An excellent Science Blogging, Soton Open Science Workshop, and Science in the 21st Century Conference Adventure, Part II

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.

Mendeley Desktop: The MVC strikes back

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! ūüėÄ

An excellent Science Blogging 2008 adventure, Part I

My jetlag is in full swing as I’m writing this from my room at the lovely Walper Terrace Hotel in Kitchener/Waterloo, Ontario. The local time is 10pm, but my inner clock (still set to GMT) tells me it’s 3 in the morning, thus lending incredible appeal to the hotel bed behind me. But I’ve decided to grim up and write about the conferences and workshops I’ve been attending in the past week, because everything whizzes by so fast that the backlog of blogworthy events is just getting bigger and bigger.

So, to start off, I participated in the Science Blogging 2008 Conference that was held on the 30th of August at the Royal Institution in London. More on that later; the conference was preceded by a “London Science Tour” on the 29th of August, led by Matt Brown, Editor at Nature Networks, writer for The Londonist and genuinely nice guy. Matt took us (a group of science bloggers + me) on a day’s walk to a number of scientific points of interest, exhibitions at the Wellcome Collection and behind-the-scenes tours the Linnean Society of London, and the Darwin Centre at the Natural History Museum. I could sit here all night enthusing about the incredible wonders nature on display there, but I’ll just say that – if you get the chance – you should see it for yourself. Here are some of the pictures I took:

Wellcome Collection – Malaria info booth

Wellcome Collection – Creepy crawlies that spread diseases

Linnean Society – Butterfly specimens collected almost 240 years ago

Linnean Society – Coleoptera of 1772, pleased to meet you

Linnean Society – 17th century books on horticulture

Darwin Centre – 8.6m squid “Archie” (Architeuthis dux)

Darwin Centre – A “really big-headed fish in a tube” (excuse my ignorance)

Darwin Centre – A “really poor, cute beaked guy in a glass” (belonging to the Tachyglossidae family? Excuse my ignorance)

Darwin Centre – Snake specimens

During the walk, I got to know some very nice people such as Heather Etchevers, Yaroslav Nikolaev, Martin Fenner (who by now has posted an interview with me on his blog), and Mo Costandi, author of the brilliant Neurophilosophy blog.

The funniest moment came later that night at a pub in Soho. Mo had just introduced me to some guy named Vaughan, and we were standing there with a pint of beer, talking about this and that. Up to that point, I had only exchanged about two sentences with Vaughan, and instead had started telling Mo about how my favourite neuroscience/psychology blog was Mind Hacks and how great Mind Hacks was – and Mo pointed over to Vaughan and said: “That’s Vaughan’s blog!”.

So I got to know the author of Mind Hacks by accident, which was completely awesome. As it turned out the next day, someone else shared my feelings. Ben Goldacre, famous Guardian Science Blogger, told a similar story about meeting Vaughan at the pub that night (“No way, you’re the author of Mind Hacks?! I LOVE Mind Hacks!”) during his opening keynote speech at the conference.

Well, so much for my plan to write about Science Blogging 2008, the Southampton Open Science Workshop, which I attended subsequently, and the Science in the 21st Century Conference, where I am now, in one go. It’s already 4.32am on my inner clock now, and I can’t resist the bed any longer. I guess this will be a multi-part post…

Mendeley Desktop 0.5.8 available now

This release mainly includes bugfixes and interface changes pointed out and requested by our members. You can download Mendeley Desktop 0.5.8 here.

Current issues on Windows only

  • Mendeley Desktop on Windows will claim to be the latest version. If it is version 0.5.7 or below, the message is a lie. We told it to tell the truth from now on.

So what has been fixed exactly since version 0.5.6?

  • Fixed order of authors for an article
  • Fixed high CPU usage on Windows when shared groups are visible
  • Fixed several crashes which could occur in the client when responding to notification of upload/download errors from server
  • Fixed authors edit field in Edit Metadata dialog being very small if there were a large number of authors
  • Fixed auto-update on Windows XP/Vista if Mendeley was installed with administrator priviledges but run without them (mainly affects Vista users)
  • Fixed several possible crashes in shared groups synchronisation
  • Fixed problem where documents uploaded to both shared groups and ‘Publications I’ve Authored’ would appear twice in ‘Publications I’ve Authored’
  • Fixed ‘Edit Metadata’ and ‘Remove Metadata’ buttons not being disabled if an article was selected and then hidden as a result of changing the filter
  • Fixed articles deleted by a non-admin user in a shared group not appearing as ‘suggested for deletion’ (with strike-through text) in other group members’ clients
  • Fixed possible problem where wrong documents would be downloaded when syncing from online library
  • Fixed documents uploaded to ‘Publications I’ve Authored’ not appearing if the document was already in the user’s Online Library
  • Fixed grey text in Tags and Notes edit fields not disappearing immediately when clicking in them
  • Fixed appearance problems with inverted themes (esp. under Linux)
  • Fixed tags and notes emblem being shown next to articles which have no tags or notes after editing an article on the server
  • Fixed Edit Metadata dialog prompting the user to save changes even if no changes had been made

What’s new?

  • Faster startup
  • Faster handling of library lists containing many articles
  • More responsive user interface during login and up/download
  • Faster synchronisation between Mendeley Desktop and Mendeley Web after clicking ‘login’ button
  • Faster upload and download of articles from Mendeley Web
  • Faster re-drawing of library list
  • Faster document deletion from server
  • Added ‘Sync’ button to refresh contents of Mendeley Web groups and Shared Groups documents instantly
  • Added ‘Tutorial’ dialog which appears on first start to provide a simple introduction to using Mendeley
  • Highlight document group under mouse when dragging an article from one group to another via the library tree
  • Show progress during PDF upload
  • Smooth per-pixel scrolling of library list
  • Display list of changes when an update for the client has been found (available from version 0.5.8 onwards)
  • More responsive user interface during document deletion
  • Prevent duplicate imports of PDFs into My Library
  • And many more minor changes…

So quite a bit has improved in the last three weeks but there is a lot left to be done. Even though Mendeley Desktop has become more responsive and quicker – speed is still our main priority. In the coming weeks major refactoring work is taking place which will allow much faster handling of thousands of library entries and faster communication to the Mendeley server. While doing this we will try to keep on fixing major bugs and implementing features.

Thank you to everyone who has been testing Mendeley and reported bugs and requested features. It has been a great help.