Comments on: Software to keep your PDFs and papers organized

By: Truong Nghiem

Truong Nghiem — Mon, 22 Feb 2010 06:16:31 +0000

I always prefer plain text and files instead of a database (I heard that zotero uses SQLite). Easy to back up, and I can sync them to Dropbox so I can access them anywhere. I also prefer BibTeX because I use LaTeX most of the time. Here is my setup:
- I use Jabref to manage a BibTeX file which contains all the papers/books references. Jabref is a very nice free software. It is written in Java (thus cross platform) and has full support for BibTeX. It can generate keys automatically (you choose the format). It can automatically search for files in a certain folder that are associated to a BibTeX entry, given that the files’ names start with the BibTeX key. Its import is not very good, so I often end up searching for BibTeX in my web browser and copy it manually to Jabref. Then I download the PDF/PS file and put it in a certain folder, rename it to the BibTeX key, then let Jabref attach it to the entry.
- I write my notes/reviews/comments of a paper in an ORG file in Emacs, save it with the same name to the same folder, and let Jabref attach it to the entry.
- On Mac OS, I use Skim to view and annotate PDF files, then save the notes in a file of the same name to the same folder, and (you guess) let Jabref attach it to the entry.

When I view an entry in Jabref, I can easily access the document and my notes/reviews by double-clicking on the files. One feature of Org-mode that I really like is links. When I write notes in Org-mode, if I need to refer to an entry in my BibTeX database, I just open the BibTeX file in Emacs, browse to the entry, press C-C l to save the location, then go back to my Org note and press C-c C-l to insert the link. Opening the link in the note will direct me to the corresponding entry in my BibTeX file. The link is dynamic: it can always find the correct entry even if the BibTeX file has changed, provided that the entry is still there. Very convenient.

By: dmj

dmj — Mon, 26 Oct 2009 07:43:56 +0000

@Knusper: Close, but I don’t use dwm but the Awesome window manager, too.

@Erwin: My environment is quite similar to Shrutarshi Basu’s. I use
the Awesome window manager on a Debian GNU/Linux system and the
network info, cpu, load etc. you noticed are simple widgets that run
in a widget box on the bottom of the screen. So it is not Screen[2]
that displays this information.

When I log into my graphical environment I start Emacs as a daemon and
spawn a graphical client for text editing. As you can see on the top
left corner of the screenshot I have two fixed “Tag” (i.e. virtual
desktops): one for text editing (“emacs”), one for browsing
(“www”). Awesome is configured in a way that firefox is always startet
on the www-tag and emacs on the emacs-tag, so I can switch between
these two applications with the cursor keys (while holding down the
“Windows”-key).

Depart from the integration of Zotero and Orgmode mentioned above I
make use of the org-protocol extensions and have a bookmarklet in one
of my firefox bars that triggers a org-remember action on the emacs
side and let me file a remember note with link and desription of a
website I find worth remembering.[3] Up to now I just took a quick
look on fireforg so I cannot tell anything about it.

The most delicious part of using window managers like dwm, Awesome,
XMonad etc. (=so called “tiling” window managers) is that they are
designed to be controlled by keystrokes so my usage of the mouse is
limited to browsing and working with Zotero.

[1] http://awesome.naquadah.org
[2] http://www.gnu.org/software/screen/
[3] What are normally websites that contain information on a topic I
deal with in orgmode.

By: Shrutarshi Basu

Shrutarshi Basu — Mon, 26 Oct 2009 03:11:35 +0000

Erwin, I don’t know where that screenshot is from, it’s not my setup. Personally, I use the Awesome window manager with Emacs for text editing. I also use GNU Screen with the XFCE terminal as my terminal setup. There is a line at the bottom of Screen which has a clock and how many terminals I have open. I don’t really use a global system line of any sort because I don’t really care about how much CPU I’m using and my laptop is normally always plugged in.

By: Knusper

Knusper — Sun, 25 Oct 2009 22:05:18 +0000

His WM is obviously DWM

By: Erwin

Erwin — Sun, 25 Oct 2009 19:03:51 +0000

Hi,
A bit off topic, but I’m very interested in setting up a minimalistic emacs environment to be used in conjunction with zotero, org-mode and fireforg.
From what I can see from
[5] http://s7b.directupload.net/images/user/090628/nqwweuf2.png
You somehow have network info and cpu info available on screen.
Might I ask to describe a bit your environment?
I’d be interested in testing a similar setup for myself.

Thanks a lot!

Erwin

By: From Xournal to org-mode notes « Delta Improvement

From Xournal to org-mode notes « Delta Improvement — Thu, 22 Oct 2009 07:42:47 +0000

[...] would appreciate any suggestions for improvements and I would like to thank Shrutarshi Basu, whose post was the starting point of this [...]

By: Jesse

Jesse — Thu, 30 Jul 2009 21:34:11 +0000

Thank you for writing such an excellent review! I do like your org-mode method, but I don’t like the idea of manually entering BibTeX information either.

Since zotero can store attachments with each record, I wonder if it would be feasible to keep a .org notes file associated with each entry. Ideally zotero searches would also look in these notes, and when you go to read a document, you could also open the .org attachment, and zotero would launch an emacs session.

Does zotero keep these attachments as plain files somewhere, or are they placed inside its sqlite database?

By: Paulo Jorge Matos

Paulo Jorge Matos — Mon, 20 Jul 2009 16:53:18 +0000

I have tried mendeley. Good piece of software, give it a try. Found, however:
- that it is not intuitive (if possible) how to export a couple of papers into a bib file;
- mendeley categories don’t match those of bib;
- you can’t change the bib description manually;

By: Mr. Gunn

Mr. Gunn — Tue, 14 Jul 2009 01:08:51 +0000

If you want PDFs, exportable BibTeX, and annotation, you should give Mendeley a try. You just feed it a directory of PDFs and it extracts the citation info for you. The new version, 0.9, also has a built-in PDF viewer that allows you to annotate the papers. It's cross-platform desktop software, so it'll work on PC, Mac, and your Linux box. That's an ingenious bit of scripting you've done, to be sure, but perhaps Mendeley could handle your reference management needs? FYI - I'm working with the guys at Mendeley, so if you have any comments or suggestions about how to make it work better for you, I can pass them along to the developers.

By: Shrutarshi Basu

Shrutarshi Basu — Mon, 29 Jun 2009 00:11:57 +0000

@Knusper: I’ll be putting my script (and others that I’ve written) on github soon
@dmj: I get most of my papers from sources that have BibTeX info readily available so I just spend a few seconds copy pasting into an Emacs buffer and changing the key to my own format. if I start having to deal with papers that don’t come with their BibTeX I’ll seriously consider Zotero and the script you linked to. Thanks for that.