<story><title>Handful of Biologists Went Rogue and Published Directly to Internet</title><url>http://www.nytimes.com/2016/03/16/science/asap-bio-biologists-published-to-the-internet.html</url></story><parent_chain><item><author>logicrook</author><text>&amp;gt; I expected that everybody would publish latex files (raw source, not PDFs) in computationally accessible formats, with raw data in easily parseable, semantic forms.&lt;p&gt;Do you realize that many researchers would be ashamed if others saw their latex code?&lt;p&gt;A friend worked for a journal, he kept a folder of the worst that he had ever seen, and could rant for hours one some gems. Including some papers that were beautifully typeset, about elegant combinatorics&amp;#x2F;type theory, and were coded on the latex equivalent of a spaceship cobbled with recycled plastic bottles, scraps and duct tape.&lt;p&gt;Do you imagine going through thousand lines macro tex file that grew over the years, when Latex is one of the worst mess ever, with conflicting packages, absurd syntactic &amp;#x27;features&amp;#x27;, and legacy crippling flaws that make debugging an horrible task?&lt;p&gt;Please, continue to compile your .tex.</text></item><item><author>dekhn</author><text>When I first found out about the web, early 90&amp;#x27;s, and it was &amp;quot;obvious&amp;quot; that the role of the web was to expand scientific publishing. I expected that everybody would publish latex files (raw source, not PDFs) in computationally accessible formats, with raw data in easily parseable, semantic forms.&lt;p&gt;That didn&amp;#x27;t really happen as expected.  In my own chosen field (biology) it happened much more slowly than I hoped- physics (with arxiv) was far better.  However, just getting PDFs on biorxiv is only a small part of the long game. I did not appreciate the huge importance placed on publishing in high-profile journals has on one&amp;#x27;s career trajectory and how large a role that would play in slowing the transition to free publication and post-publication review.&lt;p&gt;The long game is to enable the vast existing resources, and the new resources, to be parsed semantically by artificial intelligence algorithms.  We&amp;#x27;ve already passed the point where individuals can understand the full literature in their chosen field and so eventually we will need AI just to make progress.</text></item></parent_chain><comment><author>chriswarbo</author><text>&amp;gt; Do you realize that many researchers would be ashamed if others saw their latex code?&lt;p&gt;I really don&amp;#x27;t get this argument; I see it come up regarding open data for reproducibility too. TeX&amp;#x2F;LaTeX source is just an extra piece of metadata which might help someone out in a few years time. That&amp;#x27;s nothing to feel ashamed of, and it&amp;#x27;s certainly less shameful than &lt;i&gt;not&lt;/i&gt; providing the code. If the code allows flaws in the research to be exposed, that&amp;#x27;s either something to be &lt;i&gt;proud&lt;/i&gt; of, or (if it was intentional) it&amp;#x27;s not the code that&amp;#x27;s shameful.&lt;p&gt;My own LaTeX is mostly an inconsistent mixture of copypasta from stackexchange. That doesn&amp;#x27;t mean I&amp;#x27;m &lt;i&gt;ashamed&lt;/i&gt; of it, and it&amp;#x27;s all in public Git repos at &lt;a href=&quot;http:&amp;#x2F;&amp;#x2F;chriswarbo.net&amp;#x2F;git&quot; rel=&quot;nofollow&quot;&gt;http:&amp;#x2F;&amp;#x2F;chriswarbo.net&amp;#x2F;git&lt;/a&gt; if any human or bot actually cares to look.&lt;p&gt;Speaking of which, the commit histories of those Git repositories aren&amp;#x27;t very good either. Lots of commit messages like &amp;quot;Fixes&amp;quot;, or &amp;quot;Oops, typo in last commit&amp;quot;, with multiple changes bundled into single commits, atomic changes spread across multiple commits, etc. But, in the same way as my LaTeX source, it&amp;#x27;s better than having &lt;i&gt;no&lt;/i&gt; commit history, which would be the case if I set myself higher standards.&lt;p&gt;Of course, I &lt;i&gt;can&lt;/i&gt; follow higher standards, but that&amp;#x27;s when I&amp;#x27;m paid to and&amp;#x2F;or when collaboration is important. For personal stuff, I&amp;#x27;d rather invest the time I save interacting with Git on writing more tests, or refactoring, etc.</text></comment>
<story><title>Handful of Biologists Went Rogue and Published Directly to Internet</title><url>http://www.nytimes.com/2016/03/16/science/asap-bio-biologists-published-to-the-internet.html</url></story><parent_chain><item><author>logicrook</author><text>&amp;gt; I expected that everybody would publish latex files (raw source, not PDFs) in computationally accessible formats, with raw data in easily parseable, semantic forms.&lt;p&gt;Do you realize that many researchers would be ashamed if others saw their latex code?&lt;p&gt;A friend worked for a journal, he kept a folder of the worst that he had ever seen, and could rant for hours one some gems. Including some papers that were beautifully typeset, about elegant combinatorics&amp;#x2F;type theory, and were coded on the latex equivalent of a spaceship cobbled with recycled plastic bottles, scraps and duct tape.&lt;p&gt;Do you imagine going through thousand lines macro tex file that grew over the years, when Latex is one of the worst mess ever, with conflicting packages, absurd syntactic &amp;#x27;features&amp;#x27;, and legacy crippling flaws that make debugging an horrible task?&lt;p&gt;Please, continue to compile your .tex.</text></item><item><author>dekhn</author><text>When I first found out about the web, early 90&amp;#x27;s, and it was &amp;quot;obvious&amp;quot; that the role of the web was to expand scientific publishing. I expected that everybody would publish latex files (raw source, not PDFs) in computationally accessible formats, with raw data in easily parseable, semantic forms.&lt;p&gt;That didn&amp;#x27;t really happen as expected.  In my own chosen field (biology) it happened much more slowly than I hoped- physics (with arxiv) was far better.  However, just getting PDFs on biorxiv is only a small part of the long game. I did not appreciate the huge importance placed on publishing in high-profile journals has on one&amp;#x27;s career trajectory and how large a role that would play in slowing the transition to free publication and post-publication review.&lt;p&gt;The long game is to enable the vast existing resources, and the new resources, to be parsed semantically by artificial intelligence algorithms.  We&amp;#x27;ve already passed the point where individuals can understand the full literature in their chosen field and so eventually we will need AI just to make progress.</text></item></parent_chain><comment><author>soperj</author><text>It would be much easier to get better if you could view other&amp;#x27;s latex code.</text></comment>