Managing your library the modern way with tags and filters.

delicious-logoAs 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.Read More »

One on one with Bruce D'Arcus, creator of the community-driven Citation Style Language

Bruce D'ArcusMost 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.Read More »

Our first iPhone app has Arrived!

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!

The top 10 journal articles published in 2009 by readership on Mendeley

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

Publication ISI Citations Readers on Mendeley
A M. Werning, et al., “In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state,” Nature 448: 318-24, 2007. 512 26
E. Birney, et al., “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project,” Nature 447: 799-816, 2007. 618 63
A. Barski, et al., “High-resolution profiling of histone methylations in the human genome,” Cell 129: 823-37, 2007. 560 33
K.A. Frazer, et al., “A second generation human haplotype map of over 3.1 million SNPs,” Nature 449: 854-61, 2007. 588 46
K. Takahashi, et al., “Induction of pluripotent stem cells from adult human fibroblasts by defined factors,” Cell 131: 861-72, 2007. 886 64
_______________________

Pearson Correlation r = .76

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!

France’s largest science catalog adds Mendeley import button

We are very happy to announce that CAT.INIST, one of Europe’s largest scientific research catalogs, has added Mendeley’s ‘easy import button’ to its article pages. CAT INIST joins the Public Library of Science (PLoS) and ArXiv.org who have also added Mendeley’s import button to their article pages.

CNRS, “Centre National del la Recherche Scientifique” (the French National Research Institute), provides research articles and information for scientists and academics Europe-wide. The cooperation now allows users to quickly import articles to their Mendeley online library.

“CAT.INIST (established in 1973) hosts a collection of 15 million bibliographic records, held in the CNRS in Paris. The catalog provides research articles in the fields of Science, Technology, Medicine, Humanities and the Social Sciences.”

Additionally, by installing Mendeley’s Web Importer into your browser, you can easily import articles from many other databases as well, such as Google Scholar, PubMed, IEEE, ISI Web of Knowledge, etc. For a complete list of supported websites, have a look at http://www.mendeley.com/import.

For more information on CNRS’ catalog visit http://cat.inist.fr.

CAT INIST

What’s relevant to me….right now?

Total knowledge
Above is an image from a talk that I gave earlier this year. As you can see, if I lived decades ago, I could somewhat keep up with all new research that pertained to me. Today though? Forget about it. There is just way too much going on. Even if I consider myself to be in a niche research field, I should still be keeping up with cross-disciplinary material that is relevant to my research. There is just no way to keep up with all of that information. It is information overload.

Ask yourself how you find out what is relevant to you in your research field. Got it? OK, we’ll get back to that, but before we do, ask yourself what percentage of all relevant information are you actually consuming? Let’s look at that figure above in the form of a pie chart to help us answer that question. Read More »

Reminder – Mendeley ‘Open Office’ this Friday!

This is just a quick reminder of our ‘Open Office’ event this coming Friday 18 Sept from 5pm onwards – in case you haven’t seen our previous blog post from last week: we’d like to invite London users to come in to our office and chat to us directly in order to share their general feedback and their suggestions as to what they’d like to see improved in Mendeley. Drinks and snacks will be provided.

If you’re interested in coming along, please email anne@mendeley.com.

We’re looking forward to seeing you!

If you're near Toronto (and even if you're not), you should attend this event

I just got an invitation from Jen Dodd, whom I met last fall at the Science in the 21st Century Conference at the Perimeter Institute in Waterloo (what a great conference that was!). Jen is organizing a fabulous event:

Science 2.0:
What Every Scientist Needs to Know About
How the Web is Changing the Way They Work

The MaRS Centre, 101 College St., Toronto
Wednesday, July 29, 1:00-6:00 pm, with wine and cheese to follow

Wine, cheese and a speaker list like this – who could resist:

  • Choosing Infrastructure and Testing Tools for Scientific Software Projects
    Titus Brown
  • A Web Native Research Record: Applying the Best of the Web to the Lab Notebook
    Cameron Neylon
  • Doing Science in the Open: How Online Tools are Changing Scientific Discovery
    Michael Nielsen
  • Using ”Desktop” Languages for Big Problems
    David Rich
  • How Computational Science is Changing the Scientific Method
    Victoria Stodden
  • Collaborative Curation of Public Events
    Jon Udell

Here is more information about the event on the organizers’ blog.

Ironically and sadly, even though I’ll be on the right side of the pond when this event takes place, I won’t be able to attend – Jan and I will be hosting a session at this year’s Campus Technology Conference in Boston at the same time.

However, if you’re interested in these topics, here’s a little reminder about our own Science Online London Conference taking place on August 22.

Mendeley Web redesign goes live

If you knew the old site, you’ll certainly have noticed already! The main color used to be dark blue with some red-brownish hues. Our goal with the redesign was to make it brighter, airier and less cramped, with the main colors being silver-grey and deep red. We also added better explanations and illustrations of what Mendeley actually is and does!

Here’s the new homepage (the screenshot is actually matched to each visitor’s OS – e.g. if you’re using Linux, the screenshot will show Mendeley Desktop on Ubuntu):

New Mendeley homepage

And here’s the new “How it works” page, which replaces our old “Tour” page.

how-it-works

The redesign isn’t completely finished yet – we’ll be updating many more parts of the site soon, while also adding new features. Please let us know if you catch bugs or design niggles we’ve missed!

What do you think of the new look? Is it pretty enough to want to make you kiss your screen?