Bibdesk. Bibdesk as a. Bibliography. Manager. Export to Other BibTEX and Bibdesk for Beginners .. hyperlink, , Skim Notes. BibDesk is a BibTeX editor and reference manager. Because it is a BibTeX editor, it is important to understand at least a few things about the BibTeX file. Customizing the Table. You can control the order of the columns by moving them directly. To add a field that isn’t displayed, use the column management menu.
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Folks have been clamoring for a Papers vs. BibDesk post and here it is, finally. This topic has been discussed elsewhere and is sure to be visited many times in the future on AstroBetter, so consider this post just one part of a much bigger discussion.
There are different things to look for in an article management tool. I want my app to be as one-stop shopping as possible: I want to be able to search, import, organize, assign BibTeX cite keys, and annotate all in one place.
BibDesk does most of those things while, as far as I can tell, Papers really only excels at searching and importing. Also consider Mendeleywhich is both a desktop and artach article organizer. I would not buy it if I knew this in advance. Victor, re 3, you can customise the way BibDesk exports stuff. Some kind of academic database. I was just having the same problem with BibTex export — are you willing to share your script?
Does it still work? Papers can handle very well cite-keys. You can customize them yourselves, or have Papers do it bindesk you. Papers can import an existing bibtex file. That could be good or bad.
Using BibDesk to organize PDFs of research papers
I have some scripts I wrote to interface between quicksilver and ads-search without my browser. I also open my pdfs this way. Now that I see that bibdesk is open source, it provides the framework necessary to put together my dream — metadata, pdfs, ads search, astro-ph, and user notes, all within quicksilver, all while managing my bibtex behind the scenes.
Looks like I will jump on-board contributing to bibdesk!
I actually purchased a Attafh for Papers when I was writing my thesis, and transferred my bibliography over from Bibdesk to Papers. A few months ago, I switched back to Bibdesk. What I like about Ibbdesk is that it is very lightweight. Papers is too slow when dealing with thousands of references.
I find it much easier to search for references using ADS via the web browser inside bibdesk than using the search feature in Papers. Another issue is that last time I checkedPapers still did not bibdfsk custom citekeys. I like to use Author: Page, and there is no way to specify custom keys in Papers. I tried to map the Journal keywords for a bunch of articles but this produces a unpleasantly long list of singletons.
I purchased Papers about a year ago and I still use it, but only for perusing my library of PDF files.
How to insert citations with LaTeX using Bibdesk and the Google Scholar Button
When it comes to dealing with references I actually use Bibdesk to clean up the export reference file from Papers. I do agree that the power of BibDesk is ultimately its open-ness and scriptability.
One attacg that I have is replacing astro-ph articles with the published version, once the published version becomes available. An automated tool could do this; e. If someone wants to take that on, that would be awesome. BibTeX may be better at sorting and searching references, but I spend far more time reading articles than I do making citations. I hardly print anything ever anymore. I love the fact that Papers syncs with my iPhone. Tom — thousands of references?
Is this something you have written up anywhere? I am using zotero which is a add-on to firefox http: I am pretty happy with zotero. However, you can open the pdfs with only one click using your favourite pdf reader. One of my collaborators introduced me to papers. It has a generic bibtex importer and will fetch abstracts automatically from ads.
You can browse and search the references like you normally would, and it also has a category view. You can create a category tree and put any reference in as many categories as you like, and so it acts much like a bookmarks menu.
Not much in the atttach of documentation right now…. For me, Papers and BibDesk are actually complementary. I use Papers for xttach my pdf, references, etc. I just find Papers fantastic for searching within the pdfs, ior using the smart folders and collections. Then, when it comes to write a paper, I export a.
Very happy with the result so far. A major step forward would be for Papers to recognise changes made in the.
But apart from that, I really think that both are equally useful in their own way. One of the biggest diferences noone has mentioned is support for supplementary material.
Why I use BibDesk instead of Papers
Many articles may involve more than just pdfs. Bibdesk supports any type of file images, docs, bookmarks while Papers only supports pdfs. More importantly, bibdesk allows you to link all those files to the same record, which Papers still does not allow at least easily. Several of my colleagues have the same issue. I use the JabRef, which is java based.
From the description above, it sounds very similar to BibDesk. The advantage here is that it is cross-platform, and so can run on Linux, Mac or Windows. Its native database format is bibtex. So my solution is bibtex db plus the jabref. I was a Papers fan I even bought the mobile app for iOS.
Moved to Lion OS on my Mac. I would need to re-pay to get Papers 2. I consider the idea to re-pay for a minor update of Papers quite ridiculous. I will stay with BibDesk. Just run the script every week or two, and it should keep the bib library up to date. Very easy to use, and one of the last pieces missing for Bibdesk to be a perfect tool for my needs.
The very last piece is a way to make my bibliographies list the arxiv identifier for arxiv-only entries, and only for the arxiv-only entries.
This thread still seems active so a couple of updated comments may be useful. I have been a long time user of both BibTeX and Papers so my comments below are hopefully not too biased! With the previous version, I systematically had to clean my exported.
Still hoping for a two-way editing of.
Used correctly, I found it to be a fantastic tool to create a quick summary of the main points in a paper. I use this extensively and it saves me a heck of a time.
Adding PDFs to BibDesk
So, annotations is another area in which Papers has drastically improved. Papers2 has much improved after this BibTeX vs Papers review was posted. Most of the points mentioned above and very relevant at the timeare not all relevant anymore. I like to have every paper I read carefully in one place and exporting that library as a BibTeX file for citing. Simple things like switching tabs or scrolling through the list of papers involve watching a spinning beachball for multiple minutes.
ADS import used to be quick but now takes forever. It syncs iPad to desktop via Dropbox but not iCloud, but my library is way too big to fit in my Dropbox quota. I do have plenty of space to sync via iCloud. Currently I keep papers manually in an iCloud Drive folder, with macOS color-coded tags for organization, and markups syncing across devices. Notify me of followup comments via e-mail.
Let Snow Leopard Roar. Bibdesk Keywords play a starring role in BibDesk, occupying the left column in the main page while in Papers they are bibdesm in Notes. This ability to easily tag articles with multiple keywords and then search based on them is a huge advantage of BibDesk over Papers but I think Papers will catch up soon.
Preview is a can of worms that I choose to leave for tatach day.
Improved annotation functionality and integration with Skim is likely for future versions of Papers. Papers Papers auto-magically imports articles and metadata and downloads the PDF while importing an article into BibDesk is usually a multistep process. BibDesk tatach have a Papers-like single-click import for articles on arxiv. Getting this functionality built into BibDesk would rock.
Again, a full discussion of BibTeX is left for another day, but suffice it to say, being able to assign memorable cite keys to articles is important.