Journal of FUBAR and Negative Results

Last evening I attended a panel discussion entitled, “Making the Web work for Science” hosted by Science Commons. It was held at the Commonwealth Club in San Francisco and moderated by Tim O’Reilly. On the panel were Jimmy Wales, founder of Wikipedia; Stephen Friend, MD, PhD President, CEO and a Co-Founder of Sage; and John Wilbanks, VP of Science at Creative Commons.

While I was hoping more would be discussed on modeling the habits of researchers with web tools, the focus on Open Science was still a good conversation. At one point, Dr. Friend mentioned the need to publish negative results. With the ability to inexpensively self-publish and distribute data on the Web, why then, aren’t we seeing more of this?

Trying to answer from my own experience as a researcher, there are at least three reasons, or rather fears:

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A belated photo from our TechCrunch Europas Award

It just occurred to me that, because I went on vacation immediately afterward, we didn’t yet post a photo of our TechCrunch Europas Award! Two weeks ago, we won the prize for “Best Social Innovation (Which Benefits Society)”. Wonderful title, isn’t it?

Mendeley wins TechCrunch Europas Award for Best Social Innovation

A big thank you to everyone who voted for us, to the Europas jury, to event organizer Mike Butcher and Moonfruit (for sponsoring the prize), and of course our team who made this possible!

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.

And the winner is… Jonathan Peelle!

Last month, we decided to reward loyal referrers who invited at least 3 colleagues via the Mendeley invite tool and entered them into a prize draw to win an ipod shuffle.

Last week we’ve randomly drawn the winner and it is…. Jonathan Peelle from Cambridge University! He is a postdoctoral fellow at the MRC Cognition and Brain Sciences Unit researching speech and language processing in the human brain.

Here’s what he thinks about Mendeley:

Jonathan Peelle“There are three things that drew me to Mendeley. The first was the combination of desktop software and the web interface both of which are excellent and support the way I work. In particular having the web interface means my library is always accessible, wherever I am.

Second, the ability to share papers with co-workers is fantastic. It enables me to see what my colleagues are reading and saves me the trouble of typing in or searching for references they have.

Finally, being able to organize my articles by topic/folder and tags is very handy, and helps me to find those slightly more obscure references I’ve read and filed but then promptly forgotten.”

A big thank you to Jonathan and all other loyal users for spreading the word about Mendeley!

2 new full-time Mendeleyans

We are happy to announce two new members of the Mendeley family. While Carles Pina adds some Spanish flavour to Mendeley Desktop, Nicholas Jones increments the Southampton University headcount to three by bringing some award-winning expertise to the Mendeley Web table. In their own words:

Carles PinaCarles Pina is a software engineer at Mendeley. He studied computer engineering at La Salle – Ramon Llull University in Barcelona and thought working for Mendeley is a perfect reason to relocate to rainy London. Well, after growing up near Barcelona most cities feel ‘rainy’ he thinks.
In his spare time, he enjoys programming in C, Python or C++ maintaining projects like qdacco or contributing to other free software projects. He is also fascinated by attending computer meetings in general and loves traveling.
Nicholas JonesNicholas Jones is a software engineer for Mendeley Web. He studied Computer Science at the University of Southampton, graduating with a BSc in 2009. Whilst at the University of Southampton he won the Sir William Siemens Prize for “excellence and innovation on an individual 3rd year project” and the Netcraft Prize for acedemic acheivements in his 2nd year.
When not coding away at PHP and JavaScript, Nicholas enjoys trawling through social news sites such as Reddit, looking for interesting and invigorating items to read. Nicholas also has a keen interest in music and when not listening to it, may be found strumming away at his guitar.

Top 8 influential Science and Tech Stories of 2009, so far

The year 2009 is halfway through and already we’ve seen some great stuff being published, created, and predicted that could have a major impact in the future. Each of the eight items were chosen because they could influence how every one of us communicates, learns, and lives more so than any other discoveries so far in 2009. What’s that? You’re not a science or techie person? It doesn’t matter, you and everyone else are going to be affected because of the work and ideas brought forth below. So, pay attention. We start with some exclusive, never before public news from NASA, very fitting as today is the 40th anniversary of the Apollo 11 launch.

1. NASA starts project Nebula (new exclusive information) Nope, this isn’t another space probe. This is the government giving a head nod to cloud computing. They’ve wisely hired a few seasoned Internet entrepreneurs to command the mission at NASA Ames and take NASA data into the cloud. That much has been known since May. Last week I had dinner with Chris Kemp (CIO, NASA Ames) and some of the Nebula team. Here’s what Kemp agreed to reveal publicly for the first time:

”NASA collaborates with hundreds of universities, commercial partners, and other federal and international partners. The NASA Nebula cloud computing platform will dramatically increase the efficiency and productivity of these collaborations.”

How it affects you: If you’re a NASA collaborator or want to become one, then get ready. As for every day citizens, you too will reap the rewards of Nebula via the research performed. There’s also been a lot of speculation that Nebula will power data sets other than just NASA’s, such as Is this true? Let’s put it this way. Their focus, for now, is on NASA’s data. The rest is my opinion only: imagine the possibilities if we had a national or even international cloud computing platform. Remember that it was originally a similar government project called ARPANET that gave rise to today’s Internet. This could be BIG for science, tech, and planet Earth.

Hurdles to jump: Kemp and team must first get this rolling with NASA before opening it up to outsiders. And it’s government, so there’s a lot of bureaucracy and red tape to cut through to get this done and costs down. President Obama and Vivek Kundra (Federal CIO), if you’re listening, then help this team out by cutting that tape and give them carte blanche funding to get it done.

More info: Official NASA Nebula websiteFollow Nebula on Twitter

World avoided2. The ozone has been saved – sort of

Ever ask yourself what the ozone layer and our planet would look like today if we hadn’t passed some of those pesky environmental laws back in the 1980’s? Researchers, led by Paul Newman, at NASA’s Goddard Space Flight Center and elsewhere asked “What would have happened to the ozone layer if chlorofluorocarbons (CFCs) had not been regulated in 1987?” This was an important and difficult to answer question, until this year. I reached Dr. Newman for a comment to let us know the most important message from this research:

“If chlorofluorocarbons had not been regulated by the Montreal Protocol, two-thirds of the ozone layer would have been destroyed by the year 2065 with a consequent increase of surface ultraviolet radiation to extreme levels.”

How it affects you: While the conclusions were based on computer models, the importance of environmental policy cannot be overstated, and now we have proof that policy does work. Oh, and your grandkids will get to play outside in 2065. Even by 2020 it would have been pretty nasty without SPF 3 billion lathered on. Check out these neat simulations, such as the image above.

Hurdles to jump: As you may know, we still have a slight problem with a thing called “Global warming.” Lots to do in order to reduce carbon emissions.

More info: Original study

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Mendeley Desktop v0.9.1 released

This update addresses a number of issues with Mendeley Desktop v0.9.0.:

Improvements to Existing Features

  • Automatic Pubmed/Crossref title search during metadata extraction if no identifiers (DOI, ArXiv, PMID) are found
  • Hide the notification bar asking for login details when applicable
  • Improved the presentation of search results
  • Added tooltips to the document list for items that aren’t displayed in full
  • Improved detection and handling of unsuccessful responses from Mendeley Web during a sync
  • Increased stability of the internal PDF viewer (more work is to follow on this)
Bug Fixes
  • Enable lookups from Google Scholar to verify document details
  • Fixed a crash when account details were entered or changed
  • Fixed an issue with file links being lost for documents in watched folders
  • Fixed an issue where multiple copies of a note would be added when editing several documents at once
  • Fixed an issue that prevented exporting libraries as BibTeX format
  • Fixed an issue related to closing Mendeley Desktop during a document import
  • A small number of other minor bug fixes that affected the overall stability
  • Fixed a problem with the system PATH variable when installing the Word plugin

Besides releasing a new version of Mendeley Desktop we also updated our catalog of research papers, the people directory, public collection pages, and the online library.

Now you’re also able to import articles from APA PsycNET, IACR ePrints, and RePEc.

To see what has changed in previous updates of Mendeley visit our release notes page.

Server upgrade ahead

Just a quick update to let you know that we are in the process of upgrading our current server setup, which is struggling a bit lately. We’ll have much more processing power, memory, better reliability and and and … in short, the website and syncing will perform much better.

Also, another Mendeley Desktop update is on it’s way. This will fix most bugs which have been reported last week. More about that later.

Mendeley Desktop v0.9.0 released

This update introduces a lot of new features, including a PDF viewer, 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
  • 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