[ExI] Fwd: [wta-talk] Scientific literature organizational tools

samantha sjatkins at mac.com
Wed Dec 31 07:16:33 UTC 2008

Bryan Bishop wrote:
> Ah, here we go. Anyway, Zotero isn't too new, here's what I previously
> wrote on the subject.
> ---------- Forwarded message ----------
> From: Bryan Bishop <kanzure at gmail.com>
> Date: Wed, Dec 17, 2008 at 8:17 AM
> Subject: Re: [wta-talk] Scientific literature organizational tools
> To: World Transhumanist Association Discussion List
> <wta-talk at transhumanism.org>, kanzure at gmail.com
> On Wed, Dec 17, 2008 at 3:32 AM, Sergio M.L. Tarrero wrote:
>> This may be helpful to some of you who need to keep many scientific
>> articles and materials well organized...
>> http://judson.blogs.nytimes.com/2008/12/16/defeating-bedlam/?th&emc=th
> I've also struggled a bit with scientific papers and my research habits:
> http://heybryan.org/projects/autoscholar/
> Ultimately what needs to happen is the dismissal of the PDF format.
> Instead of giving everybody PDFs, there needs to be a file much like a
> zip or tar file with metadata in it, as well as the actual content,
> and then anything else that might be relevant to the paper, such as
> formatted BibTeX for the bibliographical information, contact
> information, separated figures/images/photos, any sort of software
> that they had to write for the research, etc.

I am not so sure.  PDF is based around postscript which is a pretty full 
  programming language.  Any metadata you can think of could be directly 
within a non-displayable section of the PDF file.

The other stuff needs arbitrary relationships between files and whatever 
notes and such you may want to relate or "tack on" later.  But the 
latter is not a zip.

> There's very little reason to just cram everything into a PDF.

> Also, PDFs suck as it is. I can hardly open 200 PDFs on my machines
> without things getting slow and dangerous.

Why would you have 200 pdfs open at once exactly?  You don't have the 
screen space.  And I thought I kept a clutter desktop. :-)

  Yes, as I increase system
> RAM I can open more PDFs, but that's really a stupid idea. Instead of
> just hoping that I have enough RAM and virtual memory configured, it
> should use a caching system for my paper reading pleasures. Oh well.

Then maybe write one or have some that knows how write one.

> The autoscholar software (above) was made to help fetch papers
> automatically from Google Scholar. And if I ever get around to helping
> people get past PDF and into that tar-like file format for papers,
> then it will also be able to automatically extract the BibTeX
> information :-) so that you can recursively read papers and their
> citations. Another part of the autoscholar software package is an
> automatic paper reading program. Sometime earlier this year I
> downloaded 40 GB of papers from a publisher, and so I wanted to devote
> an entire monitor to reading the papers. My reasoning was that it
> would be something to look at, be mildly entertaining and hey, of some
> educational value as well. So it just flips through papers at some
> static rate (a page every 4 seconds - this is stupid, it should keep
> track of eye gaze really).

With a mouse that has a wheel equivalent I find autoscroll works well 
for me.  A nudge to slow down or speed up periodically is easy enough. 
Of course I really want a reader that chops text into convenient width 
and length chunks for maximally fast reading.  Haven't got around to 
finding or writing such.  Any leads?

- samantha

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