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

Zibi1981 · 2009-02-09 18:37:09

Hi!
Recently I switched from KBibTex to JabRef, as the first one offered less functionality. Now I'm trying to make use of OpenOffice plugin for JabRef. I know it's not finished yet, but maybe someone know how to make it insert not only citations to the text, but also references at the end of the document. It's very important, as you all know.

mintcoffee · 2009-02-11 22:32:08

I recently stumbled upon Radical Codex ... a comic / ebook organizer. It looks like it may be good enough for categorizing papers, anybody want to try making a PKGBUILD out of it?

dcrabs · 2009-11-21 10:28:23

I know that's an old thread but there is the perfect program now: www.mendeley.org

leeyee · 2009-11-21 11:35:15

As an EE student, I would highly recommend JabRef for organizing papers in Linux, it is quite useful especially when you are using LaTeX and mostly referring to IEEE papers, because it supports automatically search bibtex entries on IEEExplore. The possible difference with iPapers(I didn't use it) is that JabRef needs to link files mannually or automatically by matching titles/bibkeys.

dcrabs · 2009-11-21 13:03:38

Did you even check out mendeley? If you would have, you would have seen that not all those features are available but it also features a fulltext search, included pdf-reader, feature extraction from pdf' and online synchronization/sharing of your pdf's with other users. There is also a plugin for openoffice.
Maybe it is only me but compared jabref is a pain to use.

Stalafin · 2009-11-21 14:04:23

dcrabs wrote:

Did you even check out mendeley? If you would have, you would have seen that not all those features are available but it also features a fulltext search, included pdf-reader, feature extraction from pdf' and online synchronization/sharing of your pdf's with other users. There is also a plugin for openoffice.
Maybe it is only me but compared jabref is a pain to use.

This is great, thank you very much! Looks a little bloated, but apart from that it seems like a very decent tool. I will definitely check it out.

Love these forums - already found lotsa useful programs just checking the forums (Impress!ve for LaTeX Beamer presentations for example ).

joaca_rj · 2009-11-21 15:52:04

Mendeley sure seems to be a real nice program.... it even search the net for related papers!..Shame it's not open source....

bender02 · 2009-11-21 15:59:42

I recently came back to zotero, a plugin for firefox. I think it's comparable with mendeley, especially the beta which allows to sync the database with the server and the linked pdf's with my own webdav, which means that I automatically have the same database and pdf's on all the computers I use (laptop and work desktop). Another thing that was critical for me is mathscinet support (which mendeley doesn't have) - it's pretty neat, you just browse mathscinet (or google scholar or I suppose other online databases as well), and when you're looking at an entry which you want to save, you click on an icon, and you've got it in the database.

big_gie · 2009-11-21 18:19:37

Mendeley has something similar. You bookmark something a scriptlet, and when you want to add the page you're on, you click that bookmark and it will add it to your database.
It's called webimporter: http://www.mendeley.com/import/

dcrabs · 2009-11-21 18:47:05

There is always the possibility to make suggestions to mendeley if a feature is missing.

bender02 · 2009-11-21 18:56:07

dcrabs wrote:

There is always the possibility to make suggestions to mendeley if a feature is missing.

yea, there's a request for mathscinet (and was there when I wanted to file one the first time I used mendeley, which could be maybe about a year ago)... still no progress
there are probably not too many mathematicians using mendeley, so there's not enough pressure on them.

R00KIE · 2009-11-21 19:59:57

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

MuPDF fails miserably with this pdf http://www.ime.tsinghua.edu.cn/szdw/bod … AS2008.pdf maybe its just a problem here but it does fail miserably. Epdfview does display it correctly ..ish there is the problem of terrible font rendering. Xpdf displays it perfectly. Also lately I've been noticing that epdfview sometimes takes a really long time to display some pages of some pdfs (seems almost like it hangs).

More on the topic, great thread here, I just don't organize anything properly but from now on I guess I'll have no excuse

MartinZ · 2009-12-08 21:20:42

dcrabs wrote:

I know that's an old thread but there is the perfect program now: www.mendeley.org

Thanks a lot, didn't know Mendeley. It is truly what I was searching for and works very good. For those who don't know, it's already available in AUR: http://aur.archlinux.org/packages.php?ID=27149

JonathanArcher · 2009-12-08 21:32:48

Yes, thank you very much, I will also try it out, sounds very promising. So far I still only use the mac with "Papers" at work.

lastpook · 2010-01-13 11:17:19

Yet another kudos for Mendeley from me. I've used it when was writing my diploma thesis in Chemistry (in windows, before switching to linux). After messing a bit with conversion of BibTeX to OO Base format I've got nice bibliography. Now it's time to organize my papers for postgraduate routine.

Last edited by lastpook (2010-01-13 11:18:06)

essence-of-foo · 2010-01-13 15:20:49

The only thing I've tested so far is http://www.citeulike.org. It's completely web based and includes some social networking functions but it's easy to stay anonymous if you don't like the social part of the site.

You can enter a URL, a pupmed-id, a DOI or ISBN and citeulike will get all the metadata for you. The references can be exported in different formats, including BibTeX.

redguardtoo · 2010-01-14 02:52:30

R00KIE wrote:

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
MuPDF fails miserably with this pdf http://www.ime.tsinghua.edu.cn/szdw/bod … AS2008.pdf maybe its just a problem here but it does fail miserably. Epdfview does display it correctly ..ish there is the problem of terrible font rendering. Xpdf displays it perfectly. Also lately I've been noticing that epdfview sometimes takes a really long time to display some pages of some pdfs (seems almost like it hangs).
More on the topic, great thread here, I just don't organize anything properly but from now on I guess I'll have no excuse

You're right. Pdf viewers based on poppler are usually more compatible with most PDFs because it has been developed for so many years. It's obvious Ranguvar's problem is among the configuration of fontconfig, try to google "fontconfig poppler" and make sure "poppler-data" package has been installed.

Here are the comparison of PDF engines.
* xpdf
Its author stop releasing latest code since version 3.02, so the xpdf's engine is a little outdated now. Its font detection method is simple and a little hackish, works in most cases but won't give you the best font matching result.

*poppler
based on xpdf and better in every respect. The only downside is it uses fontconfig to match the external fonts which is a little complicated.

*mupdf
Lightweight engine and much more efficient than poppler but supports less PDFs.

Last edited by redguardtoo (2010-01-14 02:53:07)

jack.mitchell · 2010-01-14 10:41:52

R00KIE wrote:

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
MuPDF fails miserably with this pdf http://www.ime.tsinghua.edu.cn/szdw/bod … AS2008.pdf maybe its just a problem here but it does fail miserably. Epdfview does display it correctly ..ish there is the problem of terrible font rendering. Xpdf displays it perfectly. Also lately I've been noticing that epdfview sometimes takes a really long time to display some pages of some pdfs (seems almost like it hangs).
More on the topic, great thread here, I just don't organize anything properly but from now on I guess I'll have no excuse

I've noticed a slowdown of epdfview recently, looking to change myself really.

D-Locked · 2010-01-14 20:25:57

Just tried Mendeley desktop and I'm positively impressed. However, I noticed it has a "beta" tag under it.
Does anyone know if it will remain freeware once it's out of beta?

D-Locked · 2010-01-27 23:36:29

To answer my own question:

Mendeley-FAQ wrote:

Is Mendeley free?
The straight answer would be yes and no. Yes, it's free, because: Everything you get when you sign up to Mendeley is completely free and will always remain free - including the features described in What is Mendeley?
No, it's not completely free, because: At a later point in time, we will expand upon the existing features and introduce additional ones for professional users – these will be available for a (very reasonable) fee.

mutlu_inek · 2010-01-28 03:24:53

You should really give Zotero a spin. It is fully F/OSS. Its 2.0 version is in RC and was very usable (in fact, I did not experience a single problem) even during its long beta cycle. It works really well if you work with university library online portals. It also does nice things like integrate with Openoffice or backup your entire library to WebDAV.

Last edited by mutlu_inek (2010-01-28 03:25:29)

andreamer · 2010-07-06 01:35:36

You should try Mendelydesktop http://aur.archlinux.org/packages.php?ID=27149
Its really the best i've seen for paper organization compatible with linux.

eDio · 2010-07-06 06:18:21

I like Mendeley desktop (it is available from AUR).
It is closed source but free.
Supports syncing, so your papers will be with you wherever you want.
It is veeeery simple to use. But still powerfull.
You can copy reference just by hitting ctrl+C in main window. There are many predefined styles of references, also you can create your own.
It can create references in OO.o and MS Office via supplied plugins.
It works on Windows and Mac OS too.

whacath · 2010-07-06 07:30:32

Does mendeley store any information online by default? I kinda get that impression at first glance of their site.

tkdfighter · 2010-07-06 12:34:12

whacath wrote:

Does mendeley store any information online by default? I kinda get that impression at first glance of their site.

Although you can use Mendeley Desktop standalone, the whole point of Mendeley is to share papers online. It's more of a social networking site for scientists, really. I once got to speak with one of the founders, he actually compared Mendeley to Facebook. I must say that they do take their users more seriously, though.

Arch Linux

#26 2009-02-09 18:37:09

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

#27 2009-02-11 22:32:08

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

#28 2009-11-21 10:28:23

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

#29 2009-11-21 11:35:15

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

#30 2009-11-21 13:03:38

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

#31 2009-11-21 14:04:23

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

#32 2009-11-21 15:52:04

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

#33 2009-11-21 15:59:42

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

#34 2009-11-21 18:19:37

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

#35 2009-11-21 18:47:05

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

#36 2009-11-21 18:56:07

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

#37 2009-11-21 19:59:57

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

#38 2009-12-08 21:20:42

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

#39 2009-12-08 21:32:48

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

#40 2010-01-13 11:17:19

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

#41 2010-01-13 15:20:49

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

#42 2010-01-14 02:52:30

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

#43 2010-01-14 10:41:52

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

#44 2010-01-14 20:25:57

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

#45 2010-01-27 23:36:29

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

#46 2010-01-28 03:24:53

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

#47 2010-07-06 01:35:36

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

#48 2010-07-06 06:18:21

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

#49 2010-07-06 07:30:32

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

#50 2010-07-06 12:34:12

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

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