Macs in Chemistry

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Reference Management

Bookends Updated

 

The popular reference management application Bookends has been updated. This looks to be a significant update with many bug fixes.

  • Fixed a bug that could cause mangled reference metadata to appear in the reference list.
  • Fixed a bug where editing the Notes field on the main tab would not update the Notes field in the Notes tab.
  • Fixed a bug that could cause an error to be thrown if you edited a tag while the tag cloud was showing and then clicked on the tag cloud.
  • Fixed a scanning bug that prevented the year from being output when a citation used the year-only modifier (%) and had cited pages.
  • Fixed a bug where the font size of scanned in-text citations would be different from that of the paragraph's style sheet.
  • Fixed a bug in excluding words from capitalization where words consisting of a single accented character were ignored.
  • Fixed several bugs in case conversion that affected Title Case and Sentence case.
  • Fixed a bug that resulted in malformed citations if you scanned a Word document twice in the same session with an Author-Date format.
  • Rating stars in the list view can no longer appear as white on a white background in refs that have been assigned a color label.
  • Fixed a bug in Find in This Reference.
  • Fixed a problem that prevented dropped text onto a note stream from being added to the new notecard.
  • Cited Pages once again work in scanned text files. Bookends Server works once again.
  • Fixed a problem where a Find/Replace with styles could change the style for an entire field.
  • Fixed an issue with JSTOR where the search would have to be done a second time for it to succeed.
  • Corrected the escaped BibTeX output for é.
  • Importing metadata from Web of Science in Bookends Browser works again.
  • The Key field, if shown in the reference list, will update automatically if you use Refs -> Generate BibTeX Key.
  • Fixed a bug where an author's surname was always used if a secondary order field in the format had content, even if the popup told Bookends to use the same name format as the first time.

Bookends on Tap and Bookends on Tap lit the corresponding applications for iOS are unchanged.

There is a list of reference management applications for Mac OSX here.

Comments

Papers3 for iOS updated

 

Whilst Papers3 remains an extremely popular desktop reference management application Papers3 for iOS has come in for some criticism, in particular poor synchronisation with the desktop and the use of unintelligible file names. The latest version seems to address some of those concerns.

What's New in Version 3.1.5 New:

  • Supplemental file support.
  • Sharing PDFs via email now use human readable file names.

Stability fixes:

  • Fixes a crash related to syncing.
  • Improved performance on syncing.

Other:

  • General bug fixes.
  • Improved general appearance on iPhone.

The Mobile Science website contains more science apps for iOS.

Comments

Papers3 for iOS Updated

 

I see that Papers3 for iOS has just been updated to version 3.1.1.

This version now includes article level metrics (Altmetrics) on the article you're reading now available in the landmarks view (PDF reader).

  • General bug and stability fixes.

  • Improved performance on syncing.

There are more science apps for iOS here http://www.macinchem.org/mobilescience/.

Comments

Papers 3 has just been released

 

The hugely popular reference management application Papers has just been updated. Papers 3 has a new cleaner interface and a host of new features.

Papers3

The mobile app Papers 3 for iOS has also been updated.

Comments

Reference Tracker Updated

 

The popular reference management package Reference Tracker) has been recently updated and fully supports Mavericks.

Improved ISBN lookup. Improved article search.

Fixed a bug where incomplete reference styles could be shared to the cloud. Fixed a bug where ISBN lookup results could be imported with missing data. Fixed a bug where open link buttons in documents could reposition incorrectly when the document window was resized. Fixed a bug that could cause Reference Tracker to crash on startup on OS X 10.7. Fixed tabbing between fields in the Publication Search sheet.

I also note that there is a special offer at the moment

Reference Tracker is available at a special 30 % discounted price until 30 November 2013!

There is a list of reference management applications for Mac OS X here.

Comments

Papers 3 beta

I see that the new version of the reference management application Papers is now out for beta test. Reading through the release notes this looks like it will be a major upgrade, perhaps the most significant change is the use of Dropbox for syncing between devices making it easier to get access to your references. This sounds excellent however I do know of some institutions that prohibit the use of Dropbox so I was interested to see that “other cloud based syncing services in addition to Dropbox to follow”.

In addition there is:-

  • A fresh, new user interface: the new Papers experience is simpler and more organised.
  • Navigation modes to keep your work and thoughts organised.
  • Relevant article suggestions based on the content you are reading.
  • Automatic PDF download when you import articles.
  • Better than ever metadata discovery and matching.
  • Stay connected: discover tweets and posts about the articles you are reading.
  • View and annotate supplemental files directly within Papers 3.

Papers 3 will require Mac OS X Lion and above.

There are more reference management tool here.



Comments

Pubchase Updated

PubChase is a science literature search and recommendation tool, available online and on your mobile device. It has recently been updated to include cloud-synced PDF support, making PubChase truly mobile. Users can now add/delete library PDFs on the web and iPad, with ability to view the PDFs on the iPhone as well.

They have rolled out a social network component on PubChase. This allows users to subscribe to libraries of others and to see a feed of recently-added papers by those in their network. Offering automated personal recommendations and social-based literature discovery.

They have also launched a backstage-stories series to add a personal layer to published research. This and next month, they are publishing a story per week, by invitation. However, after it is established they will open the posting to the authors themselves, thus creating an article-centered tumblr for scientists. (The first essay was http:www.pubchase.com/essay/my-break-up-nature-paper-by-meleah-a-hickman-4) An interesting idea and well worth a look.



Comments

Bookends Updated

Bookends 12 has been rewritten from the ground up. It includes configurable spell checking, database journaling, integration of the built-in browser with the library window, enhanced formatting options,.

The full release notes are here

There is a page of reference management applications here



Comments

A couple of updates

The point and click data analysis tool Wizard Pro has been updated. In particular this update address a couple of issues

  • Preserve filter selections when switching between tables
  • Correctly parse numbers surrounded by spaces in CSV files 
  • Fix a bug where a blank header cell in an Excel spreadsheet caused subsequent columns not to be imported 
  • Fix some issues with PDF export of model images
  • Fix a crash when stacking tables with indicator variables

The Reference Management package Bookends has also been updated,

  • Get DOI was updated to deal with changes made by CrossRef
  • This includes dealing with changes made in the way CrossRef encodes accented characters.
  • Updated Import From Existing Bibliography to deal with changes made by CrossRef
  • Updated Bookends browser to detect DOIs on the Google Scholar web site to deal with changes made by Google



Comments

Papers2 version 2.5 released

There has been an update to the very popular reference management application Papers2, this update introduces two new annotation styles (underlining and strikethrough). The meat of this update is focused around bug fixes and performance enhancements however, for example they have reworked spotlight indexing to be more robust, improved iOS syncing performance, and fixed a number of crashes. It also contains a number of smaller but significant improvements.

Performance improvements

  • Significantly improved performance of switching between collections.
  • Scrolling large number of collections is now smooth again.
  • Improved performance and reliability of iOS PDF syncing.
  • Improved performance of autocitekey generation.

In the release notes:-

We advise to upgrade to Papers for iOS 1.9.17, this free update is available in the iTunes App Store.

There is a list of reference management tools here.



Comments

DEVONthink 2.5

DEVONthink 2.5 now has syncing and web sharing

Sync-icon

Using multiple computers, working from different places, sharing data with coworkers: In today’s highly connected world it’s essential to always have access to the latest data. And because we know that, of course, we worked hard on creating the most versatile yet robust synchronization technology and rewriting the build-in web server of DEVONthink Pro Office. All editions of DEVONthink 2.5 synchronize databases between multiple computers and locations either directly or via Dropbox, WebDAV, file servers, or just any mountable disk. The new web server gives your PC and Linux colleagues access to the databases you want to share with them directly through their favorite web browser. And if you’re still fighting the paper flood you will like the enhancements we have made to the scan feature

There are more reference management applications here.



Comments

Bookends Updated

The reference management application Bookends has been updated to version 11.3.4 (December 23, 2012)

  • Autofill ISBN from any Amazon source In preferences, select which Amazon site (US, UK, Japan, etc.) to use to autofill references using the ISBN. This was previously limited to Amazon US. Note that many sites do not provide summary information.

  • Automatically exclude author and title from a citation or footnote If the temporary citation begins with &, Bookends will exclude the author and title (or secondary title) in the final citation or footnote.

  • The font size delta for small caps has been changed to 3 points (from 2)

  • Search Web Of Science for grant number and funding agency

  • JSTOR parser in Bookends Browser was updated to deal with changes made by JSTOR

  • Perform a Spotlight boolean NOT search by putting a minus sign directly in front of a word For example, to search for an attached pdf written by Smith and not Jones, search for "Smith -Jones" (without the quote marks).

  • Bookends Browser will detect DOIs on the Web Of Science web site and allow you to import references and pdfs by clicking on the green icon If not already present, the Web Of Science web site will be added to the Bookends Browser bookmarks.

  • Keywords shown in a column in the list view will be separated with semicolons Previously, only the first keyword was shown.

  • Bug fixes Improved check for a valid PMID in the PMID field when doing an Autofill From Internet. Fixed a bug that prevented text in fields being edited from being saved if some of the Action pop-up menu commands were invoked. Fixed a bug that could result in incorrect author-date sorts in citation groups if the name and date was separated by a space. Fixed a bug that caused an error when renaming a Type in preferences when a format window displaying that Type was open. The Reveal In Finder contextual menu now works in the reference pane view of the library window. Fixed a bug that could cause an error when syncing pdfs with Bookends On Tap. Fixed a problem where trying to open a pdf in Preview using the right-click hierarchical menu could result in an error. Fixed an error that could occur when changing the pop-up menu to select different search options in the Find dialog. Fixed an error that was generated with exporting a tab-delimited text file with attachments. Fixed a bug where the pdf display pane was not updated properly when replicating a Book as a Book Chapter.

There is a page of reference management applications here.

Comments

Papers is now officially part of Springer Science+Business media

Papers has rapidly become the application that in many ways has set the standard for reference management, winning Apple design awards for the iTunes like interface for organising your scientific references. Papers radically improved the way researchers handle their scientific literature by centralising search, downloads and organising references and documents in one tool, functioning as a personal library for research. The literature can be cited in the word processing software of choice, and can be shared with colleagues.The small team at Mekentosj rapidly gained recognition for their carefully thought out design, and as they expanded into Windows and iOS versions I guess it was clear that the team was becoming stretched, with difficult choices having to be made as to which new features could be implemented in the next release.

papers2_springer

It seems an opportunity arose for the team to get additional support and resources from Springer and the acquisition of Mekentosj was the logical step.

The fit was a natural one, and we believe that by becoming part of Springer we will be able to offer our users so much more: we can take Papers to the next level, but much faster than on our own. Backed by the second largest scientific publisher we will be able to add features quicker, react faster, provide better support, and open up a realm of new possibilities.

For those that might be worried about the future of Papers.

The Mekentosj team will remain in charge of Papers, and continue to develop Papers for each of the platforms we currently support: Mac, PC, and iOS. We will continue to bring you updates, new features, and support. All with the same dedication and excitement you are used to getting from us

What is going to happen to the other Mekentosj apps like 4Peaks, EnzymeX, etc?

The Mekentosj molecular biology apps like 4Peaks, EnzymeX, iRNAi, LabAssistant, etc. will not become part of Springer and have moved to a new home. They will also remain free. Unfortunately, as has been the case for a while, Papers takes up all our time so we can't promise any updates soon.

There are press releases here and here and a Q&A here.

There is a listing of reference management applications for Mac here.

Comments

Reference Managers Update

I’ve just noticed that a couple of the reference management applications have been updated.

Bookends is now up to version 11.3.3 with a number of bug fixes and new features including, Web of Science searches restored, autofill fields from internet, when tying to find a pdf online, if Bookends can't resolve the ip address it will skip to the next selected reference rather than showing an error dialog. There have also been some text formatting improvements.

DevonThink The maintenance release facilitates scanning documents with multiple pages using  the new scanning feature of DEVONthink, which is also available in the Personal and Pro editions, and adds support for OS X 10.8's Calendar and Reminders applications to DEVONthink Pro and up. Scanning to PDF or TIFF reveals a convenient "Combine into single document" option which, when checked, directly collects all scanned pages into a new document

Papers2 Recent papers search for Authors and Periodicals,Auto-complete of authors and sources in the inspector,Editing of multiple papers at once and duplicate merging of papers,Merge and split any duplicate or incorrectly merged sources,Displaying and navigation of notes and highlights in the inspector,Addition of tools to allow page rotation and hiding a PDF coverpage,Creating of collection hierarchies upon import of folders,Return of column mode for search results in the search section,Support for inserting footnotes in Microsoft Word,Improved Papers for iOS syncing.

Readcube A collapsible left-side panel: After many requests, we’ve finally added a button to hide the side panel, giving you extra screen real estate for reading your articles. A few new options in preferences including an option to disable the ReadCube helper app and an option to alphabetize your lists. And the ability to send articles users find with their browser straight to ReadCube.

Zotero 3.0.8.1 was released for Zotero Standalone for Mac OS X only.

Also Sente is beta testing a new synchronisation feature between desktop and iPad.

Mendeley 1.7 has been released as a preview. Probably the most important feature is the Mac Word plugin has been updated for Word 2011 on Mac. The updated plugin has a more obvious UI for inserting citations and bibliographies. It is also much faster when refreshing medium to large bibliographies.

There is a comprehensive list of reference management apps for the Mac here.

Comments

DEVONthink updated

DEVONthink has been updated to version 2.4.

Update for Mountain Lion plus support for Notification Center and the new sharing services. Share documents with one click via iMessage, Mail, Twitter, Facebook, or Airdrop or add them to Safari’s Reading List. The update also brings a completely rewritten scan feature that’s available for DEVONthink Personal and Pro

There is a list of reference management apps here.

Comments

Papers 2.2

Papers is now at version 2.2, this update includes:-

  • Recent papers search for Authors and Periodicals
  • Auto-complete of authors and sources in the inspector
  • Editing of multiple papers at once and duplicate merging of papers
  • Merge and split any duplicate or incorrectly merged sources
  • Displaying and navigation of notes and highlights in the inspector
  • Addition of tools to allow page rotation and hiding a PDF coverpage
  • Creating of collection hierarchies upon import of folders
  • Return of column mode for search results in the search section
  • Support for inserting footnotes in Microsoft Word
  • Improved Papers for iOS syncing

There is a list of reference management applications here.

Comments

Bookends Updated

The reference manager application Bookends has been updated.

Direct PubMed searches and using PubMed for autocomplete paper restored. These functions were broken by changes at PubMed.

There is a list of reference management applications here.

Comments

DevonThink updated

DevonThink has been updated.

The maintenance update to version 2.3.5 increases the visibility of the built-in tutorials, adds two new options for archiving email attachments from Apple Mail, and improves a number of other user interface details. Available from the support assistant, the one place for all support and learning resources in DEVONtechnologies apps, the tutorials explain everyday tasks step-by-step from creating databases to, e.g., importing files, searching effectively, and protecting data from prying eyes. The Internet-based content will also be extended in the coming months with even more tutorials and videos.

There is a list of reference management applications here

Comments

Papers 2 updated

The award winning reference management application Papers has just been updated to version 2.2

  • Recent papers search for Authors and Periodicals
  • Auto-complete of authors and sources in the inspector
  • Editing of multiple papers at once and duplicate merging of papers
  • Merge and split any duplicate or incorrectly merged sources
  • Displaying and navigation of notes and highlights in the inspector
  • Addition of tools to allow page rotation and hiding a PDF coverpage
  • Creating of collection hierarchies upon import of folders
  • Return of column mode for search results in the search section
  • Support for inserting footnotes in Microsoft Word
  • Improved Papers for iOS syncing

The full list of new features are described here.

There is a list of reference management applications here.

Comments

DEVONthink has been updated

DEVONthink has been updated, this maintenance release prepares DEVONthink Pro Office for the upcoming sync technology, introduces the new Activity panel, brings interface and usability enhancements, and fixes some minor bugs and glitches. It is recommended for all users of DEVONthink Pro Office.

DEVONthink Pro Office only:

  • Improved: Compatibility to eastern European languages.
  • Improved: Support for all versions of ExactScan.
  • Improved: Threading of imported email messages.
  • Fixed: Installation of Apple Mail plugin with ~/Library/Mail replaced with an alias or symbolic link.
  • Fixed: Creator and producer attributes of OCRed PDF documents.
  • Fixed: Size of date field of metadata entry window.

DEVONthink Pro and up:

  • NEW: Script Add message(s) & attachments to DEVONthink for easily importing both messages and attachments.
  • NEW: Support for categories of Atom feeds.
  • Improved: Opening multiple databases uses now one progress indicator.
  • Improved: Support for sheets, e.g. imported .csv files, with varying number of columns.
  • Improved: Scripts > Import > Del.icio.us no longer uses the discontinued keychain scripting. In addition it is able to download and set a thumbnail for the group again.
  • Improved: Encoding support for Add mailbox(es) to DEVONthink and Add message(s) to DEVONthink scripts.
  • Improved: Automator action Set Current Group.
  • Improved: Smart groups in the sidebar using the Date Opened condition are immediately updated.
  • Improved: Handling of feeds not containing dates.
  • Fixed: Issue preventing Sente 6 smart template from linking back to the original reference in Sente.
  • Removed: Obsolete script Scripts > Feeds > Apple - Latest Mac OS X downloads.

DEVONthink Personal and up:

  • NEW: Activity panel. Replaces the OCR Activity panel.
  • NEW: Copy Frame Link contextual menu command for movies.
  • Improved: Handling of Quick Look panel on OS X 10.6 Snow Leopard and later.
  • Fixed: Two issues with tabbed document windows.
  • Fixed: Crashes caused by Quick Look on OS X 10.8 Mountain Lion (workaround).
  • Fixed: Dragging linked images from Safari stored them as bookmarks since the latest Safari updates.
  • Fixed: Bookmarks to pages of PDF documents didn't always work on OS X 10.7 Lion.
  • Fixed: Duplicate shortcuts in Format popup menu of Clip to DEVONthink panel.
  • Fixed: Empty folders were not always deleted e.g. after deleting indexed items.

All editions:

  • NEW: View option View > Columns > Aliases and sorting option View > Sorting > By Aliases.
  • NEW: Number of items in groups , smart groups, and feeds is now displayed right aligned and gray.
  • NEW: Creating new documents in Tags view adds them either to the currently selected group tag or to the inbox of the database and tags them with the currently selected (ordinary) tag(s).
  • NEW: Double-clicking on entries in the Log panel reveals them or shows them in the Finder if possible.
  • Improved: Data > See Also > Classify can now also be used when the drawer is already visible, e.g. to close it using the keyboard shortcut.
  • Improved: Reliability when inserting links and attachments into rich text documents.
  • Improved: Memory management.
  • Improved: Overall reliability and performance.
  • Fixed: Some minor user interface issues on OS X 10.7 Lion.
  • Fixed: Smart groups using Item contains aliases were not always automatically updated.
  • Fixed: Mouse cursor did not show as arrow over popup and clear buttons of search fields.
  • Fixed: Reordering items in ordinary tags (inside the Tags group) wasn't possible in unsorted views.
  • Fixed: Send by Email commands were not disabled if no documents were selected.
  • Fixed: Using services or Clip to DEVONthink could cause issues while synchronizing with DEVONthink To Go.
  • Fixed: Spotlight metadata cache didn't always contain all files.
  • Fixed: Minor bugs and glitches.

There is a list of reference management applications here.

Comments

Utopia Documents

Utopia Documents is an interesting PDF reader that has a number of useful features. It allows you browse through a publications images using a screen flow like display. It also provides links to online resources to enhance the document.

There is a listing of reference management applications here.

Comments

Reference Miner

Reference Miner searches the Internet to find and display reference information from PubMed, Amazon (US, UK, Germany, France, Canada, Japan, Italy, and China), Google Scholar, JSTOR (requires access privileges and ip authentication) and the Library of Congress. The Internet search features of Reference Miner, and much more, are built into Bookends. If you own Bookends you do not need Reference Miner.

There is a list of reference management applications here.

Comments

Bookends Updated

There is a new update to Bookends (11.2.4 )

  • Updated Google Scholar direct search and Autocomplete Paper to deal with changes made by Google
  • Import abstracts from Google Scholar Note that the abstracts Google Scholar provides are incomplete, but still may be helpful.
  • Type ahead search works in the single column reference list The search is always for the author, regardless of the sort status of the list. It will only jump to an exact match of the typed characters.

There is a comprehensive list of reference management software here.

Comments

Papers2.1

I’m just catching up with things that happened over the last month or so and I noticed that the reference management application Papers has been updated to version 2.1.

If you want to know what features are currently being developed for future versions of Papers have a look at the roadmap.

There is a list of reference management applications here.

Comments

Scripting the Organic Chemistry Reference Resolver

The Organic Chemistry Reference Resolver is an invaluable web service that takes as input a text reference to a published article in a variety of formats and then finds and displays the corresponding publication.

The real beauty of a web service is that it can be accessed via a variety of means, including an applescript. This applescript uses as input either text that has been copied to the clipboard or the text the user has typed into a text box, it submits the request to the web service and displays the result in the web browser.

Comments

ReadCube added

I’ve just added ReadCube to the reference management page.

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Reference Management Applicatios

Papers2 is coming. Read More...
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Papers Update

Mekentosj released version 1.9 of Papers for iPad, and iPhone. Read More...
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EndNote Update

EndNote X4 has been updated, the new features include:- Import and Search PDFs in EndNote, You can transfer up to 10,000 references between the desktop and Web, new auto-hyperlink between in-text citations and the bibliography and more. Read More...
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WizFolio update

The latest version of the web-based reference management tool WizFolio has been released, with a Youtube video showing it in action on an iPad.

Read More...
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Papers for iPhone/iPad updated

Papers for iPhone updated Read More...
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DevonThink Update

DEVONthink and DEVONnote have been updated Read More...
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Papers for the iPad

Papers for the iPad Read More...
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Reference Management Tools

I’ve just updated the Reference Management Page and noticed a few updates Read More...
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Mendeley

Added Mendeley to the list of Reference Management Applications. Read More...
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Reference Management Updates

Snow Leopard and reference management applications compatibility. Read More...
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Papers for iPhone

Mekentosj today introduced Papers for iPhone and iPod touch. Read More...
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Tips for using Preview

Tips and tricks for using Preview Read More...
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EndNote updates

Mac market share continues to rise in June. Read More...
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Reference Management Software

It seem that there a number of updates DevonThink, Sente, and Reference Miner have all been updated.

Full listing of
reference management software here.
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Reference Managament Software

Article on reference management software in Nature. Read More...
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Papers

I see that the reference management application Papers has been updated. Read More...
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Updated Reference Management Applications

Updated Reference Management Applications page Read More...
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BibDesk

BibDesk has been updated. Read More...
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EndNote XI

EndNote has been updated to version XI Read More...
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Reference Management Applications

Page Updated

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Reference Management Applications

A list of MacOSX reference management applications.

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