Academia has a reputation for being a bit of a closed world, a walled garden of knowledge where secrets are jealously guarded. But the truth is that collaboration is at the very heart of research and scientific discovery, and that for science to advance, researchers need to get together, compare notes, disagree, and have their ideas challenged and built upon by others. Often this happens naturally – like in the cafeteria where PhD students will chat about their projects – but in such a hyper-specialized environment, chances are that people who share your particular research interests cannot be found in the same institution or even the same country. What then?

In the same way that social media has revolutionised personal and professional communication and created dynamic global conversations, platforms like Mendeley now bring academics together in groups formed around those research interests, and the implications of that are tremendous for making science more open and accelerating the pace of discovery.This is why the team here at Mendeley is particularly interested in gaining genuine, real-time insight into research collaboration.

Mendeley is involved in several research projects. Particularly fruitful has been an on-going exchange of researchers and Mendeley staff between our London HQ and the Know-Center at Graz University of Technology in Austria. All projects aim to contribute to the improved use of the wealth of Mendeley data for the benefit of our users and the scientific community in general.

Unsurprisingly perhaps, this recent investigation of research collaboration started as a Hack Day project between Mendeley staff and a visiting researcher from the Know-Center/TU Graz in the context of the TEAM project (http://team-project.tugraz.at) which is coordinated by the Knowledge Management Institute of the TU Graz. Sebastian Pöhlmann (Insights and Analytics Manager) and Piotr Drozd (Community and Business Intelligence Analyst) teamed up with Peter Kraker (PhD student, Know-Center/TU Graz) to visualise cross-country collaboration on the Mendeley platform.

An interactive map has been created that aims to shed some light into the intensity of international research collaboration across different countries. Considering that using Mendeley groups is optional for our users, we are excited to have data on 113 countries. For each of those we show the continent, the rank by user count, the number of connected countries and the proportion of foreign (= international) connections.

By browsing the map or making a selection from the list, you can visualise the connections between researchers for any given country. A connection between two countries is established if at least one of each country’s researchers are members of the same Mendeley group. Of the over 200,000 research groups on Mendeley, we’ve selected private groups with at least two members, as that tends to be the most collaborative group type. Our staff is also very active on the platform so we’ve further excluded groups owned by Mendeley staff  and connections where Mendeley staff are involved. We have further excluded countries with less than 10 total connections.

Browsing the map and the data has produced some interesting insights:

• Among BRICS countries, China, India and Russia have a high proportion of international connections whereas Brazil and South Africa seem somewhat more internally focused
• Generally speaking, North America, Europe, and Australia are very well connected, whereas Asia and South America are somewhat lagging behind.
• There are a few small countries that are very internationalized: Netherlands, Sweden, Switzerland, Belgium, Austria, and Denmark. Interestingly, these countries are also at the top of the KOF Index of Globalization: http://globalization.kof.ethz.ch/static/pdf/rankings_2012.pdf

This is early days, but we hope that by learning more about how our users collaborate with each other, we can continue to develop the best tools to help them work even more efficiently. And by sharing some of the insights on Mendeley Labs we want to contribute our part of the picture to the general knowledge of how research works.

As always, we’d love to hear your thoughts. What does collaboration mean to you and how would you go about measuring and visualizing it?

We wanted to let you know that we’ve made some changes to give our user community a better Mendeley experience. From now on all personal and Mendeley Institutional Edition accounts (apart from the ones that already have unlimited storage) will get a lot more personal library space for storing documents. Here’s how it works:

• Free plan users who currently get 1GB of storage will now get 2GB
• Plus plan and MIE users who have 2GB will now get  5GB
• Pro plan users’ limit will increase from 5GB to 10GB

This applies to all new and existing Mendeley users, and you don’t need to do anything, the new limits should already be in place on your accounts.

And for our dedicated community of Mendeley Advisors all around the world, we’ve also added an extra bonus: Each Advisor will receive – in addition to the increased personal library space – a Team package with 20GBs of group space and an unlimited number of groups with up to 10 collaborators each. This Team package is currently worth £59 ($74) a month, and is something that our community has been asking for, so we’re really pleased to make this available!

Mendeley is a collaborative platform, and we’re always looking at ways to make that collaboration easier, so although we’re only giving these enhanced group features to our advisors at the moment, we’re looking at ways to extend those benefits to all our users in the near future, so watch this space!

In the meantime let us know in the comments below what you think about the upgrades, and if you have any questions as always you can get in touch with support@mendeley.com

Photo courtesy of Kenn W. Kiser

A little while back we sent out a survey to a few of our users asking for their stories about how Mendeley had helped them in their research, and we got quite a few responses from our community. What we also found out is that now that we’ve been around for a while – actually, we launched our first beta on the 2nd April 2008, which makes Mendeley 5 years old – there are researchers out there who have used Mendeley all the way through the process of researching their PhD thesis, and many continue to use it now they’ve graduated. We’ve picked our top 10 respondents, who have all been with us for over 3 years, to share some of their favourite things about Mendeley. We’d love to see if you agree, or if you have any stories of your own you’d like to share… Usually we don’t like to toot our own horn, but hopefully since it’s our birthday you’ll forgive us!

1. “Mendeley has enabled my different collaborations to share papers and ideas, and it has enabled me to use Latex in a more efficient way. Keeping tabs on the references and results of experimental data in organic photovoltaics has been made simpler through the use of Shared Libraries and the annotations one can make in the papers.” Roberto Olivares-Amaya, Postdoctoral Research Scientist in Theoretical Chemistry from Princeton University, NJ.
2. “I use Mendeley collaboratively: We hold reading groups where everyone annotates the pdf with questions / comments on the paper coming up. During the meeting, we put Mendeley on the big screen and go through the papers / presentations bit by bit. The literature survey I had to do for one of my checkpoints was also greatly helped by Mendeley. I had an entire framework of tags that would allow me to quickly find the papers for a particular technique, the papers for a particular chapter, or even the papers that followed a similar methodology. Every paper was annotated with the key points that I had to summarize, and it made writing the survey far easier in the end. It is turning out to be pretty much the same story with my dissertation, which I’m just getting underway now.” Christian Muise, Computer and Information Science PhD Student from the University of Toronto, specializing in Artificial Intelligence.
3. “My PhD was interdisciplinary – half computational systems biology, half experimental parasitology – so I had twice the background reading to do. Mendeley helped me organise that reading and see links across the subjects.” Thomas Forth, recently completed his PhD in Systems Biology of the Malaria parasite at Leeds University.
4. “Scientists have been waiting a long time for this.  Mendeley is great, I can sync my papers across all of the different computers in our lab. When we are writing papers, everyone can have the same list of references and can actually see the same pdf files that I’m using.” Daniel Hickstein, a Physics Graduate Student specialising in Ultrafast laser spectroscopy at the university of Colorado.
5. “Mendeley has been useful throughout my whole PhD experience. Being able to highlight, put notes for when I read it again, and send that edited version to a colleague has been an excellent collaborative tool.” Alejandro Montenegro-Montero, a Biologist specializing in Molecular Science from P. Universidad Catolica de Chile in Santiago.
6. “Mendeley made it much easier to share articles with other members of my project over the years. Every time a new student joined our group, I could simply share the collection with them and point out which articles are the most important to read simply by starring them.” Joshua Middaugh, a Graduate Engineering Student at MIT specializing in Combustion and Energy.
7. “With Mendeley I can store, organize the documents and share them with others.  And this was a free software from the beginning. I find it useful that I can read and tag my documents and make a reference list for my publications.  I can find relevant articles fast using my tags. Mendeley is always useful when I need to find specific articles quickly or articles on specific topic for an example when discussing a subject with someone.” Joose Kreutzer, Engineering Researcher specializing in Microfabrication and microfluidics at the Tampere University of Technology, Finland.
8. “Mendeley works on Linux! Allows you to keep your notes attached to your pdf files and search through everything easily. There are other citing applications for Linux but they are antiquated and made the process of looking after my references more work than I had time for. Mendeley made organising my thesis references the enjoyable part.” Andrew Dunk, a Researcher in Computer and Information Science specializing in Virtual Reality and 3D User Interfaces from The University of Reading.
9. “Probably the most valuable thing Mendeley has offered me is the way to easily include original sources rather than just subsidiary results—i.e., it’s trivially easy to keep track of that 1939 Vollmer book rather than citing something that references it.  So I feel like that process makes it easier for the end user of my research to see the real provenance of ideas rather than the temptation to cite recent sources.” Neal Davis, Nuclear Engineering graduate student from the University of Illinois.
10. “The problem I have is that I read a lot of papers but when I need to recall them I cannot always remember the title or even the author. There are either phrases or other things that stick in my mind. With Mendeley I can always search these terms and retrieve the document.” Nikolaos Vasiloglou, Electrical and Electronic Engineering data scientist specializing in Machine Learning from Georgia Tech.

This week we talk to Callum (or Cally to his friends) who’s our QA Team Lead. Before landing at Mendeley he worked in publishing but in his student days he actually used to be a lifeguard. Do tell us more…

“It was probably the most boring job I’ve had, the only time I got to save anyone was when a lady got cramp during aqua aerobics – not exactly Baywatch!”

What made you apply for a job at Mendeley?
I was already working in the industry and liked how Mendeley was disrupting the marketplace

When you started working here, were things like you expected?
I expected a lot more people and processes in place – it’s a real testament to the talent and ambition of people here that we can achieve so much with so few people compared with the big players in the marketplace.

Have things changed in Mendeley since you started working here?
Kaizen is an important principle here, so things are always changing.

What’s the best thing about coming to work at Mendeley?
We get a hackday every month to experiment with new technologies and products.

Who would be invited to your perfect dinner party?
Four of my close friends and Oscar Wilde.  We would have a great laugh.

What is the one website you can’t live without?
slashdot.org  - for the pithy comments

When you were growing up, what did you want to be?
A train driver

What book are you reading at the moment and why?
For work(ish) I am reading ‘Programming Collective Intelligence’ and for pleasure I’m reading ‘Racing through the dark’, the autobiography of cyclist David Millar

What would you change about the world if you could change one thing?
Free college/university education for everyone

What was the first record you ever bought?  
Bad by Michael Jackson (on cassette)

Favourite food/drink?
Croissants dunked into coffee

Your greatest vice?
I drink far too much coffee in the afternoon

Favourite place in the world?
Saint Julienne en Beauchene (a tiny picturesque village in southern France)

Three things you would put in Room 101
Walking slowly in crowded places, crocs (the shoes), tomato ketchup

Now for a serious one worthy of the Mendeley vision: If you could give unlimited funding and resources to one area of research, what would it be and why?
I want to research decision theory in more detail.  I try to use some aspects real options pricing when prioritizing work, but learning more about the theory is something I would love to do – and actually understanding the Black-Scholes model would be nice

There’s been a lot of buzz around “Citizen Science” lately, so it’s only fair to ask whether the hype is really justified or if it’s more of a gimmick or passing fad. Taking some time to look at the projects that have already harnessed the power of the masses to advance scientific research, however, it’s difficult not to get excited.

Citizen Science, as the name suggests, is where ordinary citizens volunteer their brainpower, time, and other resources such as spare computer power, to help with research projects. From asking people to count squirrels in their backyard to encouraging you to build your own laser harp, there literally is something out there to suit everyone’s abilities, resources, and disposition. Getting involved can mean something as simple as donating some spare computer time; ClimatePrediction.net, for example, aims to produce predictions of the Earth’s climate up to 2300 by asking users to download and run a model program when their computers are on but not being used to full capacity.

For those looking to get more involved, however, there is the opportunity to hunt for stellar clusters in the Andromeda Galaxy, identify and measure the orbits of Near Earth Objects , or help researchers at Berkeley in their Search for Extraterrestrial Intelligence through the SETI@home project.

Closer to home you can view and classify pictures from the hundreds of camera traps set throughout the Serengeti National Park in Tanzania, monitor the status of bat populations, measure the evolution of tropical storms, or help survey scallop numbers in the New York Bight by analysing undersea images captured by a robot submarine named Dora. Even the humanities need not feel neglected, as nearly 800,000 people signed up so far to help the Bodleian Libraries at the University of Oxford increase access to their music collections by transcribing information from digitized sheet music. Sites like Zooniverse aggregate the largest and most popular projects, and you only need to register once to participate in as many as you like.

But while a lot of these projects only require people to view, interpret and process images, some actually ask you to actively solve puzzles, effectively turning scientific questions into games.

Ribonucleic acid (RNA) is a substance used by our cells to translate genetic information from our DNA. Folding and shape-shifting allows RNA to control cells in a predictable way, and this has huge medical and biological implications that are still to be discovered. This is where EteRNA come in: It’s a game where you design RNAs, which are then scored according to how well they fold. The best examples are added to the first large-scale library of synthetic RNA designs in the world. Similarly, Phylo is a game where participants align DNA sequences by shifting puzzle pieces as a way of achieving Multiple Sequence Alignments. A sequence alignment is a way of arranging the sequences of DNA to identify regions of similarity. From such an alignment, biologists can trace the source of certain genetic diseases. Traditionally, alignment algorithms use computationally complex heuristics to align the sequences but this is prohibitively expensive; by taking data pre-aligned by a heuristic algorithm and abstracting it into manipulating patterns consisting of coloured shapes, the game harnesses the natural human ability to recognize patterns and solve visual problems efficiently.

This is something that research institutions and charities such as Cancer Research UK are keen to capitalize upon. They are teaming up with games designers and computer programmers from tech giants such as Amazon, Facebook and Google to find a way to gamify the search for DNA mutations which lead to cancer. The data needs to be analysed by eye, as computers cannot identify the subtle differences which give the clue as to what the genetic causes of cancers might be. They are aiming to have the project up and running this summer

So it might be that this democratization of science, opening it up to ordinary citizen participation from all over the world, could aid the discovery of a cure for cancer, uncover the secrets of the universe, and help us advance knowledge in all areas of human knowledge. What do you think about it? Have you been involved in such a project or considered crowdsourcing as a way to advance your research? Or have you participated in these or any other projects as a citizen scientist? We’d love to hear your experiences, so do leave a comment or join the conversation on Twitter and Facebook.

In science it is, anyway. As Eric S. Lander- one of the eleven winners of the first Breakthrough Prize in Life Sciences – explains, this is a “staggering” amount of money for a scientist. Lander is a leader of the Human Genome Project, and in an interview quoted in the New York Times he told of how he planned on using the prize money to help pay for new approaches to teaching biology online.

The winners of what is now the world’s richest academic prize for medicine and biology – more than twice the amount of the Nobel Prize – work mostly in areas advancing cancer research, but Cornelia I. Bargmann’s work on nervous system and behaviour was also recognised, as was Dr. Shinya Yamanaka’s groundbreaking research on developing stem cells.

This follows from the establishment of the Fundamental Physics Prize – also worth $3 million – awarded to 9 scientists last July. It’s the brainchild of Russian Billionaire investor, entrepreneur and philanthropist Yuri Milner, who himself was a Physics student. Inaugural winners includedAlexei Kitaev,  Maxim Kontsevich, and Ashoke Sen.

Previous winners will help make decisions on future awards, and both prizes – as well as a $100,000 award to honour promising young researchers – will now be awarded annually to people who “think big, take risks and have made a significant impact on our lives.”

But while the physics prize was funded exclusively by Mr Milner, who personally chose the first batch of winners, for the Breakthrough Prize in Life Sciences he partnered with a select group of Internet tycoons. Apple chairman Arthur D. Levison helped in the selection process while Facebook’s Mark Zuckerberg, Google co-founder Sergey Brin and his wife Anne Wojcicki – founder of genetics company 23andMe were also involved and donated towards the $33 million prize fund.

Mark Zuckerberg told GigaOM that he believes society needs more hero scientist, researchers and engineers: “The things that we talk about in the media and the things the market rewards has a big influence on what the next generation of people growing up will choose to do and I think it’s really important that a lot of the smartest people go and choose to solve these problems and go into these lines of work.”

In a world obsessed with film, music and sports celebrities, the goal is to “move the needle” of public awareness and give scientists who have significantly contributed to the advancement of human knowledge a chance at the limelight. The foundation’s website will soon be accepting nominations for the next batch of prizes, and anyone can send one in. There are no limits as to age or how many people can share a prize. Also, people can win more than once. “If you’re Einsten,” said Mr Milner, “you will be getting three.”

Do you think that prizes such as the Life Sciences Breakthrough and the Fundamental Physics Prize have the potential to inspire more young people to pursue a scientific career? Is it fair to single out researchers for such large prizes or would it be more productive to fund their area of research directly rather than individuals? Does the fact that most winners are male and from the US represent a problem? What are your thoughts on the researchers who have been recognized so far and their contribution to science? Please let us know what you think by leaving a comment below or joining the conversation on Twitter or Facebook.

There’s been some great news for Mendeley this week. For the second time in our 4-year history, we’ve won a major award at The Europas, considered the Oscars of the European Tech scene.

Mendeley’s founders Jan, Paul, and Victor, who started Mendeley in 2009 in London, were voted the “Best Startup Founders” by The Europas Judges. They were up against high-profile competition from the founders of DataHug, Hailo, Huddle, Mind Candy, Songkick, SoundCloud, TransferWise, Wonga, and Zoopla. Mendeley had already scooped up the “Best Social Innovation Which Benefits Society” award at The Europas in 2009.

“It’s both wonderful and humbling to have won the Best Startup Founders award, especially when nominated alongside some of the most inspiring tech entrepreneurs in Europe. To me, this award is really a recognition of the passionate, creative, and dedicated team we have assembled, and the work we have done together. Thanks also go to our 1,700 Mendeley Advisors and fantastic community of over 2 million users worldwide”, said Victor, our Co-founder and CEO.

We will continue to work on making science more open and collaborative on a global scale, beginning with the recent push towards moving our infrastructure to our Open API. Thank you for your support!

A preview release of Mendeley Desktop 1.6 is available.  Improvements in this release include:

• A visual refresh on Mac and initial support for ‘Retina’ display Macs.
• Improved full-screen reading experience on Mac
• The ability to add page numbers, chapters and other kinds of location within a larger work for individual citations.
• The ability to suppress author names and add custom prefixes and suffixes for individual citations.
• Improved compatibility with various proxies in corporate and campus networks.  Mendeley will use the system proxy settings on Mac and Internet Explorer’s settings on Windows.  If you encounter any problems, please let us know in our support forum.
• When you drag and drop publications to ‘My Publications’, we now make it clearer that the documents will appear on your Mendeley profile and that the PDFs will be downloadable from there.
• Clearer ‘Getting Started’ steps after installing the Word plugins.
• Various small improvements to citation formatting.
• The Filter and QuickShare panes in the lower-left corner can now be hidden when you don’t need them.

If you’d like to test the new release, please download the preview and report any issues in our support forum.  For more screenshots, see this gallery.

This is the third of four parts announcing the top 40-ish Apps entered into the Mendeley-PLoS Binary Battle. To see the first batch of apps, check out Day One. And Day Two with the second batch is here. Check back tomorrow for the final batch of apps.

As a reminder, the top 10 apps will be announced in two weeks and the overall winners will be announced November 30th

Now, in order of entry received date, the third batch of apps to benefit science: (more…)

A preview release of Mendeley Desktop 1.1 is available.  This release includes several performance improvements in the Microsoft Word plugins alongside a number of stability and usability enhancements.

You can download the preview from the right-hand side of the downloads page.

You can give us feedback on this release in the feedback forum, the comments in this post or via our support form.

• Improved the performance of inserting citations and refreshing documents using the Word plugins (these mostly benefit the Microsoft Word for Windows plugin, but there have also been improvements to the Mac Word plugin).
• Pressing the ‘Delete’ key now removes the selected document from the current collection, instead of moving it to the trash. Pressing Shift+Delete moves the document to the trash and Ctrl+Shift+Delete removes it completely.
• Folders in the left-hand pane are now collapsed on startup.
• When a pair of documents are marked as not being duplicates in the ‘Check for Duplicates’ tool, that decision is remembered on the computer on which it was made.

• Fixed a problem which could allow multiple copies of Mendeley to run at once.
• Fixed Bibtex sync not updating the corresponding Bibtex files when documents are added to or removed from folders.
• (Mac) Reduced watched folders resource usage and fixed crash when watching a folder containing a large number of sub-folders.
• (Windows) Fixed Mendeley not being able to close Word automatically when needed on 64bit Windows.

Compatibility

• There are no compatibility changes from the previous release.  In the event of problems with the 1.1 preview, you can revert back to 1.0.