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	<title>Comments for Digifesto</title>
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	<lastBuildDate>Tue, 15 May 2012 16:18:21 +0000</lastBuildDate>
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		<title>Comment on Another rant about academia and open source by The logic bomb that helped me embrace free scientific software &#171; GCBLOG</title>
		<link>http://digifesto.com/2012/02/28/another-rant-about-academia-and-open-source/#comment-2081</link>
		<dc:creator><![CDATA[The logic bomb that helped me embrace free scientific software &#171; GCBLOG]]></dc:creator>
		<pubDate>Tue, 15 May 2012 16:18:21 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=744#comment-2081</guid>
		<description><![CDATA[[...] niche, domain-specific applications themselves.  But scientists who know some programming often aren&#8217;t very familiar with best practices in software development, and that includes licensing &#8211; many scientists, [...]]]></description>
		<content:encoded><![CDATA[<p>[...] niche, domain-specific applications themselves.  But scientists who know some programming often aren&#8217;t very familiar with best practices in software development, and that includes licensing &#8211; many scientists, [...]</p>
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		<title>Comment on Neo4j and Scala hacking notes by someonesomeonesomeone</title>
		<link>http://digifesto.com/2011/09/15/neo4j-and-scala-hacking-notes/#comment-2079</link>
		<dc:creator><![CDATA[someonesomeonesomeone]]></dc:creator>
		<pubDate>Sun, 13 May 2012 12:28:34 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=429#comment-2079</guid>
		<description><![CDATA[Regarding &quot;Application&quot;, look to the bottom of the comment in the Scala docs: &quot;It is recommended to use the App trait instead&quot;.]]></description>
		<content:encoded><![CDATA[<p>Regarding &#8220;Application&#8221;, look to the bottom of the comment in the Scala docs: &#8220;It is recommended to use the App trait instead&#8221;.</p>
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		<title>Comment on Another rant about academia and open source by Sebastian Benthall</title>
		<link>http://digifesto.com/2012/02/28/another-rant-about-academia-and-open-source/#comment-2066</link>
		<dc:creator><![CDATA[Sebastian Benthall]]></dc:creator>
		<pubDate>Wed, 09 May 2012 23:09:30 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=744#comment-2066</guid>
		<description><![CDATA[Thanks for this information about this.  It&#039;s very encouraging to see hear about so much prestigious work being done in open science.]]></description>
		<content:encoded><![CDATA[<p>Thanks for this information about this.  It&#8217;s very encouraging to see hear about so much prestigious work being done in open science.</p>
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		<title>Comment on Another rant about academia and open source by Paola</title>
		<link>http://digifesto.com/2012/02/28/another-rant-about-academia-and-open-source/#comment-2064</link>
		<dc:creator><![CDATA[Paola]]></dc:creator>
		<pubDate>Wed, 09 May 2012 10:47:33 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=744#comment-2064</guid>
		<description><![CDATA[Hi Sebastian, 
Congrats for your post, you touch an extremely interesting topic. I would like to highlight Mat Todd&#039;s example of the Univeristy of Sydney; he just started an open research project to find a feasible treatment against malaria. The results of the research will be public at least in the initial phases. A great example to follow. 
Here a brief reflection on the theme of open science, posted in www.ideasforchange.com/en:
 

The right to access existent drug products at a reasonable price is a traditional demand in developing countries and is about to be achieved, at least partially, through three complementary but different ways.

The industry cooperates and donates
Invited by Bill Gates, the largest pharmaceutical companies in the world have reached an agreement to share their research in order to eradicate forgotten tropical illnesses. They have also agreed to increase significantly the donations of medicine products that cure obsolete illnesses in the West. Bravo! Thank you.

The (Indian) State regulates
Nexavar, a drug for kidney and liver cancer patented by Bayer will be produced in India under the name of Sorafenat by the local business Natco Pharma. The Indian patent law allows local industry manufacturing if, after three years since launch, the drug is not accessible for the general citizenship at an “affordable” price.

The monthly treatment for a patient cost 4,000€ with Bayer’s drug product. The generic alternative will be available for a fraction of that price: 134€/month. 29 times less.

This means that over a 95% of the product’s price does not directly correspond to production costs. Instead, this amount includes R&amp;D, marketing, financial and structure costs.  Bayer offered it’s medicine for 475€ to certified sick patients. The authorized business will pay a 6% of sales in royalties. A necessary exception. Applicable everywhere else? Sustainable?

Scientists share
The active professor Dr. Matt Todd of the School of Chemistry at Sydney’s University has developed a methodology for open research that already has showed results: an alternative way for low cost production of a medicine that threats Bilharzia, a parasitic sickness which affects millions of people who do not have access to clean water sanitation systems.

“The challenge was that the medicine had to be produced at a very low cost and that was a challenge that academia was not going to solve”, states Todd. So he tried something different: he openly published his lab notes online while he advanced in his research and this proved to be crucial in the process.

In may he begins – with Australian government funding for three years – an open research project to find a feasible treatment against malaria using worldwide scientists that share live time results without worrying about patents. He believes that open science can achieve significant discoveries in the initial phases, before clinical trials. Free, without pardon or permission, for all.   

Open as well for existent business for collaboration, investment or cost reduction. Inspiration to  redefine their strategy and activities. Energy to to impulse new business models and new structures based on the common resource. Fresh air.]]></description>
		<content:encoded><![CDATA[<p>Hi Sebastian,<br />
Congrats for your post, you touch an extremely interesting topic. I would like to highlight Mat Todd&#8217;s example of the Univeristy of Sydney; he just started an open research project to find a feasible treatment against malaria. The results of the research will be public at least in the initial phases. A great example to follow.<br />
Here a brief reflection on the theme of open science, posted in <a href="http://www.ideasforchange.com/en" rel="nofollow">http://www.ideasforchange.com/en</a>:</p>
<p>The right to access existent drug products at a reasonable price is a traditional demand in developing countries and is about to be achieved, at least partially, through three complementary but different ways.</p>
<p>The industry cooperates and donates<br />
Invited by Bill Gates, the largest pharmaceutical companies in the world have reached an agreement to share their research in order to eradicate forgotten tropical illnesses. They have also agreed to increase significantly the donations of medicine products that cure obsolete illnesses in the West. Bravo! Thank you.</p>
<p>The (Indian) State regulates<br />
Nexavar, a drug for kidney and liver cancer patented by Bayer will be produced in India under the name of Sorafenat by the local business Natco Pharma. The Indian patent law allows local industry manufacturing if, after three years since launch, the drug is not accessible for the general citizenship at an “affordable” price.</p>
<p>The monthly treatment for a patient cost 4,000€ with Bayer’s drug product. The generic alternative will be available for a fraction of that price: 134€/month. 29 times less.</p>
<p>This means that over a 95% of the product’s price does not directly correspond to production costs. Instead, this amount includes R&amp;D, marketing, financial and structure costs.  Bayer offered it’s medicine for 475€ to certified sick patients. The authorized business will pay a 6% of sales in royalties. A necessary exception. Applicable everywhere else? Sustainable?</p>
<p>Scientists share<br />
The active professor Dr. Matt Todd of the School of Chemistry at Sydney’s University has developed a methodology for open research that already has showed results: an alternative way for low cost production of a medicine that threats Bilharzia, a parasitic sickness which affects millions of people who do not have access to clean water sanitation systems.</p>
<p>“The challenge was that the medicine had to be produced at a very low cost and that was a challenge that academia was not going to solve”, states Todd. So he tried something different: he openly published his lab notes online while he advanced in his research and this proved to be crucial in the process.</p>
<p>In may he begins – with Australian government funding for three years – an open research project to find a feasible treatment against malaria using worldwide scientists that share live time results without worrying about patents. He believes that open science can achieve significant discoveries in the initial phases, before clinical trials. Free, without pardon or permission, for all.   </p>
<p>Open as well for existent business for collaboration, investment or cost reduction. Inspiration to  redefine their strategy and activities. Energy to to impulse new business models and new structures based on the common resource. Fresh air.</p>
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		<title>Comment on Another rant about academia and open source by Sebastian Benthall</title>
		<link>http://digifesto.com/2012/02/28/another-rant-about-academia-and-open-source/#comment-2024</link>
		<dc:creator><![CDATA[Sebastian Benthall]]></dc:creator>
		<pubDate>Fri, 27 Apr 2012 18:00:59 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=744#comment-2024</guid>
		<description><![CDATA[Thanks for this.]]></description>
		<content:encoded><![CDATA[<p>Thanks for this.</p>
]]></content:encoded>
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		<title>Comment on Another rant about academia and open source by Aron Roberts</title>
		<link>http://digifesto.com/2012/02/28/another-rant-about-academia-and-open-source/#comment-2022</link>
		<dc:creator><![CDATA[Aron Roberts]]></dc:creator>
		<pubDate>Thu, 26 Apr 2012 21:57:24 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=744#comment-2022</guid>
		<description><![CDATA[Victoria Stodden included a representative listing of cloud- and desktop-based tools for sharing research code, data, and methodology on p. 14 of her talk on April 25, 2012, accessible via her Talks page:

http://www.stanford.edu/~vcs/Talks.html

Or directly via:

http://www.stanford.edu/~vcs/talks/BerkeleyNeymanApril252012-STODDEN.pdf]]></description>
		<content:encoded><![CDATA[<p>Victoria Stodden included a representative listing of cloud- and desktop-based tools for sharing research code, data, and methodology on p. 14 of her talk on April 25, 2012, accessible via her Talks page:</p>
<p><a href="http://www.stanford.edu/~vcs/Talks.html" rel="nofollow">http://www.stanford.edu/~vcs/Talks.html</a></p>
<p>Or directly via:</p>
<p><a href="http://www.stanford.edu/~vcs/talks/BerkeleyNeymanApril252012-STODDEN.pdf" rel="nofollow">http://www.stanford.edu/~vcs/talks/BerkeleyNeymanApril252012-STODDEN.pdf</a></p>
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		<title>Comment on Another rant about academia and open source by Aron Roberts</title>
		<link>http://digifesto.com/2012/02/28/another-rant-about-academia-and-open-source/#comment-2021</link>
		<dc:creator><![CDATA[Aron Roberts]]></dc:creator>
		<pubDate>Thu, 26 Apr 2012 21:54:08 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=744#comment-2021</guid>
		<description><![CDATA[Victoria Stoddert =&gt; Stodden in the post above.  With apologies to Professor Stodden, I seem to be repeatedly making this mental transposition. :-(

Her slides from that April 25, 2012 talk, among many others, can be readily found on her Talks page:
http://www.stanford.edu/~vcs/Talks.html

One of the more interesting parts of her talk (see slide 12), and relevant to the &quot;community building ethic&quot; you describe in your blog post, Sebastian, was a discussion of the results of her survey on the behavioral impediments to sharing code, data, and methodology related to research findings.

These included concerns related to: the effort and time required to package up and document these artifacts to make them useful to others; the prospect of providing ongoing support to those using these artifacts; having others use one&#039;s work without attribution, once it has been made so freely and comprehensively available; and a variety of institutional and intellectual property-related issues.  These are clearly some of the &#039;real world&#039; barriers to taking a FOSS-like approach to these artifacts.]]></description>
		<content:encoded><![CDATA[<p>Victoria Stoddert =&gt; Stodden in the post above.  With apologies to Professor Stodden, I seem to be repeatedly making this mental transposition. :-(</p>
<p>Her slides from that April 25, 2012 talk, among many others, can be readily found on her Talks page:<br />
<a href="http://www.stanford.edu/~vcs/Talks.html" rel="nofollow">http://www.stanford.edu/~vcs/Talks.html</a></p>
<p>One of the more interesting parts of her talk (see slide 12), and relevant to the &#8220;community building ethic&#8221; you describe in your blog post, Sebastian, was a discussion of the results of her survey on the behavioral impediments to sharing code, data, and methodology related to research findings.</p>
<p>These included concerns related to: the effort and time required to package up and document these artifacts to make them useful to others; the prospect of providing ongoing support to those using these artifacts; having others use one&#8217;s work without attribution, once it has been made so freely and comprehensively available; and a variety of institutional and intellectual property-related issues.  These are clearly some of the &#8216;real world&#8217; barriers to taking a FOSS-like approach to these artifacts.</p>
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		<title>Comment on Another rant about academia and open source by Sebastian Benthall</title>
		<link>http://digifesto.com/2012/02/28/another-rant-about-academia-and-open-source/#comment-2020</link>
		<dc:creator><![CDATA[Sebastian Benthall]]></dc:creator>
		<pubDate>Thu, 26 Apr 2012 05:45:52 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=744#comment-2020</guid>
		<description><![CDATA[Thanks for your thoughts.  Do you remember any of those cloud-based tools off the top of your head?

That&#039;s fascinating to hear about Darwin.  I guess the fear of a lot of academics is that some Darwin will get all the credit for their incremental work towards some grand conclusion.  It&#039;s nice to see that intellectual historians remedy this somewhat.  Hopefully, as you say, by the 22nd century their job will be a lot easier.

I think it&#039;s cool that you work on open source projects and on Berkeley&#039;s collaborative tooling.  I didn&#039;t know there were people here working on that.  I&#039;d definitely say that that is as if not more relevant as any academics&#039; work to the realization of the dream.  I&#039;d be interested in hearing more about what&#039;s going on on your end.]]></description>
		<content:encoded><![CDATA[<p>Thanks for your thoughts.  Do you remember any of those cloud-based tools off the top of your head?</p>
<p>That&#8217;s fascinating to hear about Darwin.  I guess the fear of a lot of academics is that some Darwin will get all the credit for their incremental work towards some grand conclusion.  It&#8217;s nice to see that intellectual historians remedy this somewhat.  Hopefully, as you say, by the 22nd century their job will be a lot easier.</p>
<p>I think it&#8217;s cool that you work on open source projects and on Berkeley&#8217;s collaborative tooling.  I didn&#8217;t know there were people here working on that.  I&#8217;d definitely say that that is as if not more relevant as any academics&#8217; work to the realization of the dream.  I&#8217;d be interested in hearing more about what&#8217;s going on on your end.</p>
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		<title>Comment on Another rant about academia and open source by Aron Roberts</title>
		<link>http://digifesto.com/2012/02/28/another-rant-about-academia-and-open-source/#comment-2019</link>
		<dc:creator><![CDATA[Aron Roberts]]></dc:creator>
		<pubDate>Thu, 26 Apr 2012 05:31:44 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=744#comment-2019</guid>
		<description><![CDATA[Enjoyed your thoughts, Sebastian, and particularly your characterization of the motivation of the prototypical FOSS developer.  I&#039;d be delighted if such attitudes and approaches would permeate culture, well beyond open source software development and similar endeavors, by the 22nd Century.  We may well find that a raft of oppositional human motivations make this slower going than we might both hope, however.

Heard Victoria Stoddert talk today for the first time, not far from the I-School - in the Stat Dept. in Evans.  Her talk was a handy overview of five &#039;hows,&#039; to help move us closer to reproducible research in the computational domain of research.  Among others, these included the growing availability of cloud-based tools for sharing code, data, and methodology (e.g. sharing one&#039;s runtime parameters and exact sequences of computational steps performed); and nascent requirements on the part of some funders and scientific journals to motivate such sharing.

Your comment on Darwin is what motivated this response: there&#039;s an excellent overview of the world of ideas that led to &#039;Darwinism&#039; - and beyond - in Loren Eisley&#039;s &quot;Darwin&#039;s Century&quot; (http://www.amazon.com/dp/0385081413 for reader reviews; http://0-www.worldcat.org.l0.apu.edu/oclc/168989 for Library holdings).  Theories of evolution of living organisms - and of natural selection as a driving force behind evolution - were, from what I gathered from Eisley&#039;s book, truly a decentralized, and often unguided, community effort over several centuries and in multiple countries, rather than what we might now conceive of as one dude&#039;s &#039;ism,&#039; accompanied by a posse of adherents.  By the now almost quaint 18th and 19th Century mechanisms of handwritten letters, books, journal articles, and occasional in-person talks, in an era long before blogs or social networks, these ideas gained form, and then ultimately, momentum.]]></description>
		<content:encoded><![CDATA[<p>Enjoyed your thoughts, Sebastian, and particularly your characterization of the motivation of the prototypical FOSS developer.  I&#8217;d be delighted if such attitudes and approaches would permeate culture, well beyond open source software development and similar endeavors, by the 22nd Century.  We may well find that a raft of oppositional human motivations make this slower going than we might both hope, however.</p>
<p>Heard Victoria Stoddert talk today for the first time, not far from the I-School &#8211; in the Stat Dept. in Evans.  Her talk was a handy overview of five &#8216;hows,&#8217; to help move us closer to reproducible research in the computational domain of research.  Among others, these included the growing availability of cloud-based tools for sharing code, data, and methodology (e.g. sharing one&#8217;s runtime parameters and exact sequences of computational steps performed); and nascent requirements on the part of some funders and scientific journals to motivate such sharing.</p>
<p>Your comment on Darwin is what motivated this response: there&#8217;s an excellent overview of the world of ideas that led to &#8216;Darwinism&#8217; &#8211; and beyond &#8211; in Loren Eisley&#8217;s &#8220;Darwin&#8217;s Century&#8221; (<a href="http://www.amazon.com/dp/0385081413" rel="nofollow">http://www.amazon.com/dp/0385081413</a> for reader reviews; <a href="http://0-www.worldcat.org.l0.apu.edu/oclc/168989" rel="nofollow">http://0-www.worldcat.org.l0.apu.edu/oclc/168989</a> for Library holdings).  Theories of evolution of living organisms &#8211; and of natural selection as a driving force behind evolution &#8211; were, from what I gathered from Eisley&#8217;s book, truly a decentralized, and often unguided, community effort over several centuries and in multiple countries, rather than what we might now conceive of as one dude&#8217;s &#8216;ism,&#8217; accompanied by a posse of adherents.  By the now almost quaint 18th and 19th Century mechanisms of handwritten letters, books, journal articles, and occasional in-person talks, in an era long before blogs or social networks, these ideas gained form, and then ultimately, momentum.</p>
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		<title>Comment on Another rant about academia and open source by Mel Chua &#187; Blog Archive &#187; Tracking fellow FOSS-to-academia migrants</title>
		<link>http://digifesto.com/2012/02/28/another-rant-about-academia-and-open-source/#comment-1778</link>
		<dc:creator><![CDATA[Mel Chua &#187; Blog Archive &#187; Tracking fellow FOSS-to-academia migrants]]></dc:creator>
		<pubDate>Tue, 06 Mar 2012 19:23:55 +0000</pubDate>
		<guid isPermaLink="false">http://digifesto.com/?p=744#comment-1778</guid>
		<description><![CDATA[[...] Benthall&#8217;s post about academic vs open culture reminded me that I&#8217;d like to track my fellow FOSS-to-academia migrants somewhere. Seb and [...]]]></description>
		<content:encoded><![CDATA[<p>[...] Benthall&#8217;s post about academic vs open culture reminded me that I&#8217;d like to track my fellow FOSS-to-academia migrants somewhere. Seb and [...]</p>
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