
Show HN: How I Wish Scientific Papers Were Displayed - egocodedinsol
http://egocodedinsol.github.io/raised_cosine_basis_functions/
======
rubidium
Stepping into an area about which I have strong opinions. I appreciate your
effort, I just think you're way off base.

Physical Review Letters in journal (aka pdf) format are ideal. Nothing is
especially stylish, but it's a simple, easy to read format that highlights
figures as a way to convey the meaning of the work. I much prefer the PDF to
the online version.

Some critics of your site (all in the spirit of "I hope you take this as a
challenge to do better or maybe just realize there's not a lot wrong in the
first place"): -your color contrast hurts my eyes (light grey on blue...) -the
graphs are hard to understand (no axis labels on some, no captions to
understand what's going on since that's all most people read first anyways,
lack of contrast) -typeset equations are ugly (can't beat LaTeX) -drastic font
size difference between code and text is jarring -no authors listed so I can
instantly disregard your work because I've learned not to trust your methods
(I kid, I kid... kindof) -the draggable figures did nothing for me -your
column width was too narrow. Aim for 10-14 words per line. -because I have to
scroll it's hard to quickly scan it for parts I actually want to read. When
you read 10-20 papers a day, this is important.

One thing I really like: click the Fig. # and it scrolls to be beside the
text. That is a nice feature that online journals can learn from.

In short, I think you're trying to solve a non-existent (or at least minimally
existent) problem. LaTeX is beautiful, but perhaps you don't appreciate it.
Journals in print (except for Science and Nature which blend all their
articles together) generally look really nice. The PDF's of individual
articles are the thing to read online, and I think your solution is a long way
from any sort of reasonable online reading experience.

~~~
ssivark
As a grad student who reads lots of papers (with a typical length of 30+
pages), I too have a strong opinion on this. I think PDFs do not serve the
needs of the day and such efforts are a step in the right direction.

PDFs okay if you plan to print out the papers to read and are just about
bearable if you read the papers on a large monitor. They are quite unfriendly
for tablets or smaller laptops -- starting with the multiple vertical columns,
which are taller than the screen height. The font size is dictated by the aim
of reducing printing costs rather than reading convenience. Just for starters,
a "responsive" reader with the ability to resize fonts would make a big
difference. Notes/references which appear on the side (rather than the bottom
of the page) or links to interactive data (which scientists will have to
figure out a good way of using) would drastically improve the reading
experience and the efficacy of this mode of scholarly communication.

~~~
banachtarski
You mention printing. This is the singular reason why I prefer pdfs myself.
PDFs are viewable in the browser and resizeable. They are operating system
agnostic. Most importantly, they preserve the formatting that the original
author intended.

This is not to say it can't be all done natively in a browser, with resizing
based on screen or print resolution. Just that most paper authors will not be
savvy enough to do it right. It's enough for them to learn LaTeX properly (the
_only_ option for typesetting equations) and I doubt tooling for doing what
you suggest will come any time soon.

~~~
ssivark
> PDFs are viewable in the browser and resizeable. They are operating system
> agnostic. Most importantly, they preserve the formatting that the original
> author intended.

So are most webpages.

> Just that most paper authors will not be savvy enough to do it right. [...]

I believe this can be done gracefully in a manner where the authors just
supply a source file and the software chain will generate the requisite output
formats (much like pdflatex or Pandoc do the job today). Scientists should NOT
have to muck around with HTML/CSS/JS/etc else the solution would be DOA.

~~~
banachtarski
> So are most webpages

View hacker news on multiple browsers and operating systems. It won't look the
same. My gmail looks different too. Fonts are different which means the
numbers of words per line are different.

> I believe this can be done gracefully in a manner where the authors just
> supply a source file and the software chain will generate the requisite
> output formats (much like pdflatex or Pandoc do the job today). Scientists
> should NOT have to muck around with HTML/CSS/JS/etc else the solution would
> be DOA.

Agreed but this is much much easier said than done.

------
alexholehouse
Slightly off topic, but I wish there was a change to how scientific papers
were _written_ (and this comment doesn't pertain to this article - it's just a
general comment). For some, inexplicable reason, it sometimes feels like
authors are challenging one another to write the most convoluted, unclear
account of what is actually a fairly intuitive idea.

Clearly, this is not always the case, and obviously complexity doesn't lend
itself to nice 10 word summaries (hat-tip to Jed Bartlet), but equally the
choice of language used and the pace of arguments can make a _huge_
difference. There is no need to use "big" words, when simple ones will do just
fine. There is no need to use technical language in place of standard
vocabulary where it adds nothing to further your ideas. Don't "hit the ground
running" but introduce a new idea with an analogy, or a toy example.

Write papers so humans can understand them - often the science being portrayed
is complicated enough, there's no need to further complicate your ideas to the
point where you leave English speaking audiences trying to decipher the
message, let alone what foreign readers must think.

The best papers are the papers you can read abstract-to-conclusion without
stopping and asking yourself, "What does that mean?". This is all too rare an
occurrence for me. /rant

~~~
fjdghsd
Scientific papers aren't written for you, the layman. They are written
specifically for scientists in that particular field. I'm a PhD student, and
never have I read a paper with wording that I would describe as "convoluted."

~~~
Osmium
Lucky you! I agree, though, that the problem isn't as severe as the OP
suggests, but it does exist. You see it especially in papers that aren't that
great, where the author obfuscates what they've done because the reality isn't
as impressive as they'd like (which is a shame, because that doesn't mean it's
not useful research -- and if it was presented more concisely, it'd probably
be more accessible by more people -- not everything needs to be
groundbreaking!).

------
gjuggler
A great example of a web-friendly, interactive view of a scientific paper is
the eLife Lens, example here:
[http://lens.elifesciences.org/#00380](http://lens.elifesciences.org/#00380) .
They announced the open source project back in June (blog post
[http://www.elifesciences.org/lens/](http://www.elifesciences.org/lens/)).
This is the direction that web-based paper views are moving toward, and some
publishers (notably PLOS) already have quite nice interactive components.

PubMed, the government-run biomedical abstract database, also recently
introduced its PubReader app for reading biomedical papers
([http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/](http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/)).
But my money's on eLife here — NCBI is better known for its databases than its
user interface design (to say the least).

It would be great to see some innovation here (some publishers have absolutely
_awful_ web-based journal article views). But as the main format for paper
publishing and dissemination, I think the PDF won't be going away anytime
soon.

~~~
michaelmior
Thanks for the Lens link! I may have to try this with my next paper.

~~~
i_mulvany
Lens reads JSON, and we convert from XML to JSON using this component:
[https://github.com/elifesciences/refract](https://github.com/elifesciences/refract).
We are working on updated documentation, and a getting started guide, our hope
is to make the base system flexible enough to display any "component".

~~~
michaelmior
Any existing tools to help author NLM XML?

------
timf
A great example in this vein:

[http://worrydream.com/ScientificCommunicationAsSequentialArt...](http://worrydream.com/ScientificCommunicationAsSequentialArt/)

You can mess with the sliders, etc.

Video @ [http://vimeo.com/67076984](http://vimeo.com/67076984)

~~~
egocodedinsol
I love BV!

fwiw I considered using the Strogatz paper as an example for consistency
(maybe it could become something of a standard for reimagining paper layouts),
and use tangle or knockout, but I decided to get feedback sooner rather than
later after reading a line in pg's essay today re: procrastination.

------
michael_nielsen
I like it!

Clicking on a link and having a figure appear solves a small but real problem.

In mathematical papers it'd be nice to be able to do the same with equation
references --- click on the equation number, and the equation would magically
appear in the margin. Ditto bibliography entries, theorem statements,
definitions, and so on. I guess there are possible solutions other than having
them appear in the margin, too.

~~~
egocodedinsol
Thanks! I was thinking about doing the same with bib refs since I don't like
being sent to the bottom of the page like a footnote. I really like the idea
of doing the same thing with theorems, defs, etc.

I'm a bit worried about what to do with column overload, though, if I add a
col for X, a col for Y, etc. Perhaps a hover-text is better but that would
obscure the content ...

~~~
michael_nielsen
I'm not sure I see why you'd want separate columns for X, Y, etc. Why not have
one margin, and use it for theorems, definitions, etc?

------
freyrs3
This is quite unreadable with the low contrast colors and the columns are much
too small. If you pick a random paper on the arxiv[1] and imagine how much
vertical space it will take to just to show the text you'll see the problem.

[1] [http://arxiv.org/list/hep-ex/new](http://arxiv.org/list/hep-ex/new)

~~~
egocodedinsol
I think you're right re: contrast, but I'm still conflicted about column size.
On the one hand, a wider column gives better justified results, but on the
other hand, it makes the sliding figure column more difficult on 13 in.
Screens. Which did you find more beneficial, wider columns, or sliding
figures?

~~~
vhf
Contrast[1] is too low for me as well, and text should not be justified[2]
IMO.

I too appreciate your effort, but keep in mind the differences between print-
and web- layout design. Most scientific papers are published in PDF, using
Latex. These two work great for the print. Correct hyphenation, good justified
text, etc. Browsers are not that far yet, unfortunately.

[1] [http://contrastrebellion.com/](http://contrastrebellion.com/)

[2]
[http://www.rnib.org.uk/professionals/webaccessibility/articl...](http://www.rnib.org.uk/professionals/webaccessibility/articles/Pages/justified_text.aspx)

------
zeckalpha
[http://www.ctan.org/pkg/tufte-latex](http://www.ctan.org/pkg/tufte-latex)

~~~
dfc
I came in to mention the tufte latex class. It is unfortunate that you posted
the link with no context. If you are going to post a link with no context I
would think that one of the two samples would have been a better choice:

sample handout: [http://mirrors.ctan.org/macros/latex/contrib/tufte-
latex/sam...](http://mirrors.ctan.org/macros/latex/contrib/tufte-latex/sample-
handout.pdf)

sample book: [http://mirrors.ctan.org/macros/latex/contrib/tufte-
latex/sam...](http://mirrors.ctan.org/macros/latex/contrib/tufte-latex/sample-
book.pdf)

For those looking for some context:

 _" The Tufte-LATEX document classes define a style similar to the style
Edward Tufte uses in his books and handouts. Tufte’s style is known for its
extensive use of sidenotes, tight integration of graphics with text, and well-
set typography. This document aims to be at once a demonstration of the
features of the Tufte-LATEX document classes and a style guide to their use."_

------
davidbanham
The layout is nice, but I found the text really difficult to read with the
lack of contrast. I imagine it would be next to impossible for someone with a
vision impairment.

~~~
egocodedinsol
Thanks. Did you like the auto scrolling of each column depending on what was
clicked?

re: contrast, I've found black on white is too harsh for me (I like the
'lights out' setting on project euler for instance.) Do you prefer dark text
on light bg, or light text on dark bg?

~~~
cbhl
I like black on white, because a lot of the displays I use (e.g. my mobile
phone) are too washed out to display more subtle differences in color.

Have you considered using a user stylesheet to override the default font
colors in the browser?

~~~
egocodedinsol
Ah, thanks. I considered doing a lights on/off button like project euler, but
decided not to. Part of it was that it seemed like additional complexity and I
was worried it might overload the minimalist design, and part of it was that
I'm not a javascript developer, so additional overhead is more of an issue
than it would be, say, for a n intern at the Khan Academy ;)

Ultimately, it would be great for someone to do that, but this is more proof
of concept than a product per se.

~~~
cbhl
Oh, User CSS is something you do in your browser to override what site authors
do.

Here's the docs for Opera, although I think this is also a feature in Firefox
(and maybe Chrome; I'm not as sure about that one).

[http://www.opera.com/docs/usercss/](http://www.opera.com/docs/usercss/)

------
cbhl
I don't generally read scientific papers, but I found it annoying that I had
to click on the "Figure 1" in the text to see the figure, and that the space
in the figure seemed useless until you hit the reference in the text.

Part of me wants parallax scroll, but I'm sure that would be a terrible fit
unless you had the right number of diagrams and the references to diagrams
were equally spaced out (as opposed to having two in the same line).

This also reminds me of good old <frame>s from the 90s...

Edit: I realized afterwards that you refer to some diagrams multiple times,
such as Figure 4. I guess this is a step towards not having to flip back three
pages in the PDF to get to that diagram, but I'm not sure it's a "300x
improvement" that would cause scientists/academics to switch away from LaTeX
(or use your new LaTeX module, if you went that way) any time soon.

~~~
egocodedinsol
I'm not sure what you mean re: click on "Figure 1" to see it. You could scroll
back up, but I thought that was the equivalent of flipping back pages. In a
lot of scientific papers I read the figure is not on the same page as the
first introduction. I considered fixing them to one position, or placing them
within the text like most people do, but this interrupted the flow for me.

re: "Edit" It's not a 300x improvement by any means. Definitely less cool than
the research I get to do ;) That said, I would like to see things switch away
from LaTeX as typesetting gets better on the web. I love LaTeX, and was even
offered a part-time gig as a LaTeX editor for an economist that has 3 full-
time typesetters (I'm not even kidding, he must take division of labor
seriously). But it doesn't seem to allow for the same kind of freedom we have
now as a result of newer media: it's optimized for print, even with addons
like hypertext.

~~~
cbhl
So I find that in order to see the diagram, I need to either scroll manually
(O(n) linear search) or click on the reference in the text (makes my hand
hurt).

I 100% agree with the problem you've identified, but I find your solution
confusing.

Then again, I found LaTeX confusing when I first used it, so I guess it might
just be me not being used to it.

------
Cogito
You should make the source more discoverable, particularly on your 'homepage'.

Particularly on a site like this, but also in general, in doesn't take much
more effort to write a pull request than it does to write a comment.

For example, modifying the colour scheme or layout would be a few lines
changed in the css. Encourage people to give the most useful feedback they can
- patches!

I should probably go and raise a PR implementing this now, but I've already
spent so long writing this comment... ;)

[EDIT] Adding a Readme to the repository would help people understand how
everything is organised as well (for people who want to look at the nuts and
bolts), and a License file would clarify what, if any, modification of your
work is allowed.

~~~
egocodedinsol
it's all there at github.com/egocodedinsol/egocodedinsol.github.io, or did you
mean adding a direct link to it?

I'm not sure how much it's a software project so much as a proof of concept.
If you did want it to be more of a project, what would you suggest doing?

~~~
Cogito
Sorry I missed this earlier!

I do mean explicitly adding a link to the source from the site itself. Sure,
you may not get anyone to contribute, but at least there are no excuses not
to. The best feedback almost always comes in the form of a patch :)

If you wanted to make specific components more of a project, consider
splitting them into their own repositories. If you have a branch 'gh-pages' it
will be served under username.github.io/repository

If you know of existing issues or feature requests, make use of the Github
issue tracker. This shows people that you are thinking about the future of the
code, so they feel comfortable that if they contribute it won't be wasted
effort. This also lets people know of an easy way to provide feedback that
won't get lost into the aether.

Lastly, continue to invite discussion and ask for contributions. If somebody
says "The contrast is too high" say to them "here is where the colour scheme
is defined, what should the values be?"

Hope that all helps, I really like the ideas that you have. Innovation is
always important!

------
egocodedinsol
To use: click 'text' to sync text col to reference of figure in text, multiple
times if there are multiple are multiple references, drag a figure, resize a
figure, click 'reset', click a figure reference to sync to the figure col.

I know there are a few editors that read this, I would love to see better
interfaces for your journals ;).

------
andrewcooke
what on earth is happening to the kerning? chrome/linux the line "but is
better than the hand-waving I was doing." is awful (no space between words).

edit: word-spacing: -2px; wtf?

~~~
leephillips
Narrow column + no hyphenation + justified = typesetting disaster, especially
with the crude type handling in web browsers.

------
kumarski
I wish they simply hyperlinked their sources.

------
fmsf
You guys should take a look at eLife sciences journal then... I think it is
what you want...

------
chj
Oh, why the color! I can't read anymore.

------
fdej
onfirefox22.0onwindowsthetextlookslikethis thanksbutnothanks

~~~
egocodedinsol
Odd, it doesn't do that for me on ff22windows. I originally messed with word
spacing because it looked too sparse, but I'm going to switch it back to
something safer. Thanksforthefeedback;)

