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…)

This is the fourth and final part announcing the top 40-ish Apps entered into the Mendeley-PLoS Binary Battle. To see the first batch of apps, check out Day One. And Day Two with the second batch is here. And Day Three is here.

As a reminder, the top 10 apps will be announced in two weeks and the overall winners will be announced November 30th

Now, in order of entry received date, the final batch of apps to benefit science: (more…)

This is the third of four parts announcing the top 40-ish Apps entered into the Mendeley-PLoS Binary Battle. To see the first batch of apps, check out Day One. And Day Two with the second batch is here. Check back tomorrow for the final batch of apps.

As a reminder, the top 10 apps will be announced in two weeks and the overall winners will be announced November 30th

Now, in order of entry received date, the third batch of apps to benefit science: (more…)

The Open Science Summit brings together researchers, life science industry professionals, students, patients and other stakeholders to discuss the future of collaborative science and innovation. This year features in depth sessions on new models for drug discovery and clinical trials, personal genomics, the patent system, the future of scientific publications, and more. I went last year and made some good friends and learned a lot, so I would definitely recommend it to anyone involved in scientific research.

What: Open Science Summit When: Saturday and Sunday, October 22-23rd 2011 Where: Computer History Museum, Mountain View, CA

p.s. All attendees get a special thank you gift from Mendeley, and there will also be some fun extracurricular activities, so don’t miss this.

It isn’t to obtain tenure. And it isn’t for money. Although to some, that is what publishing has become. The rationale for why we publish is (should be) to communicate results to as great an audience as possible and advance our understanding of the world around us. At Mendeley, we started to wonder how we could help communicate results and bring new models to the publication ecosystem. We think that Open Access content, where the full-text is readily accessible to all, will be the standard communication model in the future. And as such, we are rethinking how we shape our discovery algorithms. (more…)

Mendeley is now settled in our new office space in New York. We are hosting an Office Warming & Open Science Event this Friday November 19th from 6-9pm. We want to invite neighbors and colleagues – if you are interested in Mendeley and the future of open science we welcome you to join.

The evening will be a chance to share ideas, connect with others and get to know the Mendeley team better. Jan, our Co-Founder, will briefly talk about Mendeley’s journey and give an update on what we hope to achieve. The New York team will also introduce themselves along with good food, tasty drinks and fun activities.

Looking forward to meeting you!

Recently I was sitting at café Tryst in Washington D.C. along with Mendeley’s co-founders and a coffee house full of hipsters, Georgetown students, tourists, and a few politicos. In retrospect, perhaps this was the only setting possible to be discussing the future of research and our small part in it. We were surrounded by the common citizens who depend on the outputs of science, but had little to no power in changing its course for their benefit. More pointedly, they had no clue that science is being held back by the very people who are supposed to be advancing it.

We came to the conclusion that technology is finally at a point that if we don’t use it now, then we are holding back the progress of science. And what exactly are we to use technology on? Open science/data/access.

By our own hands

To understand how we (“we” meaning the research community) got here, we have to first briefly remember how the dissemination of science came to be the way it is. (more…)

“It has been described as internet dating for inventors” – well, here at Mendeley we didn’t know that we were doing this kind of stuff, but in any case it’s fantastic news that yesterday Benjamin Cohen from Channel 4 News, one of the UK’s leading news channels, reported on Mendeley! The three minute report names James Dyson, probably Britain’s most famous inventor, and Mendeley as exemplary innovators in the UK’s recovering economy.

Besides showing Mendeley in our “tiny office in London” (oh well, start-up life…), Channel 4 News also interviewed Dr. Cameron Neylon, Molecular Biologist at the Science and Technologies Facilities Council, and an Open Science advocate, in front of his mega-super-duper-luxurious four monitor set-up. Thanks Cameron for the nice quotes!

Here’s the write-up, the link to the video, and below you will find the video embedded.

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:

(more…)

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…)