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Recently there was an announcement on TechCrunch that I would be joining Mendeley as the new Research Director . Mendeley co-founder, Victor Henning, asked me to start contributing to Mendeley’s blog right away. I chose to write about journal impact factors, and how using Mendeley can change it for the better. What you get with Mendeley is the ability to track article-level impact in real-time. You can read more about it on Mendeley at Changing the journal impact factor.

I’d like to add my voice of support in encouraging academics and researchers to try out Mendeley for managing all of those PDFs on your hard drive. The fact that it has a desktop software application (Windows, OS X, Linux) means it can become really powerful, much more so than anything that is just Internet-based. In the next release update (due in June), Mendeley will finally be including a PDF reader built right into the software. That means you can read your library without having to open a separate PDF program, a major productivity booster. Rather than go further into the current list of features here, I’ll point you to the tour page.
Read more

This past Thursday the Plugg.eu competition was held in Brussels, Belgium. More than 100 startups were whittled down to just 20 and given two minutes to present to a panel of entrepreneurs and venture capitalists. The top three secured a second round 10 minute presentation. The audience award went to Myngle, which helps language tutors connect with anyone interested in affordable, live online lessons. And the overall winner was Mendeley, which complements the mission of Ologeez very well.

Mendeley gives academics and anyone with a need to organize PDFs the ability to full-text search and share such files in an iTunes-like environment. Additionally, it lets you upload and sync those PDF documents to a central server, so that, for instance, you can access the papers both at work and at home. Perhaps an even better analogy than iTunes, is to Google. Instead of indexing and organizing the web like Google, Mendeley is indexing and organizing your research library and giving you a load of aggregated stats as well. There is some huge potential with this software.

Mendeley is currently in beta, but is quickly approaching the full 1.0 release. It also recently secured $2 million in a series A funding round led by investors and the chairman from LastFM (Stefan Glaenzer), founders of Skype, and Alex Zubillaga. It is based in London, UK.

Recently I asked 100 graduate students and postdocs from Stanford University to partake in a survey in preparation for a talk I am giving. The talk is Feb. 22nd in Philadelphia and is part of the NFAIS conference. Here is the raw data for download (a 120kb Excel file). Below is the theme of my session:

Digital Natives are beginning their professional careers as faculty, scholars, researchers and business managers. Exposed for years to intuitive user interfaces, mobile devices and total connectivity, and well-versed in social networking and collaborative information sharing, they expect to enjoy a comparable information environment as they access the traditional information tools used by prior generations. Come and learn what tools they really are using, if their expectations are being met and, from their perspective, what needs to be changed in order for traditional information services to be truly useful to them.

For the survey, I was after three main things. 1) What information tools are people using most often 2) How frustrated are they with those tools and 3) What kind of organizations do they associate with good products.

This was a very limited survey, and would not be considered an SRS scientific one at that, but I still see some undeniable trends. I could have also worded some of the questions a bit better in hindsight. One thing you can’t see in the raw data is the difference in opinions based on age. For instance, more people under the age of 30 find online networks important and needing improvement than those over 30. One thing stood out in the open-ended question on social networks, everyone is uncertain if they will ever really take off and gain a large member base. I’m of the same opinion, despite having creating a site that is partly a social network for researchers. My personal feeling is that it may be more important to develop a network of labs instead of individuals and there are many sites that are trying to do just that.

And obviously open-access to journals is a major issue, especially if you’re at a small university that can’t afford the high journal fees. One of the points that I will talking about at NFAIS is how we can solve this problem with modern technology that allows full access, but maintains copyright protection. Another resolution is to simply adopt a new business model that does not depend on subscriptions, in other words shift the cost to either authors or advertisers (this is how PLoS works).

Another thing everyone seems to be in agreement on is that PubMed needs to change. A funny exercise is to take a look how the PubMed page has changed over the past eight years at the internet archive site. Hint, not much. While the design is awful, and younger people definitely notice that, the more important consideration is the user interface, and that is terrible.

Would love to hear your comments about how mainstream information technology is starting or will start to benefit science.

Rather than just listening to my diatribes on site updates, academia, and industry news, I’d like to get you as a contributor. Perspectives and unique voices are always good read, no matter what the level in academia (Student, postdoc, faculty) or expertise. So, if you’re interested then let me know.

Oh, and I am busily writing a dissertation and preparing for a defense soon, so updates might be a bit slower until I’ve gone through that gauntlet.

One of, if not the most, important reasons I started developing this site was because of how frustrated I have been with the search experience in academic databases. Either the user interface was totally boggling or search results seemed random with the relevant results tucked away.

When Ologeez launched in limited beta recently, a prototype of a stripped down PubMed search interface was available. Now that we are in full beta stage, I’ve made some updates to that search experience. The most obvious update is the “Find Related” button next to any PubMed search result. Click it and find out what happens, it’s pretty cool and your previous search results do not disappear. Try a search here then click the “View PubMed results instead” (see screenshot below).

The PubMed interface is still in beta and will undergo continued refinement. As well as the search experience for abstracts already added to the Ologeez database, either through PubMed or uploaded by you via EndNote or BibTex (coming soon).

Update: As of 2:30AM PST, PubMed servers are down. They’ve been having trouble this entire week. One more reason I’ll be importing most of the PubMed database soon. More on that later.

It’s old news now, but on June 9th, the State of California sent cease & desist letters to 13 genetic testing companies. The most prominent of the bunch were 23andMe, deCODEme and Navigenics. At least two of those 13 (23andMe & Navigenics) responded with “Hey, we’re not stopping, but we’d like to chat.”

The current argument for the C&D letter boiled down to “A state-licensed physician is required to order these at home genetic kits.” Here is my counter-argument, “Yes, regulations are needed, but not what the Department of Health has in current form.”

What the Department of Health Believes

1. Some companies are trying to fool you into “snake-oil diet remedies” based on your genetics

This is in fact true. And proper government regulation bodies are needed to watch after these companies. The majority of the 13 companies that received the C&D order though, do not fall into this category. They are legitimate businesses using state-certified testing facilities.

2. You are not capable of understanding all of that genetic data, but your doctor can

These new companies are not dumb and neither are you. That said, they are not just spitting the raw data of nucleotides and SNPs back out to you. They are combining the latest research with easy to understand diagrams and wording to give you an ample idea of what your genes do. They are taking great pains to ensure you do not overestimate or underestimate any genetic risks. The companies would tank if they couldn’t provide accurate, yet easy to understand information. 23andMe even has a demo to orientate yourself with the information involving an imaginary family’s genetic test results.

This is the information age, not the stone age. The current crop of early adopters who can afford the $1000 price tag for these at-home kits are tech savvy individuals. They are just as literate or capable of learning about their genes as their doctor, who only took a single introductory genetics course in medical school.

The argument that even scientists do not have enough data to interpret SNPs, so these companies shouldn’t be allowed, is weak. We are finally at a place where we can start to gather all that data. Why do we want to stymie it? The more people who are tested, the more we learn. Prices for these kits will eventually drop, but by that time, even the most lay people will be able to understand their genes. It won’t happen overnight, but that knowledge will be there eventually. I fail to see the bioethical argument here.

We need to start realizing that in the future everyone will be a geneticist.