Bibliography generator plugin for Microsoft Word 2008 for Mac:

This has been one of the most frequently requested features by our Mac users – now it’s here! Therefore, bibliography creation is now supported in Word and OpenOffice on all three platforms (Win, Mac and Linux). It’s just the first iteration, so we’ll continue to work on it and add more functionality. Please let us know what you think at http://feedback.mendeley.com.

Collaborative PDF annotation using sticky notes and highlights:

This has been a repeated request by research groups, labs and departments using Mendeley. PDF sticky notes and highlights are now synced with Mendeley Web, meaning that in Shared Collections you can now see each of your colleagues’ annotations separately and color-coded. In addition, there’s a major upgrade to the PDF viewer – it will now render the displayed PDF document instantly, no more pre-caching!

XMP metadata now extracted from PDFs:

This is a behind-the-scenes upgrade – Mendeley will now read embedded XMP metadata from PDFs where available (Nature and Elsevier journals, among others, now provide this routinely), boosting the metadata extraction quality. Even where there is no embedded XMP metadata, the algorithms for detecting authors and titles have also been improved.

Because of necessary changes to our server architecture, older Mendeley Desktop versions are required to upgrade to this latest beta version to continue using Mendeley’s online features – we’ll try not to make a habit of doing this.

Here is the full list of improvements and bug fixes:

• PDF annotations are now synchronized with Mendeley Web. In shared collections multiple users can add notes or highlights to documents.
• Added an importer for Ovid Reprints/Medlars format files.
• PDF import will make use of embedded XMP metadata if it is present and appears to be accurate.
• (Mac) First version of Mac Word plugin. Please note: Currently the Mac Word plugin supports Microsoft Word 2008 for Mac. Word 2004 and earlier are not yet supported.

• Added keyboard shortcuts for selecting, highlighting and adding notes.
• Newly imported documents are highlighted after import.
• The updater will now ask for the administrator password if necessary during update installation on Linux and Mac.
• Added ‘Copy LaTeX Citation’ action to documents list right-click menu.
• Improvements to accuracy of automated author and title extraction from PDFs.
• Add the ability to drag-and-drop any file type into Mendeley Desktop. If the file type is not supported by one of the importers then a new document is created with the file attached.
• Smoother scrolling in PDF viewer.
• ‘Search by Title’ and DOI lookups will now retain the full names of authors if the lookup comes back with only initials if the initials and the full names agree.

• Fixed a recent problem with links between new documents and file attachments being lost for some users when syncing and a message warning that recently synced documents had been deleted on Mendeley Web.
• Fixed crashes when exiting full-screen mode in PDF viewer.
• Fixed red border around PDF content on PowerPC Macs.
• Fixed local library data not being migrated correctly when changing email address in Mendeley Desktop.
• Added additional verification of backups before restoring to web in the ‘Restore Backup’ feature.
• File space usage shown in Preferences dialog did not update after syncing.
• Incorrect progress messages were shown in the status bar when importing a PDF.
• Fixed problem where starting a ‘Search by Title’ lookup for one document and then switching to another document before the results came back would apply the changes to the wrong document.
• Fixed crash when performing DOI lookups in ‘Add New Document’ dialog.
• The PDF viewer no longer creates temporary copies of opened PDF files on disk.
• Fixed problem where only the first page of certain multi-page PDFs were shown in the viewer.
• Fixed problem where search in a PDF viewer tab would not find matches on the last page of the PDF.
• Fixed file organiser renaming failing on Windows for documents where the title, authors or publication name contained double quotes.
• If uploading a file to Mendeley Web fails because the file is too large, the sync now continues uploading other attachments.
• Fixed a problem which could cause Mendeley Desktop to loop continuously during sync.
• Fixed PARSEFAILED error when syncing if certain characters appeared in imported documents.
• Fixed long delay when opening the citation style browser.
• Fixed long delay when opening the Tools -> Options menu on some systems.
• Fixed incorrect documents being shown when searching for certain tags.
• Fixed error about LinkToMendeleyVba.dll not being found on some Windows systems.
• Fixed various crashes when syncing after removing shared collections on the web.

If you have suggestions for improvements please let us know by visiting the feedback forum at http://feedback.mendeley.com. If you encounter any problems using Mendeley or have questions to ask please e-mail support@mendeley.com. Thanks!

Date: Tuesday, February 23rd 2010 Time: 5:00 pm GMT Presenter: William Gunn

Date: Wednesday, February 24th 2010 Time: 9:30 am GMT Presenter: Victor Henning

You’re a Mendeley power-user already? Then why not share this info with your friends and colleagues that are still looking for a free tool to manage their references and papers? They’ll thank you…

So how global is global, then? Looking at the attendees of last week’s webinars: very, very global! Mendeley is being used in so many diverse locations – there were CGIAR researchers, librarians, and knowledge management specialists from Bangladesh, Cambodia, China, Colombia, Egypt, Germany, India, Malaysia, Nigeria, the Philippines, Singapore, Sri Lanka, Syria, the UK and the USA. And it’s great to see that we can help to make research easier.

We are planning to offer more webinars very soon. If you or your organization is interested in a tailor-made web seminar, please let us know at community@mendeley.com.

When starting work on a new project, there is normally an initial phase of your work-flow that consists of performing searches on websites for available literature on the desired topic.

You query the search sites with keywords, open each link that seems of interest, read the abstract and when available download the paper (PDF document). If you happen to be searching on many sites and downloading many papers, this can be a bit repetitive.

Repetitive work is normally tedious and time is usually short. So, what if you could easily download references and their respective PDF documents (when accessible) with a simple click of the mouse?

Mendeley’s one-click web importer enables you to add references (and their PDF documents) to your Mendeley reference library from within your favorite browser. All you need to do is add the web bookmarklet to your browser bar and you will be able to easily add documents to your library from a growing selection of websites like PubMed, IEEE Xplore, Google Scholar, CAT.INIST or PLoS, just to name a few.

So I know what you are thinking: “Great, there’s a simple way to add documents to my Mendeley library while searching in my favorite browser. Show me how!”

OK, here is how…

First, you need to add the bookmarklet to your browser bookmark bar. Do this by either dragging the link directly to the bookmark bar from the Mendeley web importer page or by going to Mendeley Desktop menu Tools > Install Web Importer. Once that’s done, you should be good to go.

Let’s give it a try by opening up Google Scholar and performing a search for your favorite keyword(s). Let’s say your keywords of interest are “Synthetic Biology”, the Google Scholar results should be something like so:

Let us assume there are a few papers that you’d like to add to your library, so you click on the Mendeley web importer bookmarklet and a pop-up window opens. You are presented with a very similar list of references as those presented by Google Scholar with some extra options. Let me point a couple of these extras out (see image highlight):

Once you’re done importing the documents into your Mendeley library, they are stored in your Mendeley Web account. To be clear, the references are always stored in your library but the actual PDF files may not be imported if they are not openly accessible to Mendeley’s servers.

Side note: If the PDF documents you want to import to Mendeley are not openly accessible but you have access to them via your institutional network/proxy, there is a simple way of adding the document directly to Mendeley Desktop. Simply drag & drop the link to the PDF file and Mendeley Desktop will automatically download the file and auto-extract the document details. Let’s just call this our little secret work-around while it’s not yet fully possible via the web importer, OK?

Getting back to where we were, to have the newly imported documents made available on your computer, simply open Mendeley Desktop and click “Sync Library”.

There you go, without having to download papers one by one or opening multiple web pages, you can easily import documents into your Mendeley library using the one-click web importer.

As mentioned above, the list of supported sites keeps growing and if you would like to see another site added to the list, please feel free to contact us. The web importer also supports any sites using COinS.

Like I said before, the web importer is one of Mendeley’s features that I really enjoy using. How has your experience been using it?

Quick update: The Mendeley team is hard at work finishing up an upcoming feature for the Web Importer that will allow users to store local copies of webpages!

The top paper for 2009 was written by Uri Alon, entitled: ‘How to choose a good scientific problem’, published in the journal “Molecular Cell.” Our stats tell us that there are currently 74 Mendeley users who have read this paper, even though it was only published in late 2009.

The full list of the top ten articles published in 2009 on Mendeley (as of 28th January 2010) is:

1. Uri Alon, ‘How to choose a good scientific problem’, Molecular Cell (2009), Volume: 35, Issue: 6

2. Castro Neto et al, ‘The electronic properties of graphene’, Reviews of Modern Physics (2009), Volume: 81, Issue: 1

3. Erez Lieberman-Aiden et al, ‘Comprehensive mapping of long-range interactions reveals folding principles of the human genome’, Science (2009), Volume: 326, Issue: 5950

4. Ed Bullmore & Olaf Sporns, ‘Complex brain networks: graph theoretical analysis of structural and functional systems’, Nature Reviews Neuroscience (2009), Volume: 10, Issue: 3

5. Zhong Wang, Mark Gerstein, Michael Snyder, ‘RNA-Seq: a revolutionary tool for transcriptomics’, Nature Reviews Genetics (2009), Volume: 10, Issue: 1

6. Development Core Team, ‘R: A Language and Environment for Statistical Computing’, R Foundation for Statistical Computing (2009) Volume: 2, Issue: 09/18/2009

7. Fatih Ozsolak et al, ‘Direct RNA sequencing’, Nature, Volume: 461, Issue: 7265

8. Benjamin M Bolker et al, ‘Generalized linear mixed models: a practical guide for ecology and evolution’, Trends in Ecology & Evolution (2009), Volume: 24, Issue: 3

9. Michael Schmidt & Hod Lipson, ‘Distilling free-form natural laws from experimental data’, Science (2009), Volume: 324, Issue: 592

10. Stephen J Eglen, ‘A quick guide to teaching R programming to computational biology students’, PLoS Computational Biology (2009), Volume: 5, Issue: 8

We’d like to point out that this isn’t an authoritative list of all the ‘most read articles for 2009’. Instead, these are the ones that appear in Mendeley user libraries and show some early indications of the popularity of a journal article. We will also track the evolution of these stats over the course of 2010.

Readership complementing the impact factor

With Mendeley’s growing user base, the readership count can complement other measures, such as citation metrics, adding an extra dimension to assessing a journal article’s impact.

For example, the article “How to choose a good scientific problem” is a general interest article, rather than being specific to biology which suggests it is not likely to have a high citation count in future primary research literature.

Nonetheless, it is already the most read paper on Mendeley published in 2009, a factor that would otherwise be missed. This indicates that the readership count can allude to other ways in which articles are used within a community, and therefore increase awareness of what should be read. The next step will be to anonymously track reading time and quality rating metrics to gather the most accurate data possible for our upcoming personalized recommendation engine.

Predicting research trends?

Understanding and predicting research trends is an important part of research. The citation count, used for decades as the gold standard in article-level metrics, can verify broad trends occurring within academic disciplines such as biology. While quite accurate, official citation metrics take two years to calculate. In contrast, readership statistics may be able to predict similar trends in real-time.

For example, look at The Scientist’s list of the hottest biology papers in 2009 (all published in 2007). The readership count for these papers on Mendeley correlates with ISI’s citation count at r=.76 (two-tailed, p=.13 due to the low sample size) – a near perfect correlation, even if only based on five papers and our userbase of just over 100,000 users:

Comparison of Mendeley’s most read papers with the ISI Citations

We look forward to comparing the top 10 list shown above to the official ISI citation metrics for 2009 publications when they are calculated and released later in 2010 or 2011.

In summary, using Mendeley’s readership figures alongside the citation metrics should make it possible in the future to evaluate the scope of a journal article within the community more effectively. Finally, further refinements and understanding of readership metrics might make it possible to identify the next big trend in the academic world.

Methodology

The top 10 list was made by noting how many times a paper appears in the libraries of individual Mendeley users (readership count) and how many distinct user tags were attributed to that paper (tag count), then we filtered the results to include only papers from 2009 – done!

Seeking to provide a reading list alternative for their 2collab users, it was also announced at Science Online that Mendeley was chosen to enable the opt-in transfer of any 2collab public library folders.

How it works:

1) If you are a 2collab user and do not have a Mendeley account you will first need to sign up here for free.
2) Once registered or for those already registered on Mendeley, go to the ‘Accounts’ link located at the top of the Dashboard page after signing into Mendeley.com.
3) At the bottom of the accounts page you will see a form for entering your 2collab username details.
4) Your public folders will be imported and the next time you open or sync the Mendeley desktop software those folders will be visible. They will also be available on the Web at Mendeley.com and can be viewed by proceeding to the ‘Library’ page.
5) Within the Mendeley desktop, you will then have the option to turn those folders into ‘public collections’ so that others can continue to stay up to date with what you are reading via RSS and other means. For example, here is a feed on Norovirus.

Please contact 2collab if you need any help specific to 2collab.

We wish the 2collab team the best and know that they are already working on some great stuff at Scopus and elsewhere.

Jason Hoyt, PhD
Research Director | Mendeley

Follow Jason & Mendeley on twitter

CNRS, “Centre National del la Recherche Scientifique” (the French National Research Institute), provides research articles and information for scientists and academics Europe-wide. The cooperation now allows users to quickly import articles to their Mendeley online library.

“CAT.INIST (established in 1973) hosts a collection of 15 million bibliographic records, held in the CNRS in Paris. The catalog provides research articles in the fields of Science, Technology, Medicine, Humanities and the Social Sciences.”

Additionally, by installing Mendeley’s Web Importer into your browser, you can easily import articles from many other databases as well, such as Google Scholar, PubMed, IEEE, ISI Web of Knowledge, etc. For a complete list of supported websites, have a look at http://www.mendeley.com/import.

For more information on CNRS’ catalog visit http://cat.inist.fr.

“39 of the UK’s leading digital companies have been selected for the second annual Digital Mission to South by South West interactive (SXSWi), taking place in Austin, Texas from 11-17th March 2010. [...] The successful companies were chosen from over 120 submissions by an advisory board of industry experts drawn from the UK community including: VC’s, export specialists, journalists and industry pundits to take part in the Digital Mission to SXSWi.”

(You can find the full list of participating companies here.)

There are some great presentations in the line-up at SXSWi, some of the ones we’ll be looking out for include: Can the Real-Time Web be Realized?; Crowd Sourcing Innovative Social Change and Is The Brain The Ultimate Computer Interface?

We also hope to swot up on doing business in the US (not by watching re-runs of Dallas) but attending some special events and seminars set up for tech entrepreneurs. SXSWi brings together some of the brightest minds in the tech world and a line up of special programs showcasing websites, video games and start-up ideas. If you are planning to attend, let us know and we’ll be happy to hook up.

A big thanks to Digital Mission for making it possible and we’re looking forward to a great event!

The whole Mendeley team would like to thank you for a great year in 2009! And we promise, 2010 will be a really exciting year as well, with great plans and so many cool things in the pipeline…

And as the team arrives back in dribs and drabs following their holidays, here’s one more piece of news we’d like to share with you.

Earlier in December, Jan and Victor were presenting Mendeley at LeWeb ‘09 in Paris, and the guys over at intruders.tv took the opportunity to interview them on the latest developments at Mendeley:

Fitting all these people in our old 1,090 sq.ft. office had become quite difficult: Alright, place the new designer over here, seat the new data mining experts over there, cram in a bunch of developers in that corner and don’t forget to fill up any remaining space with interns.

Single-handedly, our very own Captain Cindy managed the whole relocation process within a mere matter of hours. Lured by corporate pizza, the whole Mendeley team pitched in highly motivated. Some ha-ha-funny guys even volunteered to carry the wireless network cables!

Our new neighbours kindly hosted a nice house warming party last Thursday. A big “Thank you” to the friendly people at IDEO and we happily accept your table soccer challenge.

Let’s hope that this time we can stay a little longer than just one and a half years.

You’re welcome to have a look: