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!

…besides improving the next version of Mendeley: Today I noticed that two particularly nice messages were pinned to the whiteboard in the developer room. So your encouraging comments are definitely noticed and appreciated - thanks!

(click for larger view)

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.

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…

We had comparatively nice weather (i.e., it didn’t rain) in London yesterday - so we seized the chance and organised a Mendeley team BBQ on the roof terrace of our office! Luckily for us, we didn’t set the building on fire, and no one fell off the roof. Here are some impressions:

Paul being happy while stealing plants for decoration:

Paul becoming even happier and pointing at things:

Smoke signals:

Pankaj, Steve and Falk discussing physics and metaphysics:

More happy Paul:

Julia, Aaron, Ben and Britton Street:

Ben apparently not moving as much as the others:

Fin!

And just in case you’re thinking, “these kids should do less BBQs and more software updates”, we’ve got you covered! Tomorrow we’ll release Mendeley Desktop beta version 0.5.8 with plenty of bugfixes, speed and stability improvements. Happy Paul will blog about it in more detail.

FOR IMMEDIATE RELEASE
August 13, 2008

Mendeley develops software for managing and sharing research papers as well as a website for discovering research trends and connecting to like-minded academics. The founders’ vision to create a “Last.fm for research” excited Skype’s former founding engineers, who became investors, and former Last.fm executive chairman Stefan Glänzer, who is now executive chairman of the company.

London, UK - When Mendeley’s founders started writing their PhDs, they wondered why there wasn’t a more convenient way of managing and sharing their collection of research papers. So they set out to develop a free research tool themselves, which is launching into public beta today.

Mendeley Desktop, a software client application available for Windows, Mac and Linux platforms, automatically extracts metadata, full-text and cited references from PDF files, builds up a personal research library, and offers sophisticated searching, tagging, and filtering functionality. It lets researchers share, synchronize and annotate their digital libraries collaboratively. Data from Mendeley Desktop is exchanged with Mendeley Web, an online research network where users can back up and access their library database, discover the most widely read papers in their academic discipline, and connect to like-minded scientists and researchers. “As the database of Mendeley Web grows, you will be able to view statistics about emerging research topics in every academic discipline, and readership statistics for each individual paper” explains Victor Henning, one of Mendeley’s co-founders. “Soon we will also include a recommendation engine. Basically, it’s like a Last.fm for research.”

This caught Stefan Glänzer’s attention. As seed investor and executive chairman, he helped Last.fm grow into the world’s largest social music network with over 20 million users. A few years earlier, he himself had been in academia, having financed his PhD through work as a DJ. “I wish I’d had a tool like Mendeley back then” says Mr. Glänzer. “There are striking similarities between the concepts: Based on its Audioscrobbler software, which helps users share and discover music, Last.fm was able to create the world’s largest open music database. Based on Mendeley Desktop, which helps users manage, share and discover research papers, Mendeley could achieve the same for academia.”

After joining Mendeley as executive chairman, Mr. Glänzer brought the team in touch with the former founding engineers of Skype, who had recently invested in academic publisher Versita through their investment fund ASI. Mendeley’s software won them over. “There are plenty of websites that want to become ‘the Facebook for researchers’” explains Eileen Broch, ASI’s investment director. “Mendeley, however, is not just another social network. It’s a truly valuable integration of software and web technologies that solves some of researchers’ day-to-day problems – which is why we decided to invest.”

About Mendeley: Mendeley develops software for managing and sharing research papers as well as a website for discovering research trends and connecting to like-minded academics. The company was founded in 2007 by Paul Föckler, Victor Henning and Jan Reichelt and is based in London, UK.

Screenshot 1: Mendeley Desktop is free academic software for managing and sharing research papers.

Screenshot 2: Mendeley Web lets researchers access their papers online, discover research trends and connect to like-minded scholars and academics.

For further information contact Victor Henning (victor.henning@mendeley.com), Tel: +44-207-2531595, or visit www.mendeley.com.
###

Today in our web developer Skype chat: Paul, Falk (brother-in-law of Paul) and Pankaj (freelance database expert).

Paul Föckler, 10:46am: I added Pankaj to our web chat
Falk Kühnel, 10:46am: hiankaj
Falk Kühnel, 10:47am: damn, my eybor is bron i guess

Cracks me up!

Let’s get the bad news out of the way first. I won’t be able to travel to the AMA Summer Conference. At this time tomorrow, I should have been at the beach of San Diego with Michael and Thorsten and a nice cold beer, but it was not to be. My cough from the viral infection hasn’t completely disappeared yet, and a weeks’ travel to California would have worsened it again… what a major bummer!

However, after a month of working from home, I have returned to the office. And as promised earlier, here’s a brief guided photo tour:

Exihibit A shows a room full of software engineers.  They occupy the west wing. They’re all so talented that they have little halos around their heads, but you can’t see them in this picture due to the backlight from the window. True story!

Exhibit B: The east wing. This is where we non-software engineers gather (notice the puny monitors and machines).

Our meeting room at lunchtime. Paul’s arm stretches out inconspicously, stealing someone’s food (or so I presume).

Our kitchen. Jan.. trying to sell me a coffee machine?!

Me in my corner, trying to take a break by hiding behind a book. Fittingly, it’s titled “Hidden Dimensions: The Unification of Physics and Consciousness“. Incredibly fascinating stuff! I’ll probably write about it on this blog later.

Outside our windows, enveloping darkness has settled in, and thus the long night of bugfixing has begun. I have witnessed a mysterious phenomenon: After dark, wherever large groups of software engineers congregate, large quantities of pizza boxes spontaneously materialize out of thin air.

Well, what can I say! The EuroScience Open Forum 2008 in Barcelona has turned out great so far. Due to its considerable greatitude and excellent greatishness, Jan decided not to let me have all the fun by myself and joined me yesterday.

On the downside, the heat and travel stress didn’t exactly help me get rid of my still-persisting cough/throat inflammation. I was barely able to sleep again for the first two nights in Barcelona, and I will need some more days rest at home when I return to London. Nonetheless, we attended some very inspiring sessions and received enthusiastic feedback on our presentation today (more on that in a later post) - let me recapitulate.

Saturday, the most interesting session was on “Open Science” or “Open Notebook Science”, on which Prof. Peter Murray-Rust from Cambridge gave a very spirited talk…

…followed by a not-so-spirited talk given by he-who-shall-not-be-named and in which every slide looked like this:

Anyhow, “Open Notebook Science” is a fairly recent idea which has gained more and more exposure in the past few months. The basic premise is that researchers should not only share their publications through Open Access outlets, but also freely publish their raw data alongside it so that it can be validated, re-purposed and aggregated.

This, of course, entails some problems: Academic careers and tenure decisions depend on publications, so how can you incentivise researchers to lay open their data before they’re certain that they have “wrung” all possible publications out of it? I believe that our “Last.fm for research” model, i.e. the chart-like tracking of which papers are being widely read, which authors are up-and-coming etc., could also be extended to raw data - thus giving credit to people who have created the raw data that others are successfully using.

Two other highlights yesterday and today were the keynote speeches by Prof. Marcus du Sautoy from Oxford and by Physiology/Medicine Nobel laureate Dr. Richard J. Roberts. Both described how they had discovered their love of science and the fields they wanted to dedicate themselves to. Little known facts:

Prof. du Sautoy originally wanted to become a spy (to get a nice black gun like his mum, who had worked for the foreign office) and thus tried to learn many different languages. By his own admission, he failed miserably because he did not find languages to be logical enough. Fortunately for him, Mathematics - and especially Symmetry, his field of expertise - offered him a way of describing and understanding the world in more logical terms. Finally, despite his obsession with symmetry, he had this wonderful quote from the 14th-century Japanese Essays in Idleness:

In everything [...] uniformity is undesirable. Leaving something incomplete makes it interesting, and gives one the feeling that there is room for growth… Even when building the imperial palace, they always leave one place unfinished.

This reminded me strikingly of the Law of Closure in Gestalt psychology which describes how the mind will try to complete figures if they are unfinished - hence deliberately leaving something incomplete will engage the mind’s creativity.

Today, then, Dr. Roberts spoke about his way from unruly, almost-expelled-from-school teenager to molecular biologist and Nobel laureate.

Dr. Roberts had actually wanted to become a professional snooker player - back in the 1960s, he was West England snooker champion. That was also when he received what he described as one of his most profound life lessons:

During a snooker tournament, he had sunk an incredible “lucky shot” - but then failed to make the next one. After the game, an old man came down from the audience and said to him:

Listen, if you sink a lucky shot like that, you have to concentrate twice as hard on your next shot. Everyone can be lucky, but if you get lucky - don’t feel bad, instead work extra hard to take advantage of it.

Seems to have worked out alright for him! After the talk, I hopped onto the stage to give Dr. Roberts a brief pitch of Mendeley, since he’s now actively involved in the Open Access movement. I’m sure that he gets loads of requests like these, but if we’re lucky, who knows - he might just find our idea interesting enough to give us some feedback.

Finally, here are two pictures of me wearing a brain helmet, looking at my brain activity (and oddly, not seeing any?!):

Phew. I should stop writing now. Must sleep. Will tell more of our exploits later. Adios!

I’ve been out of the office for a few days now. My cough/throat infection still keeps me quarantined at home and largely unable to speak (I can make uncoherent noises, though). Nonetheless, Jan, Paul and I were able to have some Skype calls to discuss current issues: They talked, and I had my microphone switched off and replied by typing answers into the chat window. I really felt like a classic Bond villain sitting behind a curtain, giving instructions to the minions of evil. Except that they weren’t really instructions, and my co-founders are neither minions nor particularly evil.

So, the crazy thing is: During my brief absence of four days, Mendeley has moved into a new office, and two more people have joined the team! I promise to do a photo tour of the new office once I’m back; meanwhile, let me introduce the two newest team members (in their own words):

——

Fred Emmott is a software engineer for Mendeley Desktop. Having spent most of his life before university at music school, he changed tracks and graduated from the University of Warwick with a degree in computer science in June 2008.

In his spare time, he works on Slamd64 (a 64-bit port of Slackware Linux) and several smaller projects. He also spends way too much time playing Guitar Hero and Rock Band.

Amir Rahbaran is a Ph.D. student in the field of strategic entrepreneurship at the University of Oldenburg. Entrepreneurial endeavors have fascinated him for a long time, which is why he’s studying them and why he is going to build up his own company in the near future.

He has joined Mendeley on a project basis as part of his Ph.D. thesis titled “Entrepreneurial Bricolage: an Ethnographic Study of Internet Start-ups”. Working for Mendeley is an integrative part of his empirical data collection as a participant-observer. Thus he observes everyone (including himself) and participates by helping to reach out to the academic community.

—–

When Amir contacted us, we were immediately fond of the idea that Mendeley itself would become part of someone’s Ph.D. research. As for reaching out to the academic community, you can see that Amir is already on the phone!

Also, I’m struck by what a musical company we’re becoming. Stefan is a former professional DJ who helped build Last.fm, Mike plays Jazz bass in his spare time, Steve plays guitar, Fred plays piano, guitar and flute, and I spent a long time playing bass and singing in Punk bands while working for Sony Music/Columbia Records and Revelation Records. Why are we writing code?! We should be writing songs!