We have been working on improvements to the importing of information from your existing libraries and documents into Mendeley for our next release.  Highlights include:

Automatic import of PDF files from selected folders:

The feature most requested by our current Mendeley users is support for importing from whole folders (rather than having to select individual files) and automatically monitoring folders for new PDFs and any other format supported by Mendeley.

The next release will include this feature across all 3 platforms (Windows, Mac, Linux)

Improved display of time since import:

In citation and table view, the time since a document was imported is now shown and you can now sort the document list by this field.  The ‘Recently Added’ folder now sorts by date added by default.

Smoother import:

The user interface is now more responsive during large import operations and the total import/automatic extraction progress is now shown in a single progress bar at the bottom of the screen.

Improved Bibtex import and export:

• We now remember the citation key and document type from the imported Bibtex library and use it when exporting modified documents back to Bibtex, regardless of whether Mendeley has its own equivalent document type.
• Better handling of the various author, editor and translator name formats supported by Bibtex
• Support for cross-references and @string entries

Improvements to the RIS and EndNote importers and exporters:

Mendeley is now more tolerant in its input handling of these filetypes and is able to import documents to Mendeley and then export back to that format again with improved fidelity.

If you have any questions or comments about importing into or exporting data from Mendeley then let us know!

I think I learned something today! As a non-software engineer, I was always puzzled beyond measure when I asked our developers to change just a minor interface detail - such as, “shift this icon up a few pixels, change the color of this frame” - and was told that this would take days upon days of work.

Today, Rob explained to me what the reason was. An interface element that you see on the screen, e.g. a toolbar, might look like it’s drawn up from a single, coherent piece of code. In reality, though, it could be cobbled together in the background from many different parts of the code that don’t have anything to do with each other. Thus, changing one pixel on the screen could require a rewrite of two huge portions of code to make them fit together.

So I said, “ah - now I get it. It’s like shadow sculptures!”. If you look at this picture, I think you’ll understand my point:

Shadow sculpture by Tim Noble and Sue Webster

If you’re a software engineer, of course this is old news. But I found it an interesting analogy! Nevertheless, as Mike pointed out in the previous post, our upcoming release (beta 0.6.0) has absolutely shiny, beautiful, well-structured code under its hood when you shine a light on it!

New About Dialogue and it’s even closable on Mac! How on earth did we get to this point?

Let me tell you a story…

Since my last post the Mendeley Desktop team has been very busy indeed!

Our “rewrite of some of the internal Mendeley code” has turned into a rewrite of almost all the code.

Why are we rewriting our code you may ask? Like many other small companies, Mendeley started with their software being written by external contractors. By the time I started in May 2008 a significant amount of code had been written which was then ported to Linux and Mac. What started life as a prototype had turned into a product which was then released to the world when we hit open beta. This means we lacked a solid architecture, any real documentation, coding standards or unit testing.

In the past few months the team has rewritten basically everything except the metadata extraction and the Citation Style Language parser (although these two have both been improved also and will probably be incrementally rewritten for further releases). As a result, we now have a much smaller, easier to read, unit-tested, documented, faster and just plain better codebase by any software engineering metric you would care to throw at it. My slightly obsessive insistence that the team meets the coding standards document and our continuous integration tool has resulted in a far higher quality product.

You might be asking why on earth you should care about everything I said above. Well the answers are in the features/bugfixes that you’ll see in the new release:

• Better performance and lower memory usage
• Adding sub-groups
• Folder monitoring
• Encrypted data transfer
• Only uses standard HTTP ports (i.e. 80 and 443) and uses your system proxy settings
• Less interface slowdown on network/import operations
• A closable “About” window on Mac, as featured at the top of this post (No, I’m not joking. To close it in 0.5.9 or below, press Escape)
• More native and more usable user interface
• More traditional Mac packaging

Anyway, I hope that is enough to get you excited about the next release. We will be retaining feature parity with 0.5.9 (i.e. no features currently existing in 0.5.9. will be dropped in 0.6.0) and 0.6.0 will fix a lot of outstanding bugs with 0.5.9.

Mendeley Desktop 0.6.0: Coming soon!

The very first steps towards a plugin for Microsoft Word are done and we thought we’d give you an early preview. It’s the first alpha and has some known bugs, but most of the time it does the job.

Known issues (which will be fixed in the next releases) are:

• Large download filesize (14.4MB)
• Several Microsoft run-time environments are being installed before the Word plugin is installed
• The plugin will only work for the user who installed it
• Removing documents from your Mendeley library which you have cited in your Word document causes blank citations
• Standard undo doesn’t work as expected after Mendeley action (eg. changing the citation style of bibliography: undo changes back each entry one by one instead of all at once)

You can download the plugin on our download page. We would really appreciate your feedback and bug-reports to improve the plugin for our next release!

Here at Mendeley we’re all working towards version 0.6.0 which will be our next major release in November with a focus on stability and scalability, many interface tweaks, and some nice new features. Version 0.5.9 is a step in this direction but is still based on the old codebase. It will be available via auto-update - if your are using Mendeley Desktop v.0.5.8 just start the application and it will automatically detect the update.

Version 0.5.9 has many bug fixes, some new features (e.g. PDF file renaming according to a chosen schema like “Author - Year - Title - Journal.pdf”), and it will hopefully be joined by an alpha version of a Word plugin in the coming days. See the complete change list below:

Change list:

• New: Auto file renaming
• New: Account usage dialog
• Fix: Speedup opening of edit metadata dialog
• Fix: Possible crash when clicking keep document button (Linux)
• Fix: Size of edit metadata window
• Fix: New documents not appearing if references dragged into my library
• Fix: Possible crash when removing documents from online library
• Fix: Crash when linking an image PDF to manually added metadata
• Fix: Table view dragging not working properly
• Fix: Initial position of edit metadata dialog
• Fix: Reference list in table view
• Fix: Possible crash when closing application if uploads or downloads are in progress
• Fix: Changes to references not appearing immediately when closing edit metadata dialog
• Fix: Problems with shared groups syncing
• Fix: Position of shared group admin buttons in table view
• Fix: Fix PDF being locked after metadata extraction (Windows)
• Fix: Remove debugging output on startup (Linux)
• Fix: Text color of deletion suggested text in table view
• Fix: Tags, notes fields and reference list not being enabled when selecting documents in the library if Mendeley starts up in table view
• Fix: Slight improvements of the citation style
• Fix: Email automatically set for trac tickets
• Fix: Reduced Mendeley power usage while idle

Long time no blog, indeed. I had wanted to write more about the numerous workshops and conferences I attended, but I didn’t get around to it because we’ve been very busy here at Mendeley HQ. Among other things, we’re planning a new release of Mendeley Desktop soon. Without giving too much away, it will include a few long-awaited and highly-requested new features. Stay tuned!

So I’ve been looking for a way to sum up my recent travels. With total disregard for Blaise Pascal’s famous quote “I would have written a shorter letter, but I did not have the time”, I concluded that Haikus might be a solution. Here goes:

In Soton I sleep
on Ben’s futon which fails, my
talk is all woozy

Said futon

Listening to Yaroslav’s talk

Moving on - my Science in the 21st Century haiku:

Waterloo WiFi
breaks during the demo yet
enthusiasm wins

Chad Orzel on Newtonian vs. Galileian science - our former landlord Michael Palin making another unexpected appearance

Collective mind-mapping exercise devised by Alex Pang

Panel with Steve Weinstein, Harry Collins, David Kaiser, Lee Smolin and impressively bescribbled blackboards

In short, I had a marvelous week at the Perimeter Institute. Thanks to Sabine for organizing such a great conference, to Mark and Eva for the many inspiring conversations, to Jen and Michael for inviting me over to dinner, to Chad, Simeon, John and Cameron for the nice evening at the brewery, to Katy for offering to help us develop data visualizations, to David and Paul for sharing their insights into the current US presidential election (and Paul giving me one of his Analog SF magazines so I’d have something to read on the plane), to Gerry for sharing his thoughts on social networking (and looking like Albert Einstein), and to Hassan for inviting me to contribute an essay about reputation systems in science to his upcoming book.

Firstly, thanks to all of you who have filed feature requests or flagged up bugs on our bug tracker, your feedback has been really useful.

After thinking about how to best accommodate your needs we’ve deciding to do a rewrite of some of the internal Mendeley code in order to get it running snappier and work better with larger libraries.

As a result of some work Fred has done on his music player we’ve decided that using Qt’s MVC framework maps extremely well to our needs and should bring us far greater performance when dealing with large libraries as well as keeping the code cleaner, better separated and making it much easier to write unit tests with decent coverage levels.

So where are we with this at the moment? Currently we have implemented most of the new non-GUI code with just our local/remote database code to finish. For those interested in this sort of thing, we are 100% documented with Doxygen (both private and public members) and have every class’s method unit-tested with around 85% test coverage.

Without revealing too much you should be excited about this and some of the new features that will see the light of day around the same time as the new, better-performing internal code. This will hopefully mean we can feasible support much larger collections than currently with a slimmer/faster application and quicker bug turnaround with less regressions than our previous releases.

Get excited, I am!

The last couple of weeks have been pretty exciting. We moved offices just in time to have enough space for all the new people who have started working for Mendeley recently. They have been working hard to optimize the software architecture, databases, interfaces, integration and usability of Mendeley Web and Mendeley Desktop.

Some of you are probably wondering why you haven’t received an invitation code yet. Well we have been working non-stop on many new features and we can’t wait to release them; so we’d rather hold off the invitations until we can present you our shiny new version. Also some major refactoring work has been done in the last weeks so we want to ensure that the version we give out is working as perfectly as possible.

Just to give you a short teaser of stuff to come…

• Linux and MAC versions of Mendeley Desktop
• Auto-installer of updates
• Shared Groups (working on tags and notes of articles collaboratively)
• Improved synchronization interface of Mendeley Desktop
• Publication handling in Mendeley Web
• Re-design and usability improvements of various areas of Mendeley Web
• Personal statistics of your library
• Speed improvements

Although there is still a reasonable amount of bugfixing left, we are trying our best to not keep you waiting too long…  as you can see, there is a lot to look forward to!

My name is Mike and I’m a software engineer. No, I won’t fix your computer. However I will get Mendeley running on it because you’re such a nice person.

I’m hard at work at the moment making Mendeley work on Linux. For those who care this involves moving from a Visual Studio based build-system to one using CMake and also fixing some of the inane rubbish that the the MSVC++ compiler seems to think should be valid C++.

At the moment you can use WINE on Linux/FreeBSD, Darwine on Apple OS X and Mendeley-shaped bread in your toaster to fulfil all your unsated academic document management needs.

Running Mendeley on Apple OS X

• Install Darwine from http://www.kronenberg.org/darwine/ into the Applications directory.
• Install TRiX from http://mike.kronenberg.org/?p=69 into the Applications directory.
• Run TRiX from Applications.
• Make sure the following options are selected: In the “General” tab: “MS Arial, Courier, Times fonts“, “MS Tahoma font (not part of corefonts)”. In the “Libraries & Runtimes” tab: “vc6redist from VS6sp4 (mfc42, msvcp60, msvcrt)”
• Press the “Install” button.
• When done (i.e. Terminal displays “All done, no errors”) install Mendeley (double click on .exe file - Darwine will do the rest. Allow it to install into the default directory: i.e. “C:\Program Files\Mendeley Beta”). If “All done, no errors” did not appear then try and click “Install” again until it does.
• Open a new Terminal.
• Run the following commands: “cd ~/.wine/drive_c/Program\ Files/Mendeley\ Beta/; /Applications/Darwine/Wine.bundle/Contents/bin/wine Mendeley.exe“
• The last command should have launched Mendeley! If it didn’t or you are having any other problems then post them here and we’ll try and help.
• KNOWN Problems: Depending on your language, “Program Files” may be something like “Programme” instead. If the above command doesn’t work then try to run “ls ~/.wine/drive_c/” and use the results to see where you should “cd” to.

Running Mendeley on Linux/FreeBSD/BeardOS

• Install Wine from your package manager.
• Download Winetricks from http://www.kegel.com/wine/winetricks.
• When downloaded run “sh winetricks” from a terminal, when in the same directory as Winetricks.
• Select “allfonts” and “vcrun6” and press “OK“. Press “OK” when the VC6 installer pops up.
• When done (i.e. the terminal displays “All done, no errors”) run “wine Mendeley-0.5.4.0.exe” when pointing at the correct downloaded installer and change the version number to be correct. Allow it to install into the default directory: i.e. “C:\Program Files\Mendeley Beta”).
• Run the following commands: “cd ~/.wine/drive_c/Program\ Files/Mendeley\ Beta/; wine Mendeley.exe“
• The last command should have launched Mendeley! If it didn’t or you are having any other problems then post them here and we’ll try and help.
• KNOWN Problems: Depending on your language, “Program Files” may be something like “Programme” instead. If the above command doesn’t work then try to run “ls ~/.wine/drive_c/” and use the results to see where you should “cd” to.

Running Mendeley on your Toaster

• Get a piece of Bread.
• Cut the piece of Bread into the shape of the Mendeley logo.
• Insert into Toaster and set heat to at least 5.
• Wait patiently for the Toast (toasted bread) to pop out of the toaster.
• Optional step: Use a Knife and a Spread (any bread-compatible spread will do) and combine them on the toast.
• Consume the toast.
• The last command should have launched Mendeley made you less hungry! If it didn’t or you are having any other problems then post them here and we’ll try and help.

Some of our beta testers have thankfully pointed out to us that we forgot to mention a tiny, yet important, detail: Currently, Mendeley Desktop only runs on Windows. Sincerest apologies to those Mac and Linux users who downloaded our software only to discover that their operating system was not yet supported!

We feel a little stupid now for not having communicated this before - a classic case of overlooking the obvious. However, we are working hard on porting the code to run properly on Linux and Mac OS X and other architectures. In the meantime, you can run Mendeley Desktop on these platforms using a virtual machine (such as Parallels or VMware) or by using the free Wine (on Linux) or Darwine (on Mac OS X) which do not require a virtual machine or a Windows license.