Mendeley Blog


Archive for the ‘academic features’ Category

28 January 2010 by Victor

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

2. Castro Neto et al, ‘The electronic properties of graphene’, Reviews of Modern Physics (2009), Volume: 81, Issue: 1
academic features The top 10 journal articles published in 2009 by readership on Mendeley

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

4. Ed Bullmore & Olaf Sporns, ‘Complex brain networks: graph theoretical analysis of structural and functional systems’, Nature Reviews Neuroscience (2009), Volume: 10, Issue: 3
academic features The top 10 journal articles published in 2009 by readership on Mendeley

5. Zhong Wang, Mark Gerstein, Michael Snyder, ‘RNA-Seq: a revolutionary tool for transcriptomics’, Nature Reviews Genetics (2009), Volume: 10, Issue: 1
academic features The top 10 journal articles published in 2009 by readership on Mendeley

6. Development Core Team, ‘R: A Language and Environment for Statistical Computing’, R Foundation for Statistical Computing (2009) Volume: 2, Issue: 09/18/2009
academic features The top 10 journal articles published in 2009 by readership on Mendeley

7. Fatih Ozsolak et al, ‘Direct RNA sequencing’, Nature, Volume: 461, Issue: 7265
academic features The top 10 journal articles published in 2009 by readership on Mendeley

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

9. Michael Schmidt & Hod Lipson, ‘Distilling free-form natural laws from experimental data’, Science (2009), Volume: 324, Issue: 592
academic features The top 10 journal articles published in 2009 by readership on Mendeley

10. Stephen J Eglen, ‘A quick guide to teaching R programming to computational biology students’, PLoS Computational Biology (2009), Volume: 5, Issue: 8
academic features The top 10 journal articles published in 2009 by readership on Mendeley

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!

25 January 2010 by Ben Romberg

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

10 December 2009 by Ben Romberg

boxed inUpload Space

When we first cleared out some room on our servers to allow you to upload PDFs to your private Mendeley Web account, we spared 500 MB per person, given that PDFs are usually around 1-2 MB, this  enables you to store 250-500 PDF documents online. In response to requests (or should we say popular demand?) as well as bulging research collections, we will increase the storage space as part of a premium package in early 2010 (we are also working on more detailed stats, a recommendation engine and some other nice features).

For the growing number of people who really can’t wait that long (hats off to those of you who have already maxed out your accounts!), please write to support@mendeley.com with a request for extra space and we’ll be happy to pass out some freebies. It will be a temporary upgrade but you won’t have to switch to a premium subscription later. Once the premium features are in place and if you choose not to upgrade, you won’t be able to add any further documents to your web account (if it is larger than 500 MB), but your data will still be accessible and safe.

Shared Collections

Taking a similar approach with shared collections – which are currently limited to ten people – we quickly found requests rolling in for collections of a much larger size, mainly for departments and labs. So, we will raise the number of people who can access a shared collection as part of a premium package and in turn make the limits flexible. Again, write to support@mendeley.com if you need more shared collection slots within your department, lab, or research group. Send us your username (e-mail address), the name of the collection, and the number of people you would like to collaborate with and we can expand your shared collection to make it a bit more sociable for the festive season.

(Image by CwThomas43)

15 September 2009 by Ricardo

School is back, so we thought it would be a good time to demonstrate how Mendeley can help professors, teachers, and alike to set up a “Recommended reading” list for their incoming students:

1) Create a new collection in Mendeley (left-side pane)
Don’t worry about the name you give the collection. If you want to rename the collection later just double click on it.

2) Select papers from your library (middle pane)

Make a selection of papers that you would like to include in your “Recommended reading” list and drag & drop them into the newly created collection. Note that you can have papers in multiple collections.

Mendeley Desktop

3) Make your newly created collection public (collections are private by default)
Click on your collection (left pane) to see the papers you’ve added to the list. You’ll notice there’s a “Edit Settings” button above the list (top-right of middle pane). Click it to change your Collection access settings from private to public. Feel free to add a short description of your collection’s content. Finally, press “Sync Library” and a link will be generated for your public collection.

4) View your public collection online and more
By clicking on the link that was created for your public collection you will be taken to your public collection web page at Mendeley Web where you’ll find the list of papers you included in your “Recommended reading” collection. So far so good.
You’ll notice on the left-hand side the title you gave your collection and your name after “Created by…”. There you also find the papers you added! (See one of my public collections here)

academic features Share recommended readings using Mendeleys Public Collections

5) Sharing the goods
You find the tools you need to easily share your public collection on the left side of the collection’s web page. “Embed on other websites” and “Subscribe to RSS”. Let’s focus on the first one, since it’s the easiest one and will allow you to add your list to your class page with a simple copy & paste of provided code.
Click on the “Embed on other websites” option and a text field will show up with code you can use to display your “Recommended reading” collection on your class site.
Notice that there is a “Preview and Customize” button that will allow you to do exactly what they say, preview your collection list or customize the color and size of the frame that will display your list.

6) Copy, paste, stay up-to-date
Once you’ve picked the right color and size for your embedded reading list, you simply copy the provided line of code in the text field and paste it into the HTML of your class page. It’s that simple!
While you’re at it, keep in mind that this is the only change you’ll have to do on your page to keep the list up-to-date. If you want to add a new paper to your reading list, just open Mendeley, import the file and drag & drop it into the public collection you created for your class and sync your library. That’s it.

So there you go, in 6 simple steps you set up your “Recommended reading” list for your class and any updates or changes from one year to the next is easily maintained within Mendeley.

This example can be adapted to a number of other situations. For example for lists of published work on a personal or lab website, a list of recently read papers on a blog, just to name a few.

If you happen to run into any issues setting up your public collection for your class (or for anything else!), please feel free to contact us at support@mendeley.com.

14 September 2009 by Paul

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!

2 September 2009 by Paul

Since we are getting closer to releasing version 1.0, we were discussing how to get even more detailed feedback from our users than we currently get through our support system.

Being able to chat with you guys face-to-face would obviously be best so we said: lets try it and do an ‘Open Office Feedback Session’. Meaning that on Friday 18 Sept at 5 pm everyone who is interested can come to our offices in London Farringdon, talk to different members of the team and tell us face-to-face what you like to see improved or added to Mendeley. You can also bring your notebooks and show us directly what’s not working for you or which feature you would like to do differently.

Mendeley office

Your feedback is very valuable to us so as a thank you we would serve drinks and snacks at our office which we could even have on our roof terrace if the weather will allow it (probably not – lets face it :) ).

If you’re interested, please drop us an email at paul@mendeley.com. We’re looking forward to meeting you!

24 August 2009 by Paul

Just a quick update: the Google Scholar lookup in Mendeley Desktop will now return improved document details. We’ll continue to work on improving this but if you have got any suggestions let us know and we’ll look into it.

As for other updates we are currently testing a portable Windows version of Mendeley Desktop which we’re hoping to release this week. We are also planning to finish all “behind the scenes” work for the next major release this week as well. More bug-fixing is needed though so the next version will probably be out around mid September.

5 August 2009 by Jan

As one of the many requested features from our feedback page, Mendeley Web now supports COinS (ContextObjects in Spans). COinS is an open and easy to use specification for publishing OpenURL bibliographic metadata in HTML. On web pages, embedded COinS can be read and processed by applications.

Also Mendeley’s Web Importer can now identify COinS embedded on other websites. This information can then be easily imported into your Mendeley research library. In addition, a COinS section is embedded in each of our article pages. This means that other bookmarklets can extract and process the information from Mendeley’s article pages.

Addendum: COinS are not only embedded in article pages but also in profile pages (own publications list) and in public collection pages.

6 July 2009 by Paul

This update introduces a lot of new features, including a PDF viewer, OpenOffice.org integration on Mac OSX and Linux, and many more. Interface issues, and a number of bugs are also addressed in this release, as well as improvements to the overall stability.

Just to give you a teaser – this is how it looks like to add notes to PDF documents:
Annotate PDFs

New Features:
  • Built-in PDF viewer for viewing PDFs directly in Mendeley Desktop
  • Support for annotating PDF files (syncing notes to and from Mendeley Web is planned for the next release)
  • Many additional online lookups (CrossRef, PubMed, Google Scholar)
  • Public document collections (reading lists) which can be embedded on other websites
  • OpenOffice.org Writer plugin for Mac OSX & Linux
  • Improved native user interface for Mac OSX
  • Individual synchronization and privacy settings for each document collection
  • Auto-save changes and undo functionality for quick document detail editing
  • Flagging documents as favorites
  • Marking a document as read, or unread
  • Detecting duplicate documents when importing library files or PDFs
  • Merging together document authors, tags, keywords or publications
  • Editing document details, or tags for multiple documents simultaneously
  • New “Trash” collection so you can restore deleted documents
Improvements to Existing Features:
  • Changes to the toolbar and terminology in light of usability tests
  • Better handling of documents with unconfirmed details
  • More robust synchronization between Mendeley Desktop and Mendeley Web
  • Search results are presented in a much easier to read format
  • Searching for documents now searches the document details, as well the PDF text
Bug Fixes:
  • Detect and handle duplicate citation keys being used when exporting to BibTeX format
  • Improved full-text indexing stability for search
  • Allow documents to be renamed without the file organizer being enabled
  • Clean up the formatting of exported citations
  • Handle tags and keywords properly when exporting to BibTex format
  • File organizer stability fixes
  • Corrections to various citation styles
  • Plus many more…

So no time to waste – visit our download page and give it a try, would be great to hear what you think! :) Also, thanks a lot for all the feedback from our leadusers who helped us polishing this new version.

Please note: As part of the upgrade process, if you have an online account already, Mendeley Desktop will need to perform a full sync when it next starts. This may take some time depending on the size of your library. It is a one-off sync that is required to ensure compatibility with an upgraded sync method.

If you have suggestions how to improve managing research papers with the Mendeley reference manager please let us know by visiting our feedback forum. If you encounter any problems using Mendeley or have questions to ask, please e-mail us at support@mendeley.com.

2 June 2009 by Jan

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.