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	<title>Comments on: Open Science/Access challenge</title>
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	<description>Bits of science</description>
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		<title>By: Walter Jessen</title>
		<link>http://blindscientist.genedrift.org/2009/11/30/open-scienceaccess-challenge/comment-page-1/#comment-2193</link>
		<dc:creator>Walter Jessen</dc:creator>
		<pubDate>Tue, 29 Dec 2009 07:49:22 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=370#comment-2193</guid>
		<description>Mine are &lt;a href=&quot;http://www.walterjessen.com/scientific-research/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Several papers are published in Open Access journals, such as EMBO Molecular Medicine, Genome Biology and BMC Bioinformatics, while others aren&#039;t.</description>
		<content:encoded><![CDATA[<p>Mine are <a href="http://www.walterjessen.com/scientific-research/" rel="nofollow">here</a>. Several papers are published in Open Access journals, such as EMBO Molecular Medicine, Genome Biology and BMC Bioinformatics, while others aren&#8217;t.</p>
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		<title>By: Cameron Neylon</title>
		<link>http://blindscientist.genedrift.org/2009/11/30/open-scienceaccess-challenge/comment-page-1/#comment-2161</link>
		<dc:creator>Cameron Neylon</dc:creator>
		<pubDate>Tue, 01 Dec 2009 20:27:58 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=370#comment-2161</guid>
		<description>Ok I&#039;ll bite. Still working to get mine up on a single website but in reverse chronological order:

Neylon C, Head in the clouds: Reimagining the laboratory record for the web-based, networked world, Automated Experimentation, http://www.aejournal.net/content/1/1/3 -OA, CC-BY

Neylon C, Wu S, Article level metrics and the evolution of scientific impact, PLoS Biology, http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000242 - OA, CC-BY

Neylon C, Catching the Wave, Nature,  http://dx.doi.org/10.1038/461881a - Not OA, can deposit after six months

Weber et al., Probing the microscopic flexibility of DNA from melting temperatures http://dx.doi.org/10.1038/nphys1371 - Not OA, can deposit after six months, someone else was lead author

Clifton LA, Neylon C, Terry AE, Dicko IC, Diddens IA, Characterizing biomaterial complexity, Materials Today - Not OA, not sure what deposition rules are, this was invited and part of a work special issue. I argued for us to retain copyright but was over-ruled

Bradley JC, Lang A,  Lindenbaum P, Neylon C, Williams A, Willighagent E, Beautifying data in the real world IN Beautiful Data, Segaran and Hammerbacher eds. O’Reilly Publishing - CC-BY version available at http://www.scribd.com/doc/17748841/Chap-16-Beautiful-Data

Neylon C, Wu S, Open science: Tools, approaches, implications. Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb09/abstracts/2009_p540.html - OA

Weber G, Haslam N, Essex JW, Neylon C, Thermal equivalence of DNA duplexes for probe design. J Phys: Condens. Matter 21(3), 2009, 034106 - Not OA, Weber is lead author

Telling MTF, Neylon C, Kilcoyne SH, Arrighi V, An-harmonic behaviour in the multi-subunit protein apoferritin as revealed by quasi-elastic neutron scattering, J Phys Chem B, 112(35), 2008, 10873-8 - ACS so definitely not OA, not my choice, Telling is lead author

Teixeira SCM et al., New sources and instrumentation for neutrons in biology. Chemical Physics 345(2-3), 2008, 133-151 - Not OA, Teixeira lead author

Haslam NJ, Whiteford NE, Weber G, Prügel-Bennett A, Essex JW, Neylon C, Optimal Probe Length Varies for Targets with High Sequence Variation: Implications for Probe Library Design for Resequencing Highly Variable Genes, PLoS ONE 3(6), 2008, e2500 doi:10.1371/journal.pone.0002500 - OA

Whiteford N, Haslam NJ, Weber G, Prügel-Bennett A, Essex JW, Neylon C, Visualising the repeat structure of genomic sequences, Complex Systems 17(4), 2008, 381-398 - Not OA, this one is a long story but not worth relating here, the paper can only be found in a few institutional repositories

Broder GR, Ranasinghe RT, She JK, Banu S, Birtwell SW, Cavalli G, Galitonov GS, Holmes D,  Martins HFP, Neylon C, Zheludev N, Roach PL, Morgan H, Diffractive micro-barcodes for encoding of biomolecules in multiplexed assays, Analytical Chemistry 80(6), 2008, 1902-9 - Not OA, Morgan lead author

Neylon C, Small angle neutron and X-ray scattering in structural biology: Recent examples from the literature, European Biophysics Journal, 37(5), 2008, 531-541 - Not OA, this is far enough back that when written I was just getting into OA, it was part of a deal to do a special issue of papers from a conference, but as I did the deal and ran the conference this is definitely down to me.

Chan L, Cross HF, She JK, Cavalli G, Martins HFP, Neylon C, Covalent attachment of proteins to solid supports and surfaces via Sortase-mediated ligation, PLoS ONE 2(11), 2007, e1164 doi:10.1371/journal.pone.0001164 - OA but full disclosure it was rejected from two non-OA journals before it was sent to PLoS ONE

Not sure whether that is a good run or not really. Its not too bad on the ones where I had control but there&#039;s an argument I should have pushed harder on the others. And like anyone, if Nature asks you for a piece you don&#039;t readily turn them down. So 6/12 in the last few years more or less &quot;proper&quot; OA.</description>
		<content:encoded><![CDATA[<p>Ok I&#8217;ll bite. Still working to get mine up on a single website but in reverse chronological order:</p>
<p>Neylon C, Head in the clouds: Reimagining the laboratory record for the web-based, networked world, Automated Experimentation, <a href="http://www.aejournal.net/content/1/1/3" rel="nofollow">http://www.aejournal.net/content/1/1/3</a> -OA, CC-BY</p>
<p>Neylon C, Wu S, Article level metrics and the evolution of scientific impact, PLoS Biology, <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000242" rel="nofollow">http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000242</a> &#8211; OA, CC-BY</p>
<p>Neylon C, Catching the Wave, Nature,  <a href="http://dx.doi.org/10.1038/461881a" rel="nofollow">http://dx.doi.org/10.1038/461881a</a> &#8211; Not OA, can deposit after six months</p>
<p>Weber et al., Probing the microscopic flexibility of DNA from melting temperatures <a href="http://dx.doi.org/10.1038/nphys1371" rel="nofollow">http://dx.doi.org/10.1038/nphys1371</a> &#8211; Not OA, can deposit after six months, someone else was lead author</p>
<p>Clifton LA, Neylon C, Terry AE, Dicko IC, Diddens IA, Characterizing biomaterial complexity, Materials Today &#8211; Not OA, not sure what deposition rules are, this was invited and part of a work special issue. I argued for us to retain copyright but was over-ruled</p>
<p>Bradley JC, Lang A,  Lindenbaum P, Neylon C, Williams A, Willighagent E, Beautifying data in the real world IN Beautiful Data, Segaran and Hammerbacher eds. O’Reilly Publishing &#8211; CC-BY version available at <a href="http://www.scribd.com/doc/17748841/Chap-16-Beautiful-Data" rel="nofollow">http://www.scribd.com/doc/17748841/Chap-16-Beautiful-Data</a></p>
<p>Neylon C, Wu S, Open science: Tools, approaches, implications. Pacific Symposium on Biocomputing <a href="http://psb.stanford.edu/psb-online/proceedings/psb09/abstracts/2009_p540.html" rel="nofollow">http://psb.stanford.edu/psb-online/proceedings/psb09/abstracts/2009_p540.html</a> &#8211; OA</p>
<p>Weber G, Haslam N, Essex JW, Neylon C, Thermal equivalence of DNA duplexes for probe design. J Phys: Condens. Matter 21(3), 2009, 034106 &#8211; Not OA, Weber is lead author</p>
<p>Telling MTF, Neylon C, Kilcoyne SH, Arrighi V, An-harmonic behaviour in the multi-subunit protein apoferritin as revealed by quasi-elastic neutron scattering, J Phys Chem B, 112(35), 2008, 10873-8 &#8211; ACS so definitely not OA, not my choice, Telling is lead author</p>
<p>Teixeira SCM et al., New sources and instrumentation for neutrons in biology. Chemical Physics 345(2-3), 2008, 133-151 &#8211; Not OA, Teixeira lead author</p>
<p>Haslam NJ, Whiteford NE, Weber G, Prügel-Bennett A, Essex JW, Neylon C, Optimal Probe Length Varies for Targets with High Sequence Variation: Implications for Probe Library Design for Resequencing Highly Variable Genes, PLoS ONE 3(6), 2008, e2500 doi:10.1371/journal.pone.0002500 &#8211; OA</p>
<p>Whiteford N, Haslam NJ, Weber G, Prügel-Bennett A, Essex JW, Neylon C, Visualising the repeat structure of genomic sequences, Complex Systems 17(4), 2008, 381-398 &#8211; Not OA, this one is a long story but not worth relating here, the paper can only be found in a few institutional repositories</p>
<p>Broder GR, Ranasinghe RT, She JK, Banu S, Birtwell SW, Cavalli G, Galitonov GS, Holmes D,  Martins HFP, Neylon C, Zheludev N, Roach PL, Morgan H, Diffractive micro-barcodes for encoding of biomolecules in multiplexed assays, Analytical Chemistry 80(6), 2008, 1902-9 &#8211; Not OA, Morgan lead author</p>
<p>Neylon C, Small angle neutron and X-ray scattering in structural biology: Recent examples from the literature, European Biophysics Journal, 37(5), 2008, 531-541 &#8211; Not OA, this is far enough back that when written I was just getting into OA, it was part of a deal to do a special issue of papers from a conference, but as I did the deal and ran the conference this is definitely down to me.</p>
<p>Chan L, Cross HF, She JK, Cavalli G, Martins HFP, Neylon C, Covalent attachment of proteins to solid supports and surfaces via Sortase-mediated ligation, PLoS ONE 2(11), 2007, e1164 doi:10.1371/journal.pone.0001164 &#8211; OA but full disclosure it was rejected from two non-OA journals before it was sent to PLoS ONE</p>
<p>Not sure whether that is a good run or not really. Its not too bad on the ones where I had control but there&#8217;s an argument I should have pushed harder on the others. And like anyone, if Nature asks you for a piece you don&#8217;t readily turn them down. So 6/12 in the last few years more or less &#8220;proper&#8221; OA.</p>
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	<item>
		<title>By: Mr. Gunn</title>
		<link>http://blindscientist.genedrift.org/2009/11/30/open-scienceaccess-challenge/comment-page-1/#comment-2159</link>
		<dc:creator>Mr. Gunn</dc:creator>
		<pubDate>Tue, 01 Dec 2009 05:16:51 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=370#comment-2159</guid>
		<description>Mine are &lt;a href=&quot;http://www.mendeley.com/profiles/william-gunn/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Nothing in an OA journal, but I did pay for open access to my dissertation. Pushing for that on a upcoming publication, as well.</description>
		<content:encoded><![CDATA[<p>Mine are <a href="http://www.mendeley.com/profiles/william-gunn/" rel="nofollow">here</a>. Nothing in an OA journal, but I did pay for open access to my dissertation. Pushing for that on a upcoming publication, as well.</p>
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	<item>
		<title>By: Neil</title>
		<link>http://blindscientist.genedrift.org/2009/11/30/open-scienceaccess-challenge/comment-page-1/#comment-2157</link>
		<dc:creator>Neil</dc:creator>
		<pubDate>Mon, 30 Nov 2009 22:36:59 +0000</pubDate>
		<guid isPermaLink="false">http://blindscientist.genedrift.org/?p=370#comment-2157</guid>
		<description>What is he up to now?  Well, &lt;a href=&quot;http://www.citeulike.org/profile/neils/publications&quot; rel=&quot;nofollow&quot;&gt;mine are here&lt;/a&gt;.

Definitely advocate OA.  I like the notion of &quot;open science&quot; (whatever that is), I don&#039;t know if I &quot;advocate&quot; it.</description>
		<content:encoded><![CDATA[<p>What is he up to now?  Well, <a href="http://www.citeulike.org/profile/neils/publications" rel="nofollow">mine are here</a>.</p>
<p>Definitely advocate OA.  I like the notion of &#8220;open science&#8221; (whatever that is), I don&#8217;t know if I &#8220;advocate&#8221; it.</p>
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