From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ramon Diaz-Uriarte Subject: Re: zotero (or mendeley) integration with org Date: Sat, 26 Mar 2011 22:06:47 +0100 Message-ID: References: <26045.1301154464@rgc.damtp.cam.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Return-path: Received: from [140.186.70.92] (port=58936 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1Q3ahI-0006ca-OA for emacs-orgmode@gnu.org; Sat, 26 Mar 2011 17:07:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Q3ah7-0007ny-Cg for emacs-orgmode@gnu.org; Sat, 26 Mar 2011 17:06:50 -0400 Received: from mail-fx0-f41.google.com ([209.85.161.41]:37960) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Q3ah7-0007nd-3c for emacs-orgmode@gnu.org; Sat, 26 Mar 2011 17:06:49 -0400 Received: by fxm18 with SMTP id 18so2266581fxm.0 for ; Sat, 26 Mar 2011 14:06:47 -0700 (PDT) In-Reply-To: <26045.1301154464@rgc.damtp.cam.ac.uk> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Stephen Eglen Cc: emacs-orgmode@gnu.org Dear Stephen, [My ---long--- comments refer only to Mendeley, not org, so maybe this should be off-list]. On Sat, Mar 26, 2011 at 4:47 PM, Stephen Eglen wrote: > There was a mail-thread lastyear about zotero and integration with org. > Now that there is an alpha release of 'org-standalone' > =A0http://www.zotero.org/blog/2011/02/ > > has anyone looked at whether this helps integrate org and zotero? > > I've not yet switched to a pdf manager (they're all stuffed into a > folder, with a few subfolders, and the only meta-data is in the > filename!), so I'd appreciate hearing what others to do to look after > their pdfs. =A0Mendeley is a possibility too (although syncing between > machines is a must, and Mendeley doesn't offer that yet.) > I've been using Mendeley for about 9 months now, after spending a few weeks examining how Mendeley, Zotero, and some other options, fitted into my habits. Here are some comments about your questions: 1. Syncing: the "orthodox" Mendeley way allows for two options: a) you sync the database of the refs (not pdfs) via their servers; b) you also sync the pdfs, which will most likely require you to pay for storage in their servers if you have a decent number of pdfs. However, I do the syncing myself. I've used rsync, then Dropbox, and for the last four months Wuala. I sync the directory where the dbs are (~/.local/share/data/Mendeley Ltd./Mendeley Desktop) and the directory where I store my pdfs. I have had this set up for the 9 months, shared between four machines, and it works fine (I try not to have Mendeley open in more than one machine at the same time, to prevent problems, but have never run into any). 2. All pdfs into a folder with a few subfolders. In Mendeley you can have each reference under its own subdirectory with some limited flexibility for the naming of the subdirectories (author, date, title, etc). Its not ideal (e.g., I dislike spaces in directory names), but I like it better than Zotero's (names of subdirectories are a random string). Keeping each ref in its own directory allows me to store other stuff (e.g., code, suppl. mat, etc) in the same place as the pdf. Now, that said, I am not all that happy with Mendeley. To begin with, Mendeley is not free software. Zotero is, but the naming of directories and the lack of a built-in pdf editor were a no-go for me. Mendeley's pdf editor allows me to underline and add notes to pdfs. At least in Linux, adding comments and underlining pdfs is not yet well solved: evince currently allows comments in the devel. version, but no underlining. Okular allows comments and underlining, but stores them in ~/.kde/share/apps/okular, which I dislike (it seems very fragile), and in okular you cannot underline a single column in papers with multi-column setup (another no-go for me). However, with Mendeley's pdf editor/viewer you can only display one pdf at a time, which is a pain if you want to compare two or more papers side by side. In fact, Mendely's pdf viewer is rather under-powered compared to, say, okular (e.g., lack of keyboard shortcuts for viewing to page or width size, difference between scrolling and moving to next page, fast searching, etc). If I only need read-only access to the pdf, even from within Mendeley, I use another pdf viewer. I thought about going back to JabRef, and using recoll for searching over all of my pdf collection (I like recoll's search much more than Mendeley's one). But that leaves unsolved the pdf commenting issue. Also, I like the ease of adding papers with Mendeley (e.g., when searching in the web, or its generally successful extraction of metadata from a paper's pdf); in fact, I find adding papers is even easier with Zotero (and friendlier also if you add things like web pages, etc). I also looked into paperpile, but I find it to be much more beta than Mendeley, and so far less flexible in almost everything. So I'd also like to know how others are dealing with pdfs. Anyway, and in spite of my complaints, since about 9 months ago I have not printed a single paper. It is great to have all those pdfs synced among my machines, be able to search them quickly, and not carry around kilograms of dead trees. Best, R. > Stephen > > --=20 Ramon Diaz-Uriarte Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz Phone: +34-91-732-8000 ext. 3019 Fax: +-34-91-224-6972