OT-Replacement for Papers from Mekentosj

< Next Topic | Back to topic list | Previous Topic >

Posted by jamesofford
Oct 29, 2014 at 10:37 AM

Good morning:
I realize that this is off-topic in that it is not about outliners or general purpose information managers, but this group has a wide experience, and I can’t really imagine any other place where the expertise to answer my question could live.

I am an academic, working in biological science at a Big Midwestern University. As an academic, my writing world consists of grants, research articles, and review articles. All of these require bibliographies, and I also maintain a large set of pdfs on my computer so that I can write and cite. In the old days, when I was in graduate school(My first computer was an IBM with two 5 1/4 floppies-I’m that old.)most of the time I schlepped over to the library, searched through paper indexes(indices?), copied the papers that I needed, and then had to enter each of them by hand to cite them. Now, in the 21st century I can search and download the pdf from my computer, and maintain my own library of pdfs for use in my writing. The creation of bibliographies is also now coming into the 21st century and there are several different programs that you can use to do your bibliography management, especially on the mac.

Endnotes was the first, and is still the most popular choice, but I don’t really like it much. It does bibliographies, but doesn’t do a good job of managing the pdfs.

For some time I have used Papers from Mekentosh(http://www.papersapp.com/). I started with version 1, and have upgraded each time an upgrade became available. Version 1 was okay, version 2 was a big upgrade, and it has worked well for me. It does everything that you need in a bibliography manager. You can search from within the program, import pdfs, the program searches out the title, author and other metadata and populates the appropriate fields. It can then help you build the bibliography in your word processor(at least in Word), and formats the bibliography for your submission. I am up to version 2.7, and it works great.

Things have gotten less rosy with version 3. There are lots of bugs, and many things that version 2.X did well, version 3 does poorly. I have had several interactions with their customer service people, and I am still not happy.

I have several big writing projects coming up including a couple of grants, a couple of papers and a review. Before I get started I thought that I would check around and try to find a new program.

I have looked at, and don’t really like Zotero and Mendeley. I prefer to have my stuff locally. I often turn off the internet when I am writing to keep distractions to a minimum so I need something that works locally.

On the mac, there are several programs that do what I want them to do. Papers, Sente(http://www.thirdstreetsoftware.com/site/Sente.html), and bookends(http://www.sonnysoftware.com/). I am thinking of moving over to one of those two.

My question-Do any of you have experience with either of these two programs? Can you point me to a good review of either, and/or a good comparison of the different programs?

My apologies for such a long post, and thanks for taking the time to read.

Jim.

Posted by Prion
Oct 29, 2014 at 05:37 PM

Hi Jim
this question is not OT in my opinion. Outlining is about structuring material and adding references is one particular (external) kind of structure you can give to your manuscript.

Reference managers…..there is a lot going on here. I have in no particular order worked with Endnote, Sente, Papers, Zotero, Bookends and Mendeley.
Papers 1 was good but lacked citation capability, Papers 2 was a big drama when (or rather how) it was released but after some months of constant fixing reached a very usable state, I enjoyed working with it. It was well thought out in that important things were easy to do and worked well. I was shocked to see history repeat itself when Papers 3 came out. If anything, it was a very early alpha, Dropbox sync never worked for me even months after it came out, support was very slow, data loss, buggy and rather haphazard metadata assignment, etc etc. Because I really liked Papers 2 I kept trying but ultimately gave up and returned to Sente. Shame, but I lost my confidence in the development team and their priorities, it seems they have moved on to develop yet another app (findings).

Sente has for a long time had rock-solid synchronization between Macs and even iOS devices. Each device has a complete database locally with all the metadata and it is up to you to decide if you also want to have all the PDFs locally, the alternative would be to store them locally on request. At this moment in time (download of pdf) you obviously have to have access to the internet but other than that everything works offline as well. Also note-taking has been solved well. If these two things (synchronization and note taking) are high on your list then take a close look at Sente. It is brilliant in what it does, synchronization works silently in the background and you don’t even have to think about it or initiate the sync. There are some things the developers have never tried doing, some of which I consider a nuisance. The document format for attachments is PDF and only PDF. Several journals in my field provide supporting information as XLS or DOC files which oddly cannot be attached. No deal breaker but strange. Also, emailing a record or PDF to someone is less well supported than what you are used to in Papers. You have to drag and drop en entry into an email that you have to initiate in mail first, hopefully the dnd gesture has the format you wanted selected or else you’ll have to fix that and then you’ll have to reveal the pdf in the file system and drag it over to the mail you have been composing. Works but could be solved more elegantly.
Targeted browsing works but duplicate detection inside the database sometimes doesn’t.
A big plus for Sente is that it makes good use of hierarchical tagging to organize papers. If you want a paper to appear in several collections at once without having to duplicate it first, Sente does it beautifully, needless to say this information is present on all your devices.
It is costly, however, and although I do consider it worth the money they are asking for it, the downside is that I cannot easily share a database or collection with my students for whom money might be more of an issue.

Bookends has perhaps the most reliable metadata detection and curating capabilities of any of the programs we are discussing here as well as undoubtedly THE best support. Synchronisation is not nearly as trouble-free as Sente’s as you will have to remember which of the computers has the most up-to-date database and will have to be designated the “master”. If you work on two different references on two different computers (adding, modifying or commenting them) then Bookends will lose the changes you did on the “slave” whilst Sente will merge the databases and retain changes done on both sides. With careful planning you might be able to trick Sente into colliding edits but in several years of usage this has never happened to me.

For the moment I am using Zotero and will see how it goes. It is free and sharing a (sub)collection with any of my students is simple.
Big plus is the informative and civilized forum. Zotero also has some features I was missing elsewhere, too: It allows indexing of the pdfs, so a search within Zotero would either search the metadata (title, author etc) or include the content of the PDFs if I so choose. BTW, the content is completely local on every machine. What you might have interpreted as an indication of online-only is merely a dedicated infrastructure you _can_ use to keep many machines in sync but you don’t have to. If you do, though, syncing is capable of looking at each entry separately rather than treating the database as a monolithic entity as Bookends. For the time being I keep the database without PDFs on Zotero’s server and sync the PDFs myself, hence I don’t have to pay because the metadata-only database is small enough for around 3000 entries to be accommodated within the free allowance.

Keep in touch, I do suspect that we are not the only ones looking into this, best of luck
Prion

Posted by Dr Andus
Oct 29, 2014 at 06:47 PM

I don’t have a Mac but I’m just flagging it up as another option: Citavi running in a virtual machine

http://support.citavi.com/forum/viewtopic.php?f=26&t=3718

http://www.citavi.com/sub/manual4/en/installing_on_a_mac.html

Back to topic list