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.

The joys and terrors of founding a company are essentially the same. You get to decide almost everything, which means that you also have decide almost everything. In the case of software development, that means the look of every interface, the wording in every dialog, the detailed function of each feature, the placement of each button etc. So, obviously, there’s plenty of room for discussion.

Such was the case again when we had to decide exactly how the Full-Screen PDF Viewer integrated into Mendeley Desktop should look and work. Here’s a preview:

The discussion centered around which features to leave out completely, and which features to retain at least as options. In the end, we left out most of the debatable features and didn’t even put them in the options menu.

You’d be surprised how many options we had in the software at earlier stages (and how emotional the discussions were that got them there). “But wouldn’t it be nice if a user could adjust the font size in the library?” - “Shouldn’t you be able to also sort the data by…”, and so on. Joel on Software captured this predicament quite nicely:

Software has a similar archaeological record, too: it’s called the Options dialog. Pull up the Tools | Options dialog box and you will see a history of arguments that the software designers had about the design of the product. Should we automatically open the last file that the user was working on? Yes! No! There is a two week debate, nobody wants to hurt anyone’s feelings, the programmer puts in an #ifdef in self defense while the designers fight it out. Eventually they just decide to make it an option.

Yet, besides the obvious point that a less cluttered interface is easier to use, there’s perhaps a deeper psychological justification for not including too many options: Too much choice can make people miserable.

There’s a great talk on this very subject by Prof. Dan Gilbert, author of “Stumbling on Happiness” - a book I thoroughly enjoyed, although it’s more a description of “the symptom, but not the cure”. In this video however, eight minutes in, he reveals the secret of happiness. Enjoy:

In order to collectively answer to a couple of questions we received during the last weeks and to shed some light on what’s behind Mendeley - we’ve set up a FAQ page on www.mendeley.com.

Check it out!

Well, I am. Currently I have six students writing their master thesis under my supervision, and if you’ve ever done this before, then you know the amount of work that goes into that job. Especially when you have to compile and distribute literature lists to each of the students, it can be quite a hassle to pluck this list from your own pool of references - depending on how well you’ve organized your library. In the end you want to have an up-to-date list of references which you can give to the student, and you also want your student to be able to directly use and analyze these references for his own work.

This is, again, one of the day-to-day problems of researchers that we’re aiming to solve with Mendeley. In Mendeley, you’ll be able to just set up document groups according to the different topics you are currently researching, and drag & drop references from your library into these groups. You could then either export a formatted list or, even better, give the student access to this group so that he would be able to import this information into his Mendeley account and start building up his own library. And every time you add a new reference to one these shared groups, your student will see this new reference in his library as well.

Obviously, this would also make the lives of research groups easier. I believe we could figure out plenty of additional scenarios which make sense in this context. If you have some ideas, just send us an e-mail and let us know!

Today was one of these days you dedicate to fixing front-end bugs and make elements of your website look good in the most popular browsers. And again, it turned into one of these days when you just pray that, on some beautiful day, everyone gets rid of the heavily outdated and terrible Internet Explorer 6. I think I’m speaking for many developers when I say that we feel absolutely tortured by having to fix all these little things just for IE 6, just because it’s not able to do standard things or displays them differently than every other browser. Please… if you are using IE 6, have a heart and follow this link! It’s for your own good!!

Even though the process of working on these tweaks is painful - the result is sheer beauty! Today it was all about the “Current & Future Locations” feature of our site, and there are just one or two tweaks missing till it’s done. With this feature, you can add locations to your profile and let others know where you are going to be in the future. For example, attending a conference overseas, giving a guest lecture, or studying abroad. Entering locations here will inform your network about your travels in their “Profile Updates” feed. If only getting accepted at a conference was that easy…

This morning in perpetually sunny London, as I walked from my flat to the Warwick Avenue tube station, I noticed something that almost made me tremble in awe and excitement. I could barely hold my iPhone still to take a picture. I’m living around the corner from the house where Alan Turing was born! ALAN TURING! Even though I’m not a programmer myself, I find that pretty awesome. Behold and rejoice, my fellow nerds:

Alan Turing, one of the fathers of computer science, formalised the concept of the algorithm through his description of Turing machines.

At Mendeley, we’re fond of algorithms. While we strive to keep our software’s user interface as simply and appealing as possible, there are quite a lot of complex algorithms huffing and puffing and toiling away in the background.

One automatically extracts the metadata from the text of an academic paper (to spare you from typing it in manually), while another takes a fingerprint from the paper’s text and anonymously matches it against other fingerprints on the Mendeley server, with the goal of improving the metadata recognition quality - so the more people use Mendeley, the better the quality becomes.

A further not-so-simple algorithm parses the cited references in the end and turns them into a machine-readable format (so you can search them, apply citation styles, and export them). An additional one matches these extracted references to documents already in your library (to automatically capture the hidden citation network already existent on your computer). Then there’s the building of the full-text index and, coming soon, the recommendation engine.

By the way, the place where Alan Turing was born is now the Colonnade Hotel. If you’re a rich nerd, you can stay there! So did Sigmund Freud, who’s got a suite named after him.