We, along with PLoS, have been overwhelmed by the huge response that academics and the developer community have given to open up science. When we announced this contest to develop science applications on top of the Mendeley and PLoS platforms last March, we were not totally sure that anyone would even be interested. Boy, were we wrong!

Tim O’Reilly, Founder and CEO of O’Reilly Media and one of five all-star judges, said this about the Binary Battle –

“I always tell developers to work on stuff that matters. It’s time to stretch beyond the consumer internet, and what better place to focus than on furthering the cutting edges of science?”

Mendeley launched the API platform in April of 2010 with the hope that it would 1) spur innovation in the science ecosystem and 2) send a signal to others that opening up data benefits everyone. To date, more than 1000 developers have applied for API keys to build on top of that data. With the Binary Battle announcement, we hoped to carry open science further and by all accounts we did.

Today we announce the winners of the 2011 Mendeley-PLoS Binary Battle. We narrowed the Binary Battle entries down to the Top 10+1, and then handed the voting over to our list of expert judges (Werner Vogels, Juan Enriquez, Tim O’Reilly, James Powell, and John Wilbanks. We also opened the vote up to the public to count as 1/6 and combined with the judges. It was great to see that both the public voting and the judges voting correlated very well. It was so close for many of the apps, but one stood out to both the judges and the public…. (more…)

At Mendeley, we are always looking for ways to make the research process more efficient. We believe in the power of big data and creative analysis to change how research is done in big and trivial ways. For example, with the massive amount of documents in our database, we have the power to analyze successful publications vs. less successful publications based on the characteristics of the documents, and then incorporate this knowledge into our product to help researchers work better. In solidarity with our brothers at Google, we feel that A/B testing on enough data will always lead to the optimal design choice, even for complex design situations. Read on to see the first fruits of our font legibility study. (more…)

We at Mendeley have now built the world’s largest open research catalog, containing over 70 million documents. This is no small feat, considering we’ve only been at it for about 2 years, and we couldn’t have done it without you (nearly a million of you!).  By bringing control of research data back to the community, we hope to make research more collaborative, open, and efficient. If you’ve ever thought, “You know, I really wish I could search the literature better” or “Wouldn’t it be cool if I could see how this idea evolved over time?” or just “I wish I had $10,001 dollars”, well, now’s your chance. (more…)

Get your work noticed! Adding your publications to your profile helps get your work found. More and more often, people aren’t looking to journal table of contents or library catalogs when they search for research. They’re watching what their friends and colleagues bookmark on social networks or add to groups on Mendeley, and they’re searching Google Scholar. In order to get your work noticed, you need to be present where people are looking. There are a few ways you can do this, but like many things, just showing up counts for more than you would think. Simply having an account and connecting to your colleagues online can position you to get found more often, but also to find more interesting things you wouldn’t have noticed otherwise. With hundreds of papers being published in my field every week, I couldn’t keep up using a pure search strategy.

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This post is the second in a series, looking back over the changes in information management over the past decade. Three major and interrelated developments are the move to querying databases of information as opposed to loading information from individual files, the practice of tagging bits of information as opposed to filing things in a hierarchical folder structure, and the representation of information as a temporal stream as opposed to a static page. This post is about the move to databases from filing systems, and how that improves your workflow. (more…)

As the year gets to the end, everyone writes “Best of” lists for the past year. I thought I would do something similar, but since we’re at the end of not only a year, but a decade, it’s worthwhile to reflect on the changes in how people manage and organize their increasingly digital stores of information. Over the next week, I’ll highlight some major developments and discuss how they’ve informed the development of Mendeley. This week it’s the practice of tagging bits of information as opposed to filing things in a hierarchical folder structure, with posts on the move to querying databases of information as opposed to loading information from individual files and the representation of information as a temporal stream as opposed to a static page to come next week. (more…)

Most of our users know that Mendeley can format citations automatically in most word processors. Some may not realize, however, that this bit of magic wasn’t developed entirely by us. Rather, we use tools that were created by a global community of academics and released for everyone to use. I recently had a conversation with the initiator of this movement, Bruce D’Arcus, on where the project is going, what it means to research, and how you can take part. (more…)

I’m thrilled to announce that we have launched our first iPhone app, and it’s free Yay!  You can head over to the app store and grab it here. This is our first app for the iPhone, and we have decided to start with a free ‘lite’ version app so that you can get the benefits right now of being able to read your papers on the go.  With that said let’s take a quick tour of the new app !

In order to use the app you will need to sign up for an account with Mendeley.  You can get build up your digital library either through the web or by using the free desktop client.  Once you have created an online digital library you can then sync that library to the iPhone app.  In order to get the sync to work you just need to install the app via iTunes, and fire it up.  You will be asked to sign in to your Mendeley account and as soon as you login the app will sync your library’s metadata.  You will be able to see all of your collections, your list of favourites, your recent items and also any shared collections that you are a member of.

Once you have your library in your pocket your can search within your collections.  In addition you can also share a citation for any item in your library via email. If you have the Pdf of a paper in your library, then there will be a ‘download’ icon to the left of the paper. You can download the Pdf straight to your device, and from there you can read it any time you like when you are offline.

You can also share the citation of a paper via email, straight from within the app.

Obviously at the moment the biggest limitation with the new app is that you can’t edit any of the metadata for your papers, but don’t worry, we will be releasing a full version of  Mendeley for iPhone in the near future, and we are also working hard on an iPad version too.  We think Mendeley is perfect for the iPad and we want to make sure that you have the best experience available for managing the information that is important to you.  We are really keen to get feedback on the app that we are releasing today so that we can make some rapid improvements.  We really hope that you enjoy the Lite version!

As a PhD student I find myself roaming the Internet quite a bit in search of literature for my research project which can be really time consuming. Looking for the right keywords, opening each relevant result into a new tab, downloading each paper of interest, finding the cryptically named PDF file and then adding it to your library in an organized fashion (phew). So anything that can cut back this strain of accessing and organizing research papers is most welcome.

In previous posts I’ve mentioned Mendeley’s web importer, which helps retrieve papers directly to your Mendeley Web account. That’s all good, but what about papers that you already have on your computer spread about in different folders or hard drives?

There are multiple ways to import files from your hard drive directly into Mendeley Desktop. You can add one file at a time, a full folder in one go or even make a specific “Watched” folder.

A “Watched” folder is basically a folder that Mendeley keeps an eye on for any new files and automatically imports new documents with minimal interaction on your behalf. Just drop or download your PDF documents into your watched folder and Mendeley will do it’s thing (I mean auto-extract it’s metadata and add it to your library!).

So we now have a web importer for online retrieval and an automated watch folder. Looks like we are set!

My references and documents are all nice and organized within Mendeley Desktop and accessible online but when I look at the files on my computer, I notice something. In fact, I notice the lack of something: meaningful file names.

As you can see in the image above, the file names are not very explanatory and whenever I have to pick a file to send to a colleague or open it directly for some reason, it becomes a guess-the-mystery-file name game. Not to mention that every time I add a file to that folder with a similar name, I get this fantastic message:

The file you are trying to copy “sdarticle.pdf” already exists. Cancel or overwrite?

Good question, do I want to overwrite sdarticle.pdf? Do I have any idea what is in that file? The most probable answer to both these questions is no. Once again, Mendeley has considered this situation and provides an effortless way to organize your files with a built-in feature called: ‘File Organizer’.

As the name suggests, this feature can organize your files for you in a few different ways. You can store your files in a centralized folder with all the files renamed to a specific format. The format is easy to customize by simply dragging the naming categories from one input box to the other.

As you can see in the image above, I chose to rename my files and keep them in one folder with the file name following the format Author – Year – Title. I did not add the journal to the file name, but could have easily done so by just dragging it down into the file name.

There’s an option to organize the files into sub-folders, however I chose not to do so. That’s just my personal choice even though I know colleagues of mine prefer to separate things into sub-folders by year.

Once I’ve picked how I want my files to be sorted and renamed, I go ahead and click apply. Folders get created, files get renamed and I’m done:

These file names are much easier to understand and are categorised how I want them. This feature has not only organized my files into a folder with proper file names, but it will keep any new documents I add in the same orderly fashion. Neat huh?

Having seen a lot of ‘top 10 lists of 2009’ around, we thought we’d throw in our two cents and give you the top 10 most read articles on Mendeley, published in 2009!

The top paper for 2009 was written by Uri Alon, entitled: ‘How to choose a good scientific problem’, published in the journal “Molecular Cell.” Our stats tell us that there are currently 74 Mendeley users who have read this paper, even though it was only published in late 2009.

The full list of the top ten articles published in 2009 on Mendeley (as of 28th January 2010) is:

1. Uri Alon, ‘How to choose a good scientific problem’, Molecular Cell (2009), Volume: 35, Issue: 6

2. Castro Neto et al, ‘The electronic properties of graphene’, Reviews of Modern Physics (2009), Volume: 81, Issue: 1

3. Erez Lieberman-Aiden et al, ‘Comprehensive mapping of long-range interactions reveals folding principles of the human genome’, Science (2009), Volume: 326, Issue: 5950

4. Ed Bullmore & Olaf Sporns, ‘Complex brain networks: graph theoretical analysis of structural and functional systems’, Nature Reviews Neuroscience (2009), Volume: 10, Issue: 3

5. Zhong Wang, Mark Gerstein, Michael Snyder, ‘RNA-Seq: a revolutionary tool for transcriptomics’, Nature Reviews Genetics (2009), Volume: 10, Issue: 1

6. Development Core Team, ‘R: A Language and Environment for Statistical Computing’, R Foundation for Statistical Computing (2009) Volume: 2, Issue: 09/18/2009

7. Fatih Ozsolak et al, ‘Direct RNA sequencing’, Nature, Volume: 461, Issue: 7265

8. Benjamin M Bolker et al, ‘Generalized linear mixed models: a practical guide for ecology and evolution’, Trends in Ecology & Evolution (2009), Volume: 24, Issue: 3

9. Michael Schmidt & Hod Lipson, ‘Distilling free-form natural laws from experimental data’, Science (2009), Volume: 324, Issue: 592

10. Stephen J Eglen, ‘A quick guide to teaching R programming to computational biology students’, PLoS Computational Biology (2009), Volume: 5, Issue: 8

We’d like to point out that this isn’t an authoritative list of all the ‘most read articles for 2009’. Instead, these are the ones that appear in Mendeley user libraries and show some early indications of the popularity of a journal article. We will also track the evolution of these stats over the course of 2010.

Readership complementing the impact factor

With Mendeley’s growing user base, the readership count can complement other measures, such as citation metrics, adding an extra dimension to assessing a journal article’s impact.

For example, the article “How to choose a good scientific problem” is a general interest article, rather than being specific to biology which suggests it is not likely to have a high citation count in future primary research literature.

Nonetheless, it is already the most read paper on Mendeley published in 2009, a factor that would otherwise be missed. This indicates that the readership count can allude to other ways in which articles are used within a community, and therefore increase awareness of what should be read. The next step will be to anonymously track reading time and quality rating metrics to gather the most accurate data possible for our upcoming personalized recommendation engine.

Predicting research trends?

Understanding and predicting research trends is an important part of research. The citation count, used for decades as the gold standard in article-level metrics, can verify broad trends occurring within academic disciplines such as biology. While quite accurate, official citation metrics take two years to calculate. In contrast, readership statistics may be able to predict similar trends in real-time.

For example, look at The Scientist’s list of the hottest biology papers in 2009 (all published in 2007). The readership count for these papers on Mendeley correlates with ISI’s citation count at r=.76 (two-tailed, p=.13 due to the low sample size) – a near perfect correlation, even if only based on five papers and our userbase of just over 100,000 users:

Comparison of Mendeley’s most read papers with the ISI Citations

We look forward to comparing the top 10 list shown above to the official ISI citation metrics for 2009 publications when they are calculated and released later in 2010 or 2011.

In summary, using Mendeley’s readership figures alongside the citation metrics should make it possible in the future to evaluate the scope of a journal article within the community more effectively. Finally, further refinements and understanding of readership metrics might make it possible to identify the next big trend in the academic world.

Methodology

The top 10 list was made by noting how many times a paper appears in the libraries of individual Mendeley users (readership count) and how many distinct user tags were attributed to that paper (tag count), then we filtered the results to include only papers from 2009 – done!