we&#8217;d be much faster &#8211; it&#8217;s the metadata and reference recognition (which also involves server interaction) that slows it down. Admittedly, we haven&#8217;t had the chance to work on this since Paulo tested it, but we&#8217;ll be experimenting with a few ideas for improvements for beta 0.7.</p>
<p>I know this won&#8217;t solve your problems with the current release, but perhaps you can give the next ones another shot and see whether things have improved for you! Thanks in any case for trying,</p>
<p>best wishes,<br />
Victor</p>
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	<item>
		<title>By: nortexoid</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1680</link>
		<dc:creator>nortexoid</dc:creator>
		<pubDate>Wed, 01 Apr 2009 16:50:28 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1680</guid>
		<description>Victor wrote &quot;Mendeley Desktop is doing a little bit more than just reading the PDF file. It extracts the full-text to make it searchable, it automatically tries to guess the correct metadata (author, title, journal, volume, issue, page numbers tc.) and extracts author-assigned keywords, and it parses each document’s cited references and turns them into machine-readable and exportable format&quot;.

The problem is that it rarely gets the metadata extraction right. So after quadrillions of cpu cycles wasted, and endless hours of thrashing away at the hard drive, you&#039;re left entering your own metadata anyway! Moreover, I notice that Copernic Desktop Search (and Google&#039;s) index the content of pdfs MUCH faster. But actually I suppose it is hard to compare because of the other stuff you mention that is simultaneously going on as it indexes the content.

I&#039;ve been trying to add my folder of pdfs (thousands) but Mendeley keeps crashing on me. This is in XP.

I like the online integration. I hate the resource-heaviness, though I&#039;m sure after the initial import it isn&#039;t so bad. If only it would get to that stage! The database &quot;structure&quot;/handling is certainly much better than Zotero&#039;s (BILLIONS of directories).</description>
		<content:encoded><![CDATA[<p>Victor wrote &#8220;Mendeley Desktop is doing a little bit more than just reading the PDF file. It extracts the full-text to make it searchable, it automatically tries to guess the correct metadata (author, title, journal, volume, issue, page numbers tc.) and extracts author-assigned keywords, and it parses each document’s cited references and turns them into machine-readable and exportable format&#8221;.</p>
<p>The problem is that it rarely gets the metadata extraction right. So after quadrillions of cpu cycles wasted, and endless hours of thrashing away at the hard drive, you&#8217;re left entering your own metadata anyway! Moreover, I notice that Copernic Desktop Search (and Google&#8217;s) index the content of pdfs MUCH faster. But actually I suppose it is hard to compare because of the other stuff you mention that is simultaneously going on as it indexes the content.</p>
<p>I&#8217;ve been trying to add my folder of pdfs (thousands) but Mendeley keeps crashing on me. This is in XP.</p>
<p>I like the online integration. I hate the resource-heaviness, though I&#8217;m sure after the initial import it isn&#8217;t so bad. If only it would get to that stage! The database &#8220;structure&#8221;/handling is certainly much better than Zotero&#8217;s (BILLIONS of directories).</p>
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		<title>By: Recent Links Tagged With "citeulike" - JabberTags</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1426</link>
		<dc:creator>Recent Links Tagged With "citeulike" - JabberTags</dc:creator>
		<pubDate>Thu, 09 Oct 2008 11:19:12 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1426</guid>
		<description>[...] public links &gt;&gt; citeulike   Mendeley: a very short review Saved by LinkOfTimemaster on Tue 07-10-2008   Science blogging at the Royal Institution, London [...]</description>
		<content:encoded><![CDATA[<p>[...] public links &gt;&gt; citeulike   Mendeley: a very short review Saved by LinkOfTimemaster on Tue 07-10-2008   Science blogging at the Royal Institution, London [...]</p>
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	<item>
		<title>By: Paulo Nuin</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1421</link>
		<dc:creator>Paulo Nuin</dc:creator>
		<pubDate>Tue, 26 Aug 2008 20:15:29 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1421</guid>
		<description>Assuming you are using C++ (Qt) 5-10 seconds to read one PDF is way too much. That number should be 1-2 seconds, with an extra second or two to I/O latency.</description>
		<content:encoded><![CDATA[<p>Assuming you are using C++ (Qt) 5-10 seconds to read one PDF is way too much. That number should be 1-2 seconds, with an extra second or two to I/O latency.</p>
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	<item>
		<title>By: Victor</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1419</link>
		<dc:creator>Victor</dc:creator>
		<pubDate>Tue, 26 Aug 2008 13:44:43 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1419</guid>
		<description>And I didn&#039;t mean to persuade you otherwise - just trying to explain.

Using 50% of CPU resources is a lot, to be sure, but that&#039;s only during automatic recognition (when all the heavy processing described above is done). Also, if it takes 5-10 seconds per PDF to do all the things I mentioned, then importing 700 files would take between 1-2 hours... But your point is taken - we&#039;ll try to speed it up in future versions.

Cheers,
Victor</description>
		<content:encoded><![CDATA[<p>And I didn&#8217;t mean to persuade you otherwise &#8211; just trying to explain.</p>
<p>Using 50% of CPU resources is a lot, to be sure, but that&#8217;s only during automatic recognition (when all the heavy processing described above is done). Also, if it takes 5-10 seconds per PDF to do all the things I mentioned, then importing 700 files would take between 1-2 hours&#8230; But your point is taken &#8211; we&#8217;ll try to speed it up in future versions.</p>
<p>Cheers,<br />
Victor</p>
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	<item>
		<title>By: Paulo Nuin</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1418</link>
		<dc:creator>Paulo Nuin</dc:creator>
		<pubDate>Tue, 26 Aug 2008 13:08:51 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1418</guid>
		<description>Still, there is no reason to use 50% of my computer CPU resources. And it shouldn&#039;t take hours to import the files. I already uninstalled it.</description>
		<content:encoded><![CDATA[<p>Still, there is no reason to use 50% of my computer CPU resources. And it shouldn&#8217;t take hours to import the files. I already uninstalled it.</p>
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		<title>By: Victor</title>
		<link>http://blindscientist.genedrift.org/2008/08/25/mendeley-a-very-short-review/comment-page-1/#comment-1417</link>
		<dc:creator>Victor</dc:creator>
		<pubDate>Tue, 26 Aug 2008 13:04:15 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=176#comment-1417</guid>
		<description>Hi Paolo,

sorry to hear that you&#039;ve had a less-than-desirable experience with our beta version. I agree that the automatic recognition you&#039;re describing could be optimized - we&#039;ll keep working on the speed and resource usage. 

If I may, I&#039;d like to add that Mendeley Desktop is doing a little bit more than just reading the PDF file. It extracts the full-text to make it searchable, it automatically tries to guess the correct metadata (author, title, journal, volume, issue, page numbers tc.) and extracts author-assigned keywords, and it parses each document&#039;s cited references and turns them into machine-readable and exportable format. It also lets you share and synchronize all this data with other users.

Cheers,
Victor</description>
		<content:encoded><![CDATA[<p>Hi Paolo,</p>
<p>sorry to hear that you&#8217;ve had a less-than-desirable experience with our beta version. I agree that the automatic recognition you&#8217;re describing could be optimized &#8211; we&#8217;ll keep working on the speed and resource usage. </p>
<p>If I may, I&#8217;d like to add that Mendeley Desktop is doing a little bit more than just reading the PDF file. It extracts the full-text to make it searchable, it automatically tries to guess the correct metadata (author, title, journal, volume, issue, page numbers tc.) and extracts author-assigned keywords, and it parses each document&#8217;s cited references and turns them into machine-readable and exportable format. It also lets you share and synchronize all this data with other users.</p>
<p>Cheers,<br />
Victor</p>
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