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.