Linux equivalent to Papers (Mac) / how are you organizing papers?

JonathanArcher · 2009-01-11 10:31:02

I guess there are some scientists here in the forum and maybe some of you know the program iPapers for Mac (http://ipapers.sourceforge.net/) which helps you organize your papers. You can use it as a browser and as far as I understood it, it can even lookup your already unorganized existing papers and lookup their titels, authors and abstract and import it into the program so you can search for those papers and have it all neatly together. So I wondered if there is some program for linux that is quite equivalent? Mostly I adore this automatic organizing, like the Musicbrainz Picard which I've also come to find really useful, do you know any program that can do this too?

At the moment I am really thinking about getting a mac because there are also other programs we use that are mainly available for mac, but that would be just for work. Personally I quite dislike the mac philosophy, so if there is any other way I'd like to try that.

And if not, sidequestion: How are you organizing your papers? At the moment I have certain folder-categories that I put them in and name the pdfs manually with "year - first author - title". Since I am writing my diploma thesis at the moment I use JabRef to organize them in a Bibtex file, but that is also all manual, which can be quite annoying over time, especially at the beginning when you know you have to file all of your dozens of papers one by one.

Late edit: I meant Papers, not iPapers, silly names...

Last edited by JonathanArcher (2009-12-08 21:33:26)

Bob Day · 2009-01-11 12:28:54

I haven't used them myself, but you might like to try:
Referencer: http://icculus.org/referencer/
Pybliographer: http://pybliographer.org/

dcrabs · 2009-01-11 12:30:28

Hi
"good" to see that other people have that problem, too. There is gpapers which tries to resemble ipapers but it is a pain to install it and it's far from finished. In the end I used kbibtex or kbib but those are similar to jabref that I didn't liked. The first two are able to look up pdf files but I never tried since it wanted me to register to the website.
I would love to start something similar to ipapers or papers for mac but unfortunately I am not familiar with gui programming.

JonathanArcher · 2009-01-11 15:40:58

gpapers I didn't know so far, at least it looks promising. And it showed me that the program I really meant is Papers, not iPapers, which my colleagues are using with great enthusiasm.

I remember that I tried out Referencer about 2 months ago, but it didn't work so well and I also didn't like the interface. And somehow I couldn't get it to recognize my papers. But maybe I just didn't use it long enough, does it work for somebody here?

Pybliographer I also didn't know, but the frontpage says, that they are looking for a new maintainer so I guess it is not active at the moment. I also couldn't find information about wether it will recognize your pdfs or if you have to do it manually.

Well dcrabs, I am not familiar with programming at all, so all I can offer is to test it if you ever come around that gui programming

Last edited by JonathanArcher (2009-01-11 15:41:19)

xen · 2009-01-11 16:16:08

I've been using Referencer for some time but I don't really use many of its features. Gpapers looks quite promising

buttons · 2009-01-11 16:30:58

ZOTERO

It's a firefox extension. It's awesome.

I also use referencer to pull bibtex from random pdfs I get. The drag and drop thing is great.

sergiocava · 2009-01-11 16:35:13

http://jabref.sourceforge.net/
pacman -S jabref

DonVla · 2009-01-11 17:01:18

i use recoll for that. it's a search and indxing tool, but very handy. i put all pdfs i have in one directory and index them with recoll.

dcrabs · 2009-01-11 18:42:34

Oh I use recall, too. Really nice program.
So it looks like the tools are there just someone has to fuse them together:

jcolinzheng · 2009-01-12 15:27:46

I don't organize papers, but if you are in CS, someone wrote a script to generate .bib file for you by querying DBLP, provided that you cite the DBLP way.

http://blog.grundprinzip.de/articles/tag/dblp/

jcolinzheng · 2009-01-12 15:43:05

DonVla wrote:

i use recoll for that. it's a search and indxing tool, but very handy. i put all pdfs i have in one directory and index them with recoll.

RECOLL looks nice, it can even index LyX files! Of course I also like the fact that it requires sane dependency to process PDF and PS documents.

mintcoffee · 2009-01-13 00:18:52

I've been using recoll for some time too to search my papers, but I really miss a tagging feature. Google Desktop had all the functionality I needed, but it really slowed my machine down as a whole.

dcrabs · 2009-01-14 12:01:00

Well, the tagging feature is in KDE4. There is nepomuk and strigi that could eventually replace recoll. It would be even better if there were a converter that could convert recoll's database or feed it to nepomuksearch.

DonVla · 2009-01-14 14:21:03

dcrabs wrote:

Well, the tagging feature is in KDE4. There is nepomuk and strigi that could eventually replace recoll. It would be even better if there were a converter that could convert recoll's database or feed it to nepomuksearch.

isn't strigi/nepomuk very slow? and they need a daemon?

Last edited by DonVla (2009-01-14 14:21:19)

dcrabs · 2009-01-14 14:33:28

DonVla wrote:

dcrabs wrote:
Well, the tagging feature is in KDE4. There is nepomuk and strigi that could eventually replace recoll. It would be even better if there were a converter that could convert recoll's database or feed it to nepomuksearch.
isn't strigi/nepomuk very slow? and they need a daemon?

Hm, it is with the redland backend but with the sesame2 it's fast.
I don't like the strigi indexing---nepomuk is not doing the indexing---so far cause it annoyed me everytime I log in. There I prefere recoll cause I decide when to do the indexing. Recoll with xapian backend seems to be very mature.
But when you are running KDE 4 you can switch strigi indexing off use nepomuk that is why I mentioned it. It would just be nice to have a converter or plugin to use the xapian db from recoll.

Basu · 2009-01-16 11:28:45

I need to make a personal project for my software engineering class next semester. I think that I could get started on a Papers-like program. The course uses C++ and Qt, so chances are it'll be a KDE program, though I need to find out a way to view PDFs first.

dcrabs · 2009-01-16 12:12:56

Basu wrote:

I need to make a personal project for my software engineering class next semester. I think that I could get started on a Papers-like program. The course uses C++ and Qt, so chances are it'll be a KDE program, though I need to find out a way to view PDFs first.

You can use okularpart for that. Unfortunately there are no examples that could help me using it. I tried using it with pykde4 but wasn't successful, probably due to my lack of gui programming skills.

Ranguvar · 2009-01-16 12:14:25

Please don't make it a KDE program and isolate those of us who use standalone WMs, or even Gnome/Xfce/LXDE, because there will then be many KDE dependencies You can make a C++ Qt app without making it a KDE app. Thanks either way though!

Last edited by Ranguvar (2009-01-16 12:14:40)

dcrabs · 2009-01-16 12:35:10

Ranguvar wrote:

Please don't make it a KDE program and isolate those of us who use standalone WMs, or even Gnome/Xfce/LXDE, because there will then be many KDE dependencies You can make a C++ Qt app without making it a KDE app. Thanks either way though!

Hm, that's true. Then I think the poppler library is enough.

Ranguvar · 2009-01-16 13:47:17

One last thing then - I've had some issues with poppler-based PDF readers (terrible quality fonts, image, but MuPDF (an enhanced version is behind the open source SumatraPDF app for Windows) has come through fabulously (as does xpdf's rendering and Adobe's). here's an example (if the link seems dead, keep refreshing): http://launchpadlibrarian.net/6805265/e … s_xpdf.png

More info here: https://bugs.launchpad.net/ubuntu/+sour … +bug/92296

Might be an idea, to try MuPDF instead of poppler

Basu · 2009-01-16 14:26:12

I'd like to avoid dependencies as much as I could (after all, if I make it a class project, I'll need to submit it and don't want my prof to have to install a bunch of dependencies). At the same time, if I integrated with KDE I could have search and indexing via Strigi, but I guess I could implement something via an SQlite db. I'll see. I haven't been very happy with native linux pdf readers in the past either. I suppose I'll have to spend some time doing my experiments with poppler and MuPDF. I'll need to talk to my prof to see if this is a viable project once I get back to college next week. I'll start making some plans in the meantime.

Last edited by Basu (2009-01-16 14:32:54)

dcrabs · 2009-01-16 17:48:28

Ranguvar wrote:

One last thing then - I've had some issues with poppler-based PDF readers (terrible quality fonts, image, but MuPDF (an enhanced version is behind the open source SumatraPDF app for Windows) has come through fabulously (as does xpdf's rendering and Adobe's). here's an example (if the link seems dead, keep refreshing): http://launchpadlibrarian.net/6805265/e … s_xpdf.png
More info here: https://bugs.launchpad.net/ubuntu/+sour … +bug/92296
Might be an idea, to try MuPDF instead of poppler

Sorry, but I have to disagree. Poppler originates from the xpdf-3.0 codebase. I think the problem of terrible fonts lies somewhere else. It is hard to believe that evince has bad fonts and xpdf good when the use the same libraries. When I had badly rendered fonts it was usually a problem of settings (antialiasing...) and it seems like evince has the problem in the bug report. Plus the bug report is quite old. Keeping Ubuntu's release cycles in mind it doesn't tell very much. That's at least what I think and experienced with Kpdf, Okular and one year of Ubuntu before I installed Arch.

Ranguvar · 2009-01-16 18:51:43

No... poppler is indeed based on xpdf, but all apps using poppler have failed me so far (evince, epdfview, okular), whereas xpdf, SumatraPDF, and Adobe work fine. This includes PDF-to-foo converters that use poppler.

Evince and xpdf do not use the same libraries - much of the xpdf code was written for the poppler libs that evince uses.

Plus, SumatraPDF/MuPDF blows away evince, etc. in terms of speed.

JonathanArcher · 2009-01-17 17:55:17

Quite some resonance here, at moment I don't have the time to test out everything since I'm in the middle of writing my diploma thesis and use JabRef for organizing. But after that I will take a look at all your suggestions.

And Basu, if you are really starting something like this, give us a call so we can test it

mutlu_inek · 2009-02-07 18:19:19

dcrabs wrote:

Basu wrote:
I need to make a personal project for my software engineering class next semester. I think that I could get started on a Papers-like program. The course uses C++ and Qt, so chances are it'll be a KDE program, though I need to find out a way to view PDFs first.
You can use okularpart for that. Unfortunately there are no examples that could help me using it. I tried using it with pykde4 but wasn't successful, probably due to my lack of gui programming skills.

FYI, Akregator uses okularpart. It opens PDFs in new tabs. You could probably have a look at its source code and find an easy way to implement it. I understand that some would be happier is a Papers clone would not depend on KDE, but recreating something like okular is not a piece of cake at all. It is a quite advanced file viewer.

And I think okular works great anyway. You can even annotate PDFs (though it does not edit them, but stores the annotations in separate files in ~/.kde4/share/apps/okular/docdata/ This has the advantage that you can give clean PDFs to others, but the disadvantage that the annotations are not easily transferable and lost (since they link to certain files), if a PDF is renamed and moved. I am using a fixed directory hierarchy for the PDFs (actually, I use Zotero, it is really great), so that is not a problem.

Arch Linux

#1 2009-01-11 10:31:02

Linux equivalent to Papers (Mac) / how are you organizing papers?

#2 2009-01-11 12:28:54

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#3 2009-01-11 12:30:28

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#4 2009-01-11 15:40:58

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#5 2009-01-11 16:16:08

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#6 2009-01-11 16:30:58

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#7 2009-01-11 16:35:13

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#8 2009-01-11 17:01:18

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#9 2009-01-11 18:42:34

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#10 2009-01-12 15:27:46

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#11 2009-01-12 15:43:05

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#12 2009-01-13 00:18:52

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#13 2009-01-14 12:01:00

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#14 2009-01-14 14:21:03

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#15 2009-01-14 14:33:28

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#16 2009-01-16 11:28:45

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#17 2009-01-16 12:12:56

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#18 2009-01-16 12:14:25

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#19 2009-01-16 12:35:10

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#20 2009-01-16 13:47:17

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#21 2009-01-16 14:26:12

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#22 2009-01-16 17:48:28

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#23 2009-01-16 18:51:43

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#24 2009-01-17 17:55:17

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

#25 2009-02-07 18:19:19

Re: Linux equivalent to Papers (Mac) / how are you organizing papers?

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