Victor Henning, Mendeley Co-Founder, speaks at the ScienceBusiness Awards 2012 in Brussels (Photo by ScienceBusiness)

The existing Mendeley offering will continue to be free, so that we can continue to grow our user base as we have in the past, and we will also integrate Mendeley into Elsevier’s existing offerings like ScienceDirect or Scopus to increase their value. This actually means that we’re now under less short term pressure to monetize Mendeley’s individual users. When we were an independent start-up, we had to think about charging for every new or additional feature, in order to get to break even. Now, we can think more about the long term again.

For example, this enabled us to double our users’ storage space for free immediately after the Elsevier announcement. We had previously also planned to make the sync of highlights & annotations in our forthcoming new iOS app a premium feature – today, we decided instead that it will be free for all users, and thus also free for all third-party app developers to implement. And, as mentioned above, we are currently reviewing our collaboration features to see if we can expand them for free, too.

This week we have released a new version of Mendeley with some major updates. The major new feature in Mendeley 0.9.8.1 is public collaborative groups.

What are groups?

Groups are a simple way for you to collaborate with your colleagues to create a shared collection of documents. Groups allow members to put together a list of papers and share notes. There are three types of groups:
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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!

Some may have already heard the news that 2collab, a product of Elsevier, is no longer accepting new users and will be shutting down in due time (updated). 2collab and Scopus Product Manager, Michael Habib, announced this on January 16th at the Science Online conference in Raleigh, North Carolina.

Seeking to provide a reading list alternative for their 2collab users, it was also announced at Science Online that Mendeley was chosen to enable the opt-in transfer of any 2collab public library folders.

How it works:

1) If you are a 2collab user and do not have a Mendeley account you will first need to sign up here for free.
2) Once registered or for those already registered on Mendeley, go to the ‘Accounts’ link located at the top of the Dashboard page after signing into Mendeley.com.
3) At the bottom of the accounts page you will see a form for entering your 2collab username details.
4) Your public folders will be imported and the next time you open or sync the Mendeley desktop software those folders will be visible. They will also be available on the Web at Mendeley.com and can be viewed by proceeding to the ‘Library’ page.
5) Within the Mendeley desktop, you will then have the option to turn those folders into ‘public collections’ so that others can continue to stay up to date with what you are reading via RSS and other means. For example, here is a feed on Norovirus.

Please contact 2collab if you need any help specific to 2collab.

We wish the 2collab team the best and know that they are already working on some great stuff at Scopus and elsewhere.

Jason Hoyt, PhD
Research Director | Mendeley

Follow Jason & Mendeley on twitter

In piphilology, one hundred thousand is the current world record for the number of digits of pi memorized by a human being (well, that’s according to Wikipedia). So, as happy as we are at Mendeley to have 100,000 users onboard, we regret to say that it is now beyond our limits for us to remember every single user on our site (but good to see that you keep on writing and helping to improve Mendeley). In the same week we crossed a second milestone of 8 million research articles uploaded to our database in less than a year. Currently Mendeley’s article database continues to expand as researchers, students and scientists from around the world upload, collaborate and share their research using Mendeley. In April 2009 we reached the 1 million article mark, which means the number of articles in our database has doubled in size every ten to twelve weeks. To give a little context: the world’s largest online research database by Thomson Reuters took 49 years to reach 40 million articles.

A big thank you to Techcrunch’s Sean O’Hear who wrote: “Mendeley could be the largest online research paper database by early 2010″ and James Glick from The Next Web who wrote: “Mendeley ‘the last.fm of research’ hits new heights”.

And congratulations to our growing community of users!

Image by Jorel314

Roughly three and a half months after our announcement that we would plan to collaborate with CiteULike it’s even better news to announce that the first step is live – Mendeley users can now access their CiteULike data from within Mendeley. As we said in our previous blog post,

Your CiteULike account will show up as a “Document Group” in our Mendeley Desktop software, thus making your CiteULike metadata available to you in a desktop interface – from where you can manage them offline or insert citations and bibliographies into Microsoft Word, for example.

Follow these steps to activate the integration of CiteULike with Mendeley:

• On your settings page, scroll to the bottom and enter your CiteULike username. Then click OK, and allow any pop-up blocking messages displayed by your browser — if any.
• You will be taken to an activation message on CiteULike’s site — confirm this action.
• This will take you to your Edit Profile page with a check-box displayed next to Enable Mendeley. You will find this at the bottom of the form, highlighted. Click Update Profile to save this.
• You will now see your CiteULike profile page. Don’t worry if you don’t see any confirmation — this is normal. The synchronization is now set up successfully.

You can enable, or disable, Mendeley synchronization by going to your Edit Profile page on CiteULike, and checking, or unchecking, the check-box labelled Enable Mendeley. If you don’t login to Mendeley once every 30 days, this sync will be disabled. You can re-enable it by re-checking this box.

This is obviously just a first step – together with the guys at CiteULike we are now working on a two-way synchronization. Our reference manager Mendeley Desktop now already offers a wide selection of import/export options (plus a Web Importer to grab citations off the web), and if you have any additional suggestions or comments, have your say on our feedback page.

[Victor:] Completing our trinity of Community Liaison Goodness, may I introduce Brandon King! He is a Ph.D. student in neuroscience at Brown University, doing fascinating research on brain-computer interfaces (so don’t mess with him, or his army of cyborgs will come and get you. No, I just made that up. He’s as nice and funny as they come). We’re excited to have him on our team! Here’s his introduction in his own words:

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I graduated college 2001, the year that journals were just beginning to become available online. So, for the vast majority of my undergraduate existence, I was forced to do the unthinkable: go to libraries and pull articles from the stacks. “I don’t get it. I’m looking for small bits of constantly updated text, so for my uses, the whole library could be replaced by a web page and a search box.” Of course, this was back when saying you read something on the internet was akin to citing facts from a fictional work.

After spending five years in ‘industry’, I decided to return to academia to continue research on brain-computer interfaces. When I discovered that I could download almost any paper on any topic I could imagine, I was like a kid in a candy store. I could hear my Windows machine cry when the indexer hit my “Papers” folder. As I honed in on my eventual project/thesis topic, I began to amass a big collection of PDFs. “No problem,” I thought. “I’ll just sit down for a whole day at some point and organize it all!”

That was when my papers were numbering around 200. After discovering RSS feeds and launching a blog, that number quickly ballooned up into the thousands. As I type this, there are ~3,700 papers in my library. Yes, it is impossible for me to have read them all, but having read at least the abstracts from each, the interplay of all these ideas and the trends in topics over time have played a major role in shaping my understanding of my field of interest.

Did I mention that none of these PDFs have file names? Well, they didn’t, unless you consider sdarticle(122).pdf to be a useful identifier.

As I started working on my project proposal, I knew I had to find some way to keep this mountain of information in order. It should be easy enough to spend a couple hours tediously searching for each paper in one of those ‘reference manager’ programs, right? Or someone must have come up with a really snazzy web app to take care of references, right? Wrong and wrong. At least that’s what I thought until a member of the Mendeley team brought their program to my attention.

Maybe I dismissed it at first because of the beta moniker or the funny name, but as soon as I installed Mendeley and started to play with it, I was hooked. The hours, nay, days, it saved me made it instantly one of my ‘must have’ programs.

I saw huge potential in Mendeley, and started submitting suggestions and bug reports (it was in version 0.5 at the time) and when Victor came to the States to talk with university librarians, we arranged to meet. I walked away thinking Mendeley could easily be a game changer in the same way online journal access changed research.

We came up with the idea of adding the position I am now starting at because realizing the potential of this awesome tool is only possible by engaging the people that are going to use it. Each lab, each researcher, and each student has their own system of compensating for the near Paleolithic Era reference management tools they have access to. To make Mendeley the most useful program out there, we have to get your feedback on how we can better adapt Mendeley to the way YOU work while at the same time gently nudging people away from the status quo in which reference managing is tedious but necessary. I want to make Mendeley as much a source for creating ideas and new connections between ideas as it is for simply managing references. I think one of the unspoken lessons of research is that you have to stop looking at papers as files or a limited set of ideas, and understand instead how the work fits into the topic of interest as a whole. My hope is that Mendeley will allow researchers to bridge old ideas, inspire new ones, and provide a platform for sharing the information that led them to a novel insight. You know. Small goals, like change everything.

Hurray! William Gunn has joined us as Community Liaison! Ricardo Vidal became our first Community Liaison two weeks ago, so with William we have now doubled the brains and talent behind our outreach efforts. William has just completed his Ph.D. on adult stem cells and bone biology at Tulane University. On his blog Synthesis, he has also been writing about open science and social research software. Here’s the story (re-posted from Synthesis) on how he came to join us, in his own words:

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Reference managers and I have a long history. All the way back in 2004, when I was writing my first paper, my workflow went something like this:

“I need to cite Drs. A, B, and C here. Now, where did I put that paper from Dr. A?” I’d search through various folders of PDFs, organized according to a series of evolving categorization schemes and rifle through ambiguously labeled folders in my desk drawers, pulling out things I knew I’d need handy later. If I found the exact paper I was looking for, I’d then open Reference Manager (v6, I think) and enter the citation details, each in their respective fields. Finding the article, I’d select it and add it to the group of papers I was accumulating.

If it didn’t find it, I’d then go to Pubmed and search for the paper, again entering each citation detail in its field, and then do the required clicking to get the .ris file, download that, then import that into Reference Manager. Then I’d move the reference from the “imported files” library to my library, clicking away the 4 or 5 confirmation dialogs that occurred during this process. On to the next one, which I wouldn’t be able to find a copy of, and would have to search Pubmed for, whereupon I’d find more recent papers from that author, if I was searching by author, or other relevant papers from other authors, if I was searching by subject. Not wanting to cite outdated info, I’d click through from Pubmed to my school’s online catalog, re-enter the search details to find the article in my library’s system, browse through the system until I found a link to the paper online, download the PDF and .ris file (if available), or actually get off my ass and go to the library to make a copy of the paper.

As I was reading the new paper from the Dr. B, I’d find some interesting new assertion, follow that trail for a bit to see how good the evidence was, get distracted by a new idea relevant to an experiment I wanted to do, and emerge a couple hours later with an experiment partially planned and wanting to re-structure the outline for my introduction to incorporate the new perspective I had achieved. Of course, I’d want to check that I wouldn’t be raising the ire of a likely reviewer of the paper by not citing the person who first came up with the idea, so I’d have some background reading to do on a couple of likely reviewers. The whole process, from the endless clicking away of confirmation prompts to the fairly specific Pubmed searches which nonetheless pulled up thousands of results, many of which I wasn’t yet aware, made for extraordinarily slow going. It was XKCD’s wikipedia problem writ large. (more…)