University of Glasgow

Roderic Page

PLoS recently announced [a dedicated iPad app, that covers all the PLoS
Journals](http://everyone.plos.org/2010/06/15/plosipadapp/), and which
is available [from the App
Store](http://itunes.apple.com/us/app/plos-reader/id370880976?mt=8).
Given the statement that \"PLoS is committed to continue pushing the
boundaries of scientific communication\" I was expecting something
special. Instead, what we get (as shown) in the video below is a PDF
viewer with a nice page turning effect (code
[here](http://github.com/brow/leaves)). Maybe it\'s Steve Job\'s fault
for showing iBooks when he first demoed the iPad, but there desire to
imitate 3D page turning effects leaves me cold (for a nice discussion of
how this can lead to horribly mixed metaphors see iA\'s [Designing for
iPad: Reality
Check](http://informationarchitects.jp/designing-for-ipad-reality-check/)).  
  
  

::: {style="text-align:center"}
[PLoS iPad Demo](http://vimeo.com/12287509) from
[PLoS](http://vimeo.com/plos) on [Vimeo](http://vimeo.com).
:::

  
  
But I think this app shows that PLoS really don\'t grok the iPad. Maybe
it\'s early days, but I find it really disappointing that page-turning
PDFs is the first thing they come up with. It\'s not about recreating
the paper experience on a device! There\'s huge scope for interactivity,
which the PLoS app simply ignores --- you can\'t select text, and none
of the references. It also ignores the web (without which, ironically,
PLoS couldn\'t exist).  
  
Instead of just [moaning about
this](http://everyone.plos.org/2010/06/15/plosipadapp/#comment-742),
I\'ve spent a couple of days fussing with a simple demo of what could be
done. I\'ve taken a PLoS paper (\"Discovery of the Largest Orbweaving
Spider Species: The Evolution of Gigantism in Nephila\",
[doi:10.1371/journal.pone.0007516](http://dx.doi.org/10.1371/journal.pone.0007516)),
grabbed the XML, applied a XSLT style sheet to generate some HTML, and
added a little Javascript functionality. References are displayed as
clickable links inline. If you click on one a window pops up displaying
the citation, and it then tries to find it for you online (for the
technically mined, it\'s using OpenURL and
[bioGUID](http://biogid.info/openurl/)). If it succeeds it displays a
blue arrow --- click that and you\'re off to the publisher\'s web site
to view the article.  
![reference.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/TBoxT1tC0kI/AAAAAAAAArA/WFLiM6PyimQ/reference.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="199"}  
  
Figures are also links, click on and you get a
[Lightbox](http://www.lokeshdhakar.com/projects/lightbox2/) view of the
image.  
You can [view this article
live](http://iphylo.org/~rpage/ipad/example1.html), in a regular browser
or in iPad. Here\'s a video of the demonstration page:  

::: {style="text-align:center"}
[PLoS paper on the iPad](http://vimeo.com/12643047) from [Roderic
Page](http://vimeo.com/rdmpage) on [Vimeo](http://vimeo.com).
:::

  
  
This is all very crude and rushed. There\'s a lot more that could be
done. For references we could flag which articles are self citations, we
could talk to bookmarking services via their APIs to see which citations
the reader already has, etc. We could also make data, sequences, and
taxonomic names clickable, providing the reader with more information
and avenues for exploration. Then there\'s the whole issue of figures.
For graphs we should have the underlying data so that we can easily make
new visualisations, phylogenies should be interactive (at least make the
taxon names clickable), and there\'s no need to amalgamate figures into
aggregates like [Fig
.2](http://dx.doi.org/10.1371/journal.pone.0007516.g002) below. Each
element (A-E) should be separately addressable so when the text refers
to Fig. 2D we can show the user just that element.  
  
![journal.pone.0007516.g002.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/TBoxV2hqTPI/AAAAAAAAArE/LJWnNdvylSc/journal.pone.0007516.g002.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="337"}  
  
The PLoS app and reactions to Elsevier\'s \"Article 2.0\" (e.g.,
[Elsevier\'s \'Article of the Future\' resembles websites of the
past](http://onlinejournalismblog.com/2009/07/27/elseviers-article-of-the-future-resembles-websites-of-the-past/)
and [The "Article of the Future" --- Just Lipstick
Again?](http://scholarlykitchen.sspnet.org/2009/07/21/the-article-of-the-future-lipstick-on-a-pig/))
suggests publishers are floundering in their efforts to get to grips
with the web, and new platforms for interacting with the web.  
  
So, PLoS, I challenge you to show us that you actually \"get\" the iPad
and what it could mean for science publishing. Because at the moment,
I\'ve seen nothing that suggests you grasp the opportunity it
represents. Better yet, why not revisit [Elsevier\'s Article
2.0](article20.elsevier.com/) project and have a challenge specifically
about re-imagining the scientific article? And please, no more page
turning effects


PLoS recently announced a dedicated iPad app, that covers all the PLoS Journals, and which is available from the App Store. Given the statement that "PLoS is committed to continue pushing the boundaries of scientific communication" I was expecting something special.

PLoS doesn't "get" the iPad (or the web)

![best_experience_20100127.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/S2MLTZsXFvI/AAAAAAAAAmU/ayovV3f-nDc/best_experience_20100127.png?imgmax=800){border="0"
width="200" align="right"}  
OK, first of all, I want one, I want one real bad.  
  
There\'s been a general sense of disappointment about the
[iPad](http://www.apple.com/ipad/), which I suspect is only natural
given the enormous hype leading up to the
[announcement](http://www.apple.com/quicktime/qtv/specialevent0110/), as
well as the fact that the applications shown were fairly conventional.
Personally I don\'t think book reading is where the action is. For
time-sensitive stuff like newspapers, and rich, complex documents such
as scientific papers, sure, but physical books strike me as a piece of
technology that we\'re not really going to improve on, rather like
knives and forks.  
  
But some grasp that [this is
magic](http://www.xconomy.com/national/2010/01/29/whats-so-magical-about-an-oversized-iphone-plenty-and-theres-more-to-come/?single_page=true).
What I hope the iPad will do is finally move some visualisation tools
into the main stream (as much as phylogenetics can be thought of as
mainstream). The challenge of [visualising large
phylogenies](http://iphylo.blogspot.com/2007/08/viewing-very-large-trees.html)
has yielded some cool tools which, sadly, remained under-developed, such
as TreeJuxtaposer, which seems clunky and counter-intuituve when using a
mouse, but with a touch screen would just be awesome.  
  

  
  
Tools such as
[Paloverde](http://loco.biosci.arizona.edu/paloverde/paloverde.html)
would also be more intuitive to use, as would the magnifier feature in
[Dendroscope](http://www-ab.informatik.uni-tuebingen.de/software/dendroscope).
Imagine \"pinch and zoom\" in TreeJuxtaposer or Dendroscope, or for
viewing large a sequence alignments.  
  
Then there\'s the existing tabletop tools that I [blogged about
earlier](http://iphylo.blogspot.com/2009/10/co-located-collaborative-tree.html):  
  

  
  
And of course there\'s [Perceptive
Pixel\'s](http://www.perceptivepixel.com/index.html) view of a taxonomic
classification:  
  

  
  
There would be some work involved porting these tools to the iPad (e.g.,
porting code from Java to Objective C in the case of TreeJuxtaposer and
Dendroscope), but the person who does this is going to have an impact on
this field comparable to Maddison brothers when they released
[MacClade](http://macclade.org/macclade.html) in 1986.  


OK, first of all, I want one, I want one real bad.There's been a general sense of disappointment about the iPad, which I suspect is only natural given the enormous hype leading up to the announcement, as well as the fact that the applications shown were fairly conventional.

Postagens de Rogue Scholar

PLoS doesn't "get" the iPad (or the web)

Why I want an iPad