

OpenJournal - Discuss academic papers (open source) - mekarpeles
http://hackerlist.net:1337

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streptomycin
When I read papers, I often write short notes to myself about them, as I
imagine most people do. I could imagine these notes as also being comments on
a site like this, particularly if it's all open and community-run. However, if
the paper I'm reading is some 10 year old paper in some niche subfield, which
ultimately is the majority of what scientists end up reading, I'm just going
to be talking to myself there, so what's the point? I'm not going to submit a
paper there that I know no other readers will care about.

How do you overcome that barrier? It's not even network effects alone, it's
like extreme network effects because the tail is so long in science. I guess
it's really the barrier between being high-level discussion about only the
latest big-name science news in certain fields, and being a central hub for
all kinds of relatively short comments on scientific papers. Seems like a
difficult problem to solve.

Have you thought about maybe pre-populating your database with all papers,
ready for discussion, rather than having it as a Reddit-like discussion of
only recently submitted things? Or is there some other kind of grand vision
for where this will go?

~~~
jayunit
Not to speak for Mek, but one hope I have is that these small personal notes
automatically make their way onto places like OpenJournal and start to seed
conversations. Something like a cross between ScienceBlogs and Twitter, with
enough mini metadata to tie to the paper and paragraph.

Do you use a library management tool like Zotero or Mendeley for notetaking,
or writing on printouts, or something else?

~~~
streptomycin
I used to use plain text files. Recently I started using Mendeley because it's
so damn convenient and it has a very nice UI, but my problems with Mendeley
are (1) comments are private and (2) it's proprietary.

<http://www.researchblogging.org/> is a great website that aggregates more
long-form posts about papers, but it has a really shitty UI and it doesn't do
anything for short comments on random papers by random non-bloggers.

~~~
mekarpeles
Let's see what inspiration we can draw from researchblogging.org -- I've read
a bunch of data driven / research oriented blogs (or blogs about
[understanding] research) and found them helpful.

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jayunit
Mek, this is great. Thanks for sharing & open-sourcing it. I love the idea of
bringing together paper discussions online - whether post-publication peer
review like f1000research.com or more casual discussion like r/science.

One challenge I've found is that it's often difficult for discussion sites to
gain sufficient traction to build a critical mass of discussion -
<http://plasmyd.com>, <http://papercritic.com>, <http://scicombinator.com>,
<http://chemfeeds.com>.

I wonder if focusing on supporting existing small-group interactions (real-
life journal clubs) would help?

I took a slightly different approach when I wrote
<http://www.papernautapp.com> and chose instead to aggregate existing
discussions about academic papers (mostly blogs, a few news sites, HN, and
r/science, with a goal to cover to more sites and mailing lists). It's also
freely licensed, and there are some interesting things I discovered that might
be useful to OpenJournal (looking at your TODO list and GH issues):

* CrossRef.org runs a ton of cool lookup/crossref/deref services at <http://labs.crossref.org/>

* They also have some great libraries at <https://github.com/crossref/> \- who wouldn't geek out at this: <http://labs.crossref.org/pdfextract/>

* If you want to do some auto-identification on webpages, the <https://github.com/zotero/translators> project is great and actively maintained by the Zotero community.

(Some notes on how Papernaut is put together, if you're interested:
[http://jayunit.net/2013/01/06/papernaut-exploring-online-
dis...](http://jayunit.net/2013/01/06/papernaut-exploring-online-discussion-
of-academic-papers) )

Lastly, if you're fostering discussion and feedback on papers, there's
overlapping interest with the <http://altmetrics.org> and
<http://altmetric.com> folks.

~~~
ejstronge
I think the issue of getting enough traction might be mitigated by restricting
the papers that could be discussed. HN is a good example of this - very few
posts engender discussions but those that seem promising (by the number of
upvotes) are given a spotlight on the front page.

I think an improvement to the services you linked to would be to add a few new
articles each week from very selective journals/conferences in each field. I
imagine existing measures like a journal's impact score or the number of a
conference's attendees would be a good start and tracking blogposts (as you're
already doing) could be a good supplement.

This might help pull older or less visible publications out of obscurity; if
something published in a domain-specific journal is germane to a discussion, a
commenter might point this out while discussing a more highly visible article.

~~~
mekarpeles
Thanks ejstronge and great idea. I'll see if I can get a group of hackers
together to post one recommended paper a week.

Do you have any interest in being informed? Also, do you know anyone who may
be interested in helping curate / contribute?

~~~
ejstronge
Hey mekarpeles, thanks for responding. I'm a biologist by training and would
be interested in joining if that's a field you'd be featuring - I think an
environment where people could discuss recent, high-impact biology articles
would be great.

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yliu
Something like this is long overdue, I think. Great work. Open academic
publication models have had a difficult time for a number of reasons, but
systems like this are very helpful in making the case for openness.

One thing that always bothers me with a purely Reddit-style, point-based
system for surfacing academic discussions across domains, though, is that it's
unclear what kind of papers are being surfaced: a very good paper in a very
niche space may not get the attention that a mediocre paper written for a mass
audience (for some definition of "mass") would. Is that an acceptable drawback
for openjournal? Or should there be some way for niche papers to gain
exposure? Forking openjournal and making your own "sub-openjournal" for your
research domain? Weighted voting mechanisms?

Also, like reddit, it might be useful to have a mechanism to demonstrate,
emphasize, and/or sort by specific commenters' backgrounds, training, and
credentials. For many domains, peer review and commentary from people in the
same field might be more useful than general commentary.

As a minor wish, I've always wanted to see a mechanism for encouraging sharing
of implementations, test code, and other raw experimental results along with
the actual papers. 'Cause really, for most cases, I'm not going to implement a
multi-page algorithm just to verify a conclusion or make use of an insight.
But if I can fork and compile a github repo associated with the paper...

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robrenaud
Why use this instead of a subreddit?

I'd love a great solution to this problem and I'd even consider trying to
build one, but I am not sure there is any money in it.

One thing I'd love in an academic paper reader is something that allowed
comments/annotations inline with the paper. For example, if a paper in the
future contradicts something that is stated, you could add a comment linking
to the contradiction. Or you could merely ask and provide clarifications, or
comment on simpler alternatives to given part of the paper.

Also, I'd like to be able to rate papers for say, readability or difficulty,
tag them as theoretical or empirical, etc.

I'd also like if cited papers were automatically dereferenced so I didn't have
to hunt down the references myself.

Personalization would also be a nice feature. EG, recommend other papers by
the same author, or other highly cited papers that cite/are cited a given
paper, or frequent co-authors of some author that I like.

I'd love to be able to download a bunch of papers easily for offline viewing.

~~~
mhluongo
We launched <http://scholr.ly> in January- we've still got plenty of issues,
but we handle some of your use cases, like citation linking. We also first-
class authors so you can see an easy summary of a researcher's work. We're
still working on personalization and have kicked around tagging/rating for
some time- I'd love your feedback.

It seems like the rest of your issues could be solved by Mendeley- WDYT?

~~~
mekarpeles
mhluongo -- Love that you specialize in search and have author profiles.

You guys should get in touch with the peer library guys, send me an email if
you'd like an intro. I'd love to see more collaboration in the space.

Internet Archive (archive.org) is also interested in contributing to the space
and has been super helpful in aiding our efforts at open journal.

I think the three biggest problems in the space are (1) discovery +
accessibility (including open-access), (2) collaboration (sharing, commenting,
contributing), and (3) quality assurance (maintainability, scm-backed,
repeatable research).

There are many solutions to target discovery and accessibility but I'm (as an
academic) personally dissatisfied with the level
sharing/collaboration/openness, the lack of community, and the lack of
standards in academic research. I think the world needs for academia and
research what github did for social programming.

~~~
mhluongo
mekarpeles - an intro to the PeerLibrary team would be awesome- I'll do that.

I've loved the GitHub for science analogy ever since it first surfaced a
couple years ago- I couldn't agree more.

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nhaehnle
The academic world could benefit from a place that allows commenting on any
paper (you can have too many comments; not sure how moderating such a system
would work).

To this end, it would be great if this were written in such a way that it
implicitly considers papers from all the "standard" academic sources as part
of the system, ideally with duplicate removal.

That is, automatically add articles from arXiv and major currently existing
journals and conferences, try to automatically detect duplicate papers
(perhaps add a concept of versions of papers).

In addition, such a site could really benefit by having "virtual journals",
where users collect topical collections of must-read papers.

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mtrn
This is great and I would use this. I even think about
porting/forking/stealing this for a German audience.

The only thing that would keep such a site from growing is the relative
reservation of less technical crowds (at least that has been my observation).
HN, proggit, SO: they are all useful and fun for the technical minded. Similar
sites for other segments (excluding cats, cats always win) are much less
active and sometimes fail to attract some critical mass.

~~~
mekarpeles
Please do, let me know how I can help you with it.

m@hackerlist.net

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mekarpeles
Would love feedback.

Please feel welcome to submit issues on github and I will try to deal with
them in realtime: <https://github.com/mekarpeles/openjournal/issues>

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mekarpeles
Also, thanks for your patience, it's running on a micro EC2 and I haven't put
too much effort yet into optimizing request handling (just using waltz over
web.py at this point)

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stillbourne
RSS/Atom please.

~~~
mekarpeles
Adding this to the github issue tracker, I'll get this setup for you as soon
as I have a break in my schedule today. Thanks!

~~~
mekarpeles
Issue oppened -- thanks! <https://github.com/mekarpeles/openjournal/issues/16>

