7 ms·

OpenJournal - Discuss academic papers (open source)

63 points by mekarpeles 14y ago

mekarpeles 14y ago
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 https://github.com/mekarpeles/openjournal/issues
mekarpeles 14y ago
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)
stillbourne 14y ago
RSS/Atom please.
- mekarpeles 14y ago
  https://hackerlist.net:1443/rss https://hackerlist.net:1443/rss -- done, please let me know if you'd like it in a different format or if there are any mistakes. Thanks, stillbourne!
- mekarpeles 14y ago
  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 14y ago
    Issue oppened -- thanks! https://github.com/mekarpeles/openjournal/issues/16 https://github.com/mekarpeles/openjournal/issues/16
  - deleted 14y ago
    [deleted]
robrenaud 14y ago
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.
- mekarpeles 14y ago
  rob, not really interested in the monetary aspects of this problem, more interested in the open-access nature. There is a subreddit for academic papers, I figured it would make sense having something ultra-targeted for computer science papers and I didn't feel like the right community was using the subreddit (the results quality wasn't great). It did teach me that a lot of people like requesting papers, so this is something I am considering. Also, this was a good opportunity for me to attack a problem I am really passionate about while testing out a web framework I've been writing (waltz). Finally, I did the project for sentimental reasons. I was talking to Aaron Swartz about open journal a while back over skype and was looking forward to working with him on it, so I thought it would be nice to finish it in his honor :o) You have some great ideas (mass download is something I've seen requested by some of my friends from my phd program). There's a team called peer library who's attacking many of these problems and I'll be giving them as much support as I can. Thanks for your kind remarks + great feedback
- mhluongo 14y ago
  We launched http://scholr.ly 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?
nhaehnle 14y ago
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.
streptomycin 14y ago
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 14y ago
  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?
  - mekarpeles 14y ago
    I'm a fan of plaus, academia, and mendley, etc. I wish there was more of an outlet/community for people to contribute their own research (in a way that made the research repeatable and improvable)
  - streptomycin 14y ago
    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/ 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.
jayunit 14y ago
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://plasmyd.com, http://papercritic.com http://papercritic.com, http://scicombinator.com http://scicombinator.com, http://chemfeeds.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 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/ http://labs.crossref.org/ * They also have some great libraries at https://github.com/crossref/ https://github.com/crossref/ - who wouldn't geek out at this: http://labs.crossref.org/pdfextract/ http://labs.crossref.org/pdfextract/ * If you want to do some auto-identification on webpages, the https://github.com/zotero/translators 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-discussion-of-academic-papers http://jayunit.net/2013/01/06/papernaut-exploring-online-dis... ) Lastly, if you're fostering discussion and feedback on papers, there's overlapping interest with the http://altmetrics.org http://altmetrics.org and http://altmetric.com http://altmetric.com folks.
- ejstronge 14y ago
  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.
mtrn 14y ago
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 14y ago
  Please do, let me know how I can help you with it. m@hackerlist.net
yliu 14y ago
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...

63 points by mekarpeles 14y ago

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 https://github.com/mekarpeles/openjournal/issues

mekarpeles 14y ago

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)

stillbourne 14y ago

RSS/Atom please.

mekarpeles 14y ago
https://hackerlist.net:1443/rss https://hackerlist.net:1443/rss -- done, please let me know if you'd like it in a different format or if there are any mistakes. Thanks, stillbourne!
mekarpeles 14y ago
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 14y ago
  Issue oppened -- thanks! https://github.com/mekarpeles/openjournal/issues/16 https://github.com/mekarpeles/openjournal/issues/16
- deleted 14y ago
  [deleted]

robrenaud 14y ago

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.

mekarpeles 14y ago
rob, not really interested in the monetary aspects of this problem, more interested in the open-access nature. There is a subreddit for academic papers, I figured it would make sense having something ultra-targeted for computer science papers and I didn't feel like the right community was using the subreddit (the results quality wasn't great). It did teach me that a lot of people like requesting papers, so this is something I am considering. Also, this was a good opportunity for me to attack a problem I am really passionate about while testing out a web framework I've been writing (waltz). Finally, I did the project for sentimental reasons. I was talking to Aaron Swartz about open journal a while back over skype and was looking forward to working with him on it, so I thought it would be nice to finish it in his honor :o) You have some great ideas (mass download is something I've seen requested by some of my friends from my phd program). There's a team called peer library who's attacking many of these problems and I'll be giving them as much support as I can. Thanks for your kind remarks + great feedback
mhluongo 14y ago
We launched http://scholr.ly 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?

nhaehnle 14y ago

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.

streptomycin 14y ago

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 14y ago
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?
- mekarpeles 14y ago
  I'm a fan of plaus, academia, and mendley, etc. I wish there was more of an outlet/community for people to contribute their own research (in a way that made the research repeatable and improvable)
- streptomycin 14y ago
  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/ 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.

jayunit 14y ago

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://plasmyd.com, http://papercritic.com http://papercritic.com, http://scicombinator.com http://scicombinator.com, http://chemfeeds.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 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/ http://labs.crossref.org/ * They also have some great libraries at https://github.com/crossref/ https://github.com/crossref/ - who wouldn't geek out at this: http://labs.crossref.org/pdfextract/ http://labs.crossref.org/pdfextract/ * If you want to do some auto-identification on webpages, the https://github.com/zotero/translators 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-discussion-of-academic-papers http://jayunit.net/2013/01/06/papernaut-exploring-online-dis... ) Lastly, if you're fostering discussion and feedback on papers, there's overlapping interest with the http://altmetrics.org http://altmetrics.org and http://altmetric.com http://altmetric.com folks.

ejstronge 14y ago
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.

mtrn 14y ago

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 14y ago
Please do, let me know how I can help you with it. m@hackerlist.net

yliu 14y ago

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...