Macs in Chemistry

Insanely Great Science

Reference Management

Papers Update


The latest update to Papers 3 (version 3.4.16)

  • Adds support for Microsoft Word version 16
  • Adds Citations support for Scrivener
  • Resolves issues with PDF annotations

There are more reference management apps here.


Scripting the Organic Chemistry Reference Resolver


Some time ago I published an AppleScript that allowed users to make use of the excellent Organic Chemistry Reference Resolver.

The Chemistry Reference Resolver serves to quickly direct you to a publisher's webpage that contains the article you are looking for: You type-in the reference The Resolver determines whether it is a journal citation, a DOI, a Sigma-Aldrich chemical search, or something more esoteric Based on the input, it then redirects you to the publisher's webpage – straight to the paper (or its nearest approximation) Many formats are supported including vaguely defined "lazy citations", such as "perkin1 2002 2733".

I was really delighted to hear recently that Brian Myers had customised the script to fit in better with his workflow. Simply copy the reference text to the clipboard and when you activate the script you can search for the reference immediately. Both versions of the script are available here.



oaDOI Safari Extension


With Safari 5 one of the most interesting new features is the support for Extensions and there are now many different [extensions availabl(

There are a section of extensions that might be of interest to scientists and I've started listing the here.

I've just created a new extension that might be of interest.

Ever come across an interesting paper that is behind a paywall? Many of these publications may also be available via green open access.

Self-archiving, also known as green open access, refers to the practice of depositing articles in an institutional repository or a subject repository such as arXiv.

However locating the open version can be a bit hit and miss given there are so many potential repositories. Fortunately oaDOI provides a simple way to search for open access versions

You can simply paste the DOI into the search engine at, however this web service is ideal for linking to a Safari Extension.

Read more…


Serious bug in Evernote


A reader just alerted me to a serious bug in Evernote effecting Mac users.

We have identified a bug in some versions of Evernote for Mac that can cause images and other attachments to be deleted from a note under specific conditions. We've released an updated version of Evernote for Mac, version 6.9.1, to resolve this. Please open Evernote and navigate to Evernote > Check for updates… to get this latest version. If you are using the Mac App Store version of Evernote, this new release has been submitted for approval with Apple, and is estimated at being available for download from the App Store next week.

More comments in the Evernote forum


Papers updated


The very popular reference management application Papers has been updated. to version 3.4.5 (512).

Release Notes

  • Match with Selection now works in the Reader mode.
  • Papers no longer crashes if an incorrect EZProxy address is entered in the Access preferences.
  • General stability improvements.


There are more reference management applications here.


Bundle offer for Finding, Papers and more


There is an interesting bundle offer running at the moment.

"A collection of seven fantastic Mac apps to help you be more productive. Focused around writing, editing, researching and organising, these apps are the perfect companion to all researchers and scientists. The best part? This selection of Mac apps normally cost $305, but during this promotion (which won't last for long), the whole bundle is just $49.99!”

The apps are:-

Papers $80 Your personal library of research designed for your Mac. Papers ​is a multiple a​ward winning​ application developed for researchers. It turns your messy heap of PDFs into your personal library. It helps you collect, curate and stay up to date with your field.

Manuscripts $40 A writing tool like nothing you have seen before. Manuscripts is a writing tool for complex documents unlike any you have seen: it helps you with a complex writing project from outline to editing, proof reading and publishing stages, all within a beautiful Mac app.

Records $30 Records is a delightful and easy to use personal database. The perfect companion for everything you want to collect and organize in life, from your favorite movies to your customer invoices, offering a great balance between easy of use and powerful features.

Soulver $11 Soulver helps you work things out. It's more than a spreadsheet, and smarter than a calculator. Soulver helps you do quick calculations and work things out. Use Soulver to play around with numbers, do "back of the envelope" calculations, and solve day-to-day problems.

DEVONagent Pro $50 Your smart Internet (re)search assistant. DEVONagent Pro helps you search more efficiently on the web. It searches multiple sources, frees you from hunting for the really relevant results, and gives you power tools for your research.

TextSoap $45 Automate tedious text document cleaning. Automatically remove unwanted characters, fix messed up carriage returns, and pretty much anything else you can think. Stop manually fixing text documents and emails. TextSoap can automate away that tediousness.

Findings $49 Your research notebook, reinvented.

All 7 applications for $49.99


Readcube acquire Papers


ReadCube, best known for their innovative software serving researchers, publishers, academic and commercial organizations, today acquired Papers from global academic publisher Springer Nature.

Papers is a very popular multi-platform reference management tool.

There is a listing of reference management tools here.


Papers 3 for iPhone and iPad, now available for free!


As of today, Papers for iPhone and iPad is available for free! Full functionality, no in-app purchases or small print.

Awesome news.


Shazino software


I recently became aware of a new company specialising in software for scientists Shazino have developed a number of interesting applications for both Mac OS X and iOS.

The best known app is PaperShip an iPad, iPhone, and Mac application designed to help you keep your articles organized with your Mendeley or Zotero library. However they also provide a couple of smaller apps that make life easier in the lab.

Laboratory Timer, Fast Counter and SciKey a scientific keyboard.

The latest addition is an electronic labNotebook called Hivebench, this is available for both MacOSX and iOS. Looking at the website it seems to be aimed at molecular biologists/biochemists, and there is a free version that allows unto 10 scientists to collaborate.



Wi-Fi syncing in Papers 3


The Papers Team have just announced that Wi-Fi syncing is now available in Papers 3, available in Papers 3.3.0 for Mac and iOS or later.

Whilst many of our users find Dropbox syncing convenient for keeping their Papers library in sync across multiple devices, users have also been asking for more flexibility. Wi-Fi library syncing is easy-to-use and keeps your devices in sync without being bound by the Cloud storage limits of services like Dropbox.


Papers for Mac updated


The popular reference management application Papers have been updated to version 3.2.7. This update includes improved syncing between multiple devices, Mendeley integration, when importing your Mendeley library, collections, annotations and keywords (tags) are now included.

Performance & Stability:

  • App startup: Improvements to how the app accesses the user's library to reduce the likelihood of slow startup times, as well as improved performance during general app usage.
  • Dropbox Sync: Improvements to reliability. Previously when syncing after launching the app, UI refreshes for subsequent sync operations that changed the metadata of library items that had been changed during the first sync would often not occur until relaunching the app.
  • Reduces the likelihood of a crash during application startup.
  • Reader: No longer crashes when closing all Reader tabs using Cmd+W after launching the app in Reader mode.
  • Federated Search: No longer crashes when selecting "Others" when previously having one of the Favourite search engines selected.
  • Citations: No longer crashes when generating an example citation of a single publication.
  • Stability: Addressed the cause of a memory leak that could occur in certain scenarios.
  • Smart Collections: Nested Smart Collections are no longer shown in the pop-over when using the "Add to collection" option. This was incorrect and improves app performance with large libraries with many Smart Collections.
  • Keywords: When in the Labels mode, filtering now works correctly in the Keywords search bar.
  • Dropbox Sync: Author metadata for papers newly imported on another device is now display correctly in the Info Inspector without needing to relaunch the app.
  • Finder integration: Several improvements to the Finder Spotlight search feature.
  • Spotlight Search: Improvements to index rebuilding to prevent a crash in rare circumstances.
  • Papers 2 Import: Improvements to reliability during the import operation.
  • Author editing: Resolves a bug in the Authors screen where it was possible for the "Me" author to become un-editable.
  • Collections: Correct identation style for nested collections when viewed in the "Add to collection" pop-over from the Overview Inspector.
  • Freehand annotations: Improvements to the selection of previously drawn freehand annotations.

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


Papers 3 Updated


The extremely popular reference management application Papers has been updated.

New Features

  • Keyboard shortcuts: Adds "Add Review" & "Add Keywords" menu items (keyboard shortcuts ⇧⌘R and ⇧⌘K respectively) under the "Paper" menu, previously available in Papers 2.

Performance & Stability

  • Paper management: Choosing "New Paper From Reference…" when viewing a paper in the Reader no longer results in a crash.
  • Reduces the likelihood of app crashes in rare circumstances, for example when editing note annotations.
  • Papers Online: Changes to star rating, color labels or general notes for papers in Papers Online collections are now shown consistently.
  • Library Search: Complete library metadata is now available when using the Search tab and "Papers Library" as the search engine.
  • Papers Online: Improvements to error handling when signed in to Papers Online.
  • Multiple authors or keywords can now be added or deleted without the "Add Author" & "Add Keyword" pop-over views being dismissed automatically.
  • Library Export: All exporters now respect currently-selected papers regardless of which tab is selected, rather than only exporting any previously-selected papers in the Library tab.
  • Dragging a metadata file onto the Overview inspector for a paper will now correctly offers the ability to replace the paper's metadata.
  • Citekeys are now unlocked when they are deleted, reverting back to a universal citekey. Previously, blank citekeys would be exported.
  • Spotlight Indexing: When switching to a different library, the Spotlight Search Index is automatically re-built if one does not exist.
  • When closing the last paper in the Reader tab, the app will now return to the previously open tab before entering the Reader.
  • QuickLook improvements: More filetypes are now compatible for previewing via QuickLook within Papers 3 for Mac.
  • Improved handling of non-roman characters that require multiple keystrokes to type (such as Chinese, Japanese or Korean characters).
  • Improved Library search bar typing responsiveness on OS X 10.10 Yosemite.
  • Minor UI tweaks to menus & layout.

Papers 3 for teams


I've just added Papers 3 for teams to the mobile science site. This app has been designed for teams, departments, companies and institutions to offer the same flexibility and easy management of Papers 3 to users with iOS devices as there is with desktop volume licenses.


Papers updated


The popular reference management application Papers has been updated.

Freehand annotations that were added using Papers 3 for iOS are now synched and displayed on Papers 3 for Mac! (Freehand annotation editing on Papers 3 for Mac will be added in a future update). Dragging one or more papers from your library into a note annotation will now add the citekey references to that note. Scripting API: It's now possible to set a publication's authors or editors via a string of person names:

tell application "Papers"
    set selectedPapers to selected publications of front library window
    set author names of first item of selectedPapers to "Griekspoor, A.C.; Neefjes, J.J.; Groothuis, T.A.M."
end tell

I’m delighted to see that they are already addressing bugs that have arisen in OS X 10.10 (Yosemite).


Chemistry document classifier


The latest issue of J Cheminformatics has an article entitled “A document classifier for medicinal chemistry publications trained on the ChEMBL corpus”, Journal of Cheminformatics 2014, 6:40 doi:.

The large increase in the number of scientific publications has fuelled a need for semi- and fully automated text mining approaches in order to assist in the triage process, both for individual scientists and also for larger-scale data extraction and curation into public databases. Here, we introduce a document classifier, which is able to successfully distinguish between publications that are ‘ChEMBL-like’ (i.e. related to small molecule drug discovery and likely to contain quantitative bioactivity data) and those that are not. The unprecedented size of the medicinal chemistry literature collection, coupled with the advantage of manual curation and mapping to chemistry and biology make the ChEMBL corpus a unique resource for text mining.

The models, workflows and tools are freely available for download.


Applescript in the future


Applescript has had to take a bit of a back seat in recent years but there have been a couple of posts recently that will be of significant interest to all scripters.

Papers is a multi-award winning reference management application that hugely popular with scientists. I saw a very interesting entry on their blog.

The latest beta version of Papers for Mac adds support for scripting. This allows you to automate tasks or fetch and manipulate data in your Papers library by using AppleScript, or JavaScipt in Yosemite. Papers 3 features extensive AppleScript support that allows data to be fetched from a Papers library. You can also execute commands, like import and export. You can even create new data and set its most important properties. Some parts of the UI can be automated as well: the current selection can be changed, as well as the current view mode.

The importance of adding Applescript support to applications is nicely illustrated in an article by Brent Simmons, Making Your Mac App’s Data Scriptable.

Scripting isn’t a matter of automating button clicks; it’s about exposing the model layer to people who could use your app in their workflows.

There have been many concerns that the introduction of “sandboxing” will compromise the ability of applescripts to automate complex multi application workflows. There has been a recent article that shows the current best practices for controlling another app using AppleScript, Scripting from a Sandbox.

This comment sums things up nicely

While that’s usually a small minority of users (who use applescript), they’re power users — the kind of people who recommend apps to friends and family. They blog and tweet about apps, and people listen to them. They can be your app’s biggest evangelists.

And of course it is easy to share applescripts. I’ve added the links to the Applescript Resources page.


Bookends Updated


The reference management software Bookends has been updated. The update includes

  • New PDF viewer with search, markup, and annotation

  • Tight integration between PDF notes and the Bookends note stream

  • Move groups between folders with a hierarchical menu

  • Watch folders work when the default attachment folder is not on the boot HD

  • Use AppleScripts to set the contents of a field

  • Bibliography generation is faster

  • Set text output style (e.g. Styled Text, BibTeX, HTML, etc.) in Preferences, Scan & Bib tab

  • Worked around a Mendeley XML incompatibility with EndNote XML so that reference Types are imported correctly

  • The keyboard shortcut for Autofill From Internet has been changed to Shift-Command-A

  • If Bookends can't find an assigned attachment folder, the factory default folder will be used

  • JSTOR search and Autocomplete Paper were updated to deal with changes made by JSTOR

  • The number of references you can import from Google Scholar at once has been reduced from 50 to 20

  • Updated Google Scholar parsing to deal with changes made by Google

  • Existing font styles will be preserved when pasting decomposed Unicode text into a text field

  • Smarter handling of Title Case

There is a comprehensive listing of reference management software for Mac OSX here.


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.


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.


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

The Mobile Science website contains more science apps for iOS.


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


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.


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


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.


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.


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 An interesting idea and well worth a look.


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


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


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.


DEVONthink 2.5

DEVONthink 2.5 now has syncing and web sharing


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.


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.


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.


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.


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 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.


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.


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.


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.


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


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.


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 > 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.


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.


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.


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.



Now I have a new MacBook Pro I've decided to install VMware so that I can test more of the Opensource scientific applications under Linux, any that look interesting I'll look at compiling under MacOSX.

I've just installed Ubuntu and whilst doing so I came across one tip I thought I'd pass on, during the installation you lose the mouse cursor, however you can still navigate menus/options using the arrow keys. Took me a little time to realise :-)

VMware Fusion (Mac)

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.


ReadCube added

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


Reference Management Applicatios

Papers2 is coming.

Papers Update

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

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...

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.


Papers for iPhone/iPad updated

Papers for iPhone updated

DevonThink Update

DEVONthink and DEVONnote have been updated

Papers for the iPad

Papers for the iPad

Reference Management Tools

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


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

Reference Management Updates

Snow Leopard and reference management applications compatibility.

Papers for iPhone

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

Tips for using Preview

Tips and tricks for using Preview

EndNote updates

Mac market share continues to rise in June.

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.

Reference Managament Software

Article on reference management software in Nature.


I see that the reference management application Papers has been updated. Read More...

Updated Reference Management Applications

Updated Reference Management Applications page


BibDesk has been updated.

EndNote XI

EndNote has been updated to version XI

Reference Management Applications

Page Updated


Reference Management Applications

A list of MacOSX reference management applications.