

Authorea: Write research papers inside your browser - synparb
https://www.authorea.com/

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ank286
Landing page comment: "Write research papers, right inside your browser" As a
researcher, I immediately ask "Why?" What is wrong with my Latek utils and
fabulous MS Word that my research lab gave me for free. Then, where are some
templates for the journals/conferences I could possible use with Authorea. You
can reach far more people if you included templates from most
journals/conferences. Then I can see this taking off.. Otherwise it is nothing
but a fancy text-editor to me with Latek support and is trying to be like
arXiv. As it is, arXiv has a lot of noisy publications.

~~~
matteocantiello
Thanks for the feedback. This is still work in progress, and we are planning
to improve the export function to publication-ready format (as you suggest).
This said, we want to bring the authoring process to the web principally for 2
reasons: 1) It makes collaboration easier 2) It expands dramatically the
possibilities of sharing scientific content respect to a 'static' PDF format,
ultimately impacting transparency and reproducibility of scientific results.

~~~
ank286
I just want templates for different journals/conferences for the same topic.
All their formats are annoying, but at the end of the day, every
PI/researchers wants to publish in something that is peer-reviewed. In a
university setting, paying to read/download a publication is an after-thought.
The entire transparency/reproducibility of scientific results is a good goal
but is very long-term goal.

Some entities like ScholarOne/Cambridge Journals wants you to individually
upload your images and your text separately. Since a user is just writing
their paper on Authorea, maybe, you can keep track of what journals they are
aiming for and reformat the publication for multiple journals in ONE SHOT.
That'd be the biggest time saver ever.

At the end, doing research is fun but publishing is a painful process, and you
are judged based on publications. Reduce the pain.

~~~
matteocantiello
I totally hear you. And this is part of what we want to accomplish. As for the
transparency/reproducibility I do not think this is too much long-term:
already now if you prepare a paper on Authorea and publish it on a refereed
journal, you can include a link to the Authorea repository. Which means even
if the Journal version is static, it links to a 'dynamic' repository which
contains the sources of your scientific work. So I believe Authorea is already
pretty close to achieving that goal.

~~~
ank286
What if the Journal asks for a transfer of copyright? Does that violate some
kind of law/thing for all the previous (including the final) version of the
manuscript stored on Authorea? Would the author have to take down their final-
manuscript from Authorea so they can transfer the copyright to the
publisher/Journal.

~~~
apepe
hi there- by and large, authors are allowed to publish the pre-print and post-
print versions of their published manuscripts (pre-print being the version
right before editor proof-reading, and post-print any version following
publication). Authorea articles are essentially "enriched" pre-prints so they
do not interfere with the passing of the copyright to publishers.

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xaa
Something like this is sorely needed. Google Docs is the best compromise
between simplicity and collaboration that my group has come up with, but of
course it doesn't have reference support.

It is very visually appealing and has good features. However, for me, it seems
very sluggish and unresponsive.

~~~
JohnHammersley
This is really neat, a good combination of Markdown & LaTeX.

As one of the founders of <https://www.writelatex.com>, one of the interesting
differences is the fact you're editing the "output" file rather than the
source - takes a bit of getting used to! Looking forward to seeing it develop
:-)

~~~
apepe
Thanks John. Authorea founder here. First off, I have tried writelatex for the
first time just a couple of weeks ago and it really works great to create
beautiful documents. Great work.

Yes, we (and most scholars in general) are very used to editing a source
(Latex mostly) and compiling it to something else (a PDF output, or similar).
We are trying to streamline that process using the web as the canvas, and
render directly to HTML5. In a way you are right, it feels like you are
editing directly the HTML output. Which is fine! Our hope is that researchers,
especially the ones who already work and write on the web will quickly get
used to such a workflow.

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natejenkins
Our goal is to reinvent the article online.

One thing that really needs to change is that figures need to come to life.
While there are a few ways too accomplish this, one is by using javascript
libraries such as d3.js to render dynamic images.

As an example of things to come, have a look at:
<https://www.authorea.com/522>

Does not work in Firefox at the moment.

~~~
jimmaswell
If it doesn't work in Firefox you're probably not following standards. Why?

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natejenkins
It uses the sandbox feature for an iframe in html5. It doesn't seem to be
supported yet in Firefox. Although if it is I'm sure someone will correct me.

~~~
numair
<http://caniuse.com/iframe-sandbox>

Might want to update your browser detection script.

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krcz
That's a great idea and really good implementation. The only thing I'd miss
from Google Docs are comments that are not part of a text (in Docs these are
rendered on right side of document). You could implement it by come special
syntax for comments, which wouldn't render when exported and on site, and in
edit mode, it would show just a little icon. GUI option to click somewhere to
add comment in this place would make it even easier. It allows further
capabilities, like easy inline peer review.

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xur17
Looks great! One quick comment - the links on the left hand side of an article
should only take up enough space to fit the text for the links, so more space
can be dedicated to the article.

Ex: <https://www.authorea.com/users/1/articles/483/_show_article>

Otherwise, it looks great - I'm going to be starting to write my thesis soon,
and I plan to try this out.

~~~
apepe
thanks for the tip! You are right indeed. Not the best use of whitespace
there. We are still polishing up the front end a bit. It would be wonderful if
you gave Authorea a try for your thesis. Feel free to get in touch for support
as rendering a very long document in the browser may be more cumbersome than
regular academic papers.

~~~
xur17
Will do!

I think some other people mentioned this too, but I'd love the ability to
connect this to my own git repository so I can store / have access to all of
my changes.

~~~
apepe
yep, git access and offline mode are two features that are coming real soon.
thanks again!

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synparb
I'm curious how easy it's going to be to (1) download the git repo from the
backend, and (2) format the articles to meet specific journal requirements for
submission.

~~~
natejenkins
Hi, Authorea co-founder here. A bit surprised to see us on the front page.

1\. Full access to the git repository will be added soon. It wasn't our main
concern initially as we wanted it to be easy to work on articles for an
academic researcher who wasn't familiar with git.

2\. This currently requires some post-authorea cleanup. We are also working on
making this much easier. The main pain point that we are trying to solve
currently is making collaboration on articles easy.

~~~
synparb
Great to hear that these things are planned. I think #2 is really quite
important, because if there isn't a simple path to preparing a submission-
ready document, then there is still a major point of friction in the process.

~~~
matteocantiello
Hi, Authorea consultant here. I completely agree. It's important to provide a
seamless way to export Authorea articles to submission-ready format, for
example by including the relevant Journal style file (or even giving users the
option to chose from a list). Work in progress.

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skyahead
Latex is free! Authorea is NOT. This is the main problem I see.

And the second problem, who will write papers in public before publication?

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jclos
These two problems are related - I don't mind having the final product in
public (it's bound to get there eventually) and thus not having to pay too
much (or even use the free tier), but putting everything in public before
publication is insane and I doubt it will be used for anything but blog posts
for that reason.

~~~
apepe
hi jclos, I don't think that putting out research content out in the open is
insane, as you say. While privacy is indeed a good and a safe idea in a number
of contexts, for most research projects, sharing the full sources from the
very beginning is only advantageous. For example, less secrecy encourages
collaboration, rather than competition. Also, it is a way for authors to claim
their ideas and work as soon as they have it. Why wait months before getting
something published when we have a fast modern content publication system
right in front of our eyes? I have a vision, and I may be wrong. But my vision
is to use the web to publish and disseminate scientific content: science you
can fork, clone, reproduce, and interact with, from the very first word you
jot down in a paper, up to the last equation. My hope is that Authorea is a
step in the right direction.

~~~
jclos
I understand, and I agree to some extent, but the truth is that it is too
risky.

In my country at least, but I'm sure it is the same for most, researchers
survive by putting their quota (fixed by the ministry of research) of
publications in well renowned journals. The risk of having someone "steal"
your idea (in the very loose definition) and beat you to the publication, for
instance by having a bigger research team, thus putting you out of a job, is a
real one.

In an ideal world your system would be perfect, putting the advancement of
knowledge before everything else (as open source does with software), but
researchers have to look out for themselves before all, considering how their
performance is evaluated and how that affects their livelihood. Unlike open
source software, there aren't a lot of ways to monetize scientific
publications. I would enjoy seeing things change, but change is slow to come.
Especially in an area as pachydermic and anchored in traditions as academia.

I really like Authorea and I will use it for non-published work, but I feel
that limiting private publications so much is going to limit adoption. But
then again what do I know, I guess we will see how it goes.

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rdw
The LaTeX support seems very nice. Nice job! The concept of a paper as a DVCS
repository is a very natural one, and it's exactly how I would write my papers
back in the day.

I'm curious how the "host the data and the code" comes in. Perhaps you're
supposed to clone the backing git repository and add the code to that, but I
don't see how to do that yet. Early days.

~~~
natejenkins
Hey, thanks for the compliment! Much appreciated.

If you look at a figure in an article, for example
<https://www.authorea.com/483>, you'll notice that the figure reference has
been pulled out of the latex source. We did that so that in the online version
of an article we can make figures cooler, like attaching data to them. Figures
exist in their own folders, and we have big plans for those folders.

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goldfeld
This is a great answer to all this "open up the papers" movement, and going
forward a much better solution than those apps that cropped up for asking for
a given research paper. If things remain open, that is. A github for papers
sounds great, and an actual natural extension of the idea of github. Whereas
github is pragmatic projects, authorea is the step before that.

~~~
matteocantiello
Exactly! And at the same time we can exploit the power of the web, which
unfolds into an easier approach to collaboration and a wider range of
possibilities in terms of ways to show / plot / share the data and any other
products of the scientific research. "Papers" haven't changed at all in the
last few hundred years, but research and technology has dramatically. It's
time to keep up.

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interconnector
ShareLaTeX is also worth checking out: <https://www.sharelatex.com/>

~~~
matteocantiello
Notice though the big conceptual difference between any online (collaborative)
LaTeX editor and Authorea. In Authorea articles are written in a browser and
live in the browser (as HTML5 pages). There is a huge potential to be
exploited by such a paradigm shift.

~~~
sciurus
If I'm writing a paper, it's great for collaboration if it can be written in
the browser. Being able to preview my paper in the browser sounds nice too,
but to publish it I need to be able to compile it into a PDF.

~~~
apepe
yes, we (scientists and scholars) still rely on the exchange of PDFs to
communicate research. This is a pity. The problem is that a scholarly paper in
PDF, even when it is on the web, it is essentially a photograph of a
(physical, analog) paper. As such, a PDF fails to expose the living, dynamic,
interactive nature of research. The baseline motivation for Authorea is to
expose such nature: to expose the data underlying plots and images, to allow
articles to be forked and cloned, to enable web-native data visualizations, to
get version control right, and so on. We are trying to move in this direction!

~~~
neumann
I hear what you are yearning for - I remember trying to convince my supervisor
that researchers need to look towards github for progress.

His response stuck with me: While scientific research is continuous and never
complete, the whole point of publication is that it is a record in a fixed
point in time. The results and discussion cannot be altered, or reused: it is
a milestone, a historical record of a novel contribution to knowledge. Sure,
you might reanalyse your data, rework an image with new parameters what have
you, but the nature of sharing your work with your scientific community
requires it to be static.

~~~
apepe
I partly agree with your supervisor. While publications are indeed milestones
and are great for obtaining recognition in the scholarly community, they can
still exist and accomplish their function alongside their "rich" counterparts:
online versions of those publications with live, dynamic, executable data and
images, to allow forking, cloning, and interaction. We now produce research in
a much more dynamic environment than even just a decade ago. My hope is that
10 years from now a scientific paper "locked" in a PDF format will look
obsolete. I may be wrong, but I sincerely hope that.

~~~
Thrymr
Indeed. A snapshot could be a tag, and a reference contains that tag. Looking
up a reference would let you see the paper in the state that is being
referenced, but also allow you to easily move forward to later versions.

We are a long way from that now, but it is appealing.

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yannis
Strange enough I had a very similar idea see
[http://tex.stackexchange.com/questions/83588/latex-mark-
up-a...](http://tex.stackexchange.com/questions/83588/latex-mark-up-as-a-
generic-mark-up-language) and made a prototype. Would be glad to share ideas
if you want. Please contact via tex.sx chat.

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icelancer
Thank god. I have been planning on writing a bunch of papers to publish on my
website and all of the options have been awful.

So far, it looks great. Thanks for the service. Can't wait to try it out.

~~~
matteocantiello
Thanks. Please try and give us feedback. We are very happy to hear from users!

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lsiebert
I'm on mobile, but does this have zotero integration?

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natejenkins
not yet (sorry), but it's on the list.

~~~
lsiebert
Awesome. Thank you for making something cool.

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RichardPrice
Authorea is a great project. I love the idea of helping academics write their
papers natively for the web. Good luck Nate and Alberto!

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apepe
Thanks Richard! I am so glad you like Authorea. It was great chatting about
Academia.edu last month at the Berkman. I look forward to meeting up soon.
--Alberto

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toomim
FUCK YHEAAAAAHHHHHHHHH!!!!!!!

I'M GOING TO USE THIS RIGHT NOW!!!!!!!!!!!!!!

Just like, update to the internet, man. I want my articles to look beautiful
on the web, not just in antiquated print journals!!!!!

Why, in 2013 do references need to look like this (Johnson-Kines et al., 1533)
when we have HYPERLINKS on the web??? And you can show a little snippet in a
tooltip--or the actual quote or line of the document that you're referencing?

Where are my embedded videos?

~~~
toomim
ACK. I tried using it. Too many bugs! UI needs polish.

When you fix this, please announce it to me. I want to use a version that
works!

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apepe
hi toomim, yes we are still a bit rough around the edges. We are only a few
months old. If you can let us know what bugs you found, it'd be great. And we
will definitely announce it again as soon as we are ready for a more official
launch. Thanks for checking us out

