Next Generation Science

Here at NGS, we’re getting reading for the ScienceOnline2010 conference this coming weekend. I’ll be in RTP on Thursday evening and will be posting updates here as well as on my personal Twitter account.

Graham posted some great tips for those attending the conference virtually over at his blog yesterday. To help keep you connected with the conference without actually being there, we’ve added the ScienceOnline2010 Twitter hashtag (#scio10) feed to the NGS sidebar. This way, everytime you visit NGS over the weekend, you can easily see what’s being talked about.

It’s simple to post automatic updates from the ScienceOnline2010 hashtag feed on your WordPress blog. The code below will import and display items using the built-in WordPress function, wp_rss(), which provides WordPress with feed-fetching and feed-parsing functionality. All you need to do is place the following code below (download here) where you want the feed displayed within your theme template file (e.g., sidebar.php for the homepage or sidebarsingle.php for single article pages). You can customize the number of items posted on line 11.

For FriendFeed users, we’ve also added real-time discussion from the ScienceOnline2010 FriendFeed group further down the sidebar.

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CureHunter is a web accessible, fully integrated scientific search, data retrieval and analysis engine. Developed by a team of scientists with expertise in medical data mining, artificial intelligence software development, computational linguistics and computational biology, CureHunter “reads” the entire U.S. National Library of Medicine Medline Archive and automatically extract and quantifies the evidence for successful clinical outcomes of all known drugs for all known human diseases.

Hope had an opportunity to talk with Judge Schonfeld, CEO and Chief Scientist of CureHunter. In part II of their interview below, Hope focuses on the users and uses of CureHunter; Judge discusses the differences between CureHunter and Wolfram|Alpha, and compares search results from CureHunter to novo|seek, GoPubMed and PubMed.
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CureHunter is a web accessible, fully integrated scientific search, data retrieval and analysis engine. Developed by a team of scientists with expertise in medical data mining, artificial intelligence software development, computational linguistics and computational biology, CureHunter “reads” the entire U.S. National Library of Medicine Medline Archive and automatically extract and quantifies the evidence for successful clinical outcomes of all known drugs for all known human diseases.

Hope had an opportunity to talk with Judge Schonfeld, CEO and Chief Scientist of CureHunter. In part I of their interview below, Judge talks about the development of CureHunter, the definition of “autonomous search” and the difference between CureHunter and other authoritative online reference services.
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Physicist Stephen Wolfram’s computational knowledge engine Wolfram|Alpha goes live tonight, documenting the event in real time. Drawing on terabytes of curated data to produce new combinations and presentations, Wolfram|Alpha is designed to answer questions, make projections, solve equations and provide insights on top of factual knowledge. If all goes well tonight and this weekend, the company will declare the web application officially launched on Monday, May 18th.

In an age of federated and semantic search engines such as Mednar and DeepDyve, which provide links to a variety of pages on the Internet, Wolfram|Alpha instead responds to specific queries using its own detailed store of factual information and a family of algorithms found using the NKS system.

This is something altogether different than an index of the web.

Taken from Wolfram’s 2002 book, A New Kind of Science – NKS for short – the NKS system is based on the idea that each natural phenomenon can be regarded as a computation that has a very simple underlying rule. Stephen Wolfram sees Wolfram|Alpha as tool to systematize knowledge, to make the world computable.

Although many are skeptical of the project, I for one and excited about Wolfram|Alpha. My initial training in the sciences was in physics. I spent a great deal of time developing mathematical models of natural processes, so I’m very comfortable with the idea of using algorithms to take what we know and determine something new.

I’m confident the system will work (heck, even Google can do simple computation). However, I think more important questions are “what are its limits to extend beyond mathematical computation” and “how well will it interpret natural language queries?”

According to the Wolfram|Alpha Blog, they’ll start webcasting preparations at 7pm CDT on justin.tv and include behind-the-scenes views of what it’s taken to create Wolfram|Alpha.

For more on Wolfram|Alpha, check out Rudy Rucker’s in-depth interview with Stephen Wolfram.

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Hope has just posted a lengthy review of DeepDyve on AltSearchEngines:

Okay, a search engine or business strategy has to be really intriguing or really powerful to get me out of bed in the middle of the night to write about it as I am doing right now with DeepDyve.

DeepDyve delivers.

I am also a sucker for catchy slogans, like DeepDyve’s, “search for research.” DeepDyve not only offers some pretty impressive technology, it is also developing just out and out brilliant marketing strategies that create win-wins for publishers, authors and those of us like medical librarians, other information professionals and academics who make a living from and live for the fun of the fastest possible acquisition and provision to patrons, clients and peers of the best data possible.

Please, please take notice scientific and technical publishers. There is a vast potential and in many cases deep-pocketed audience for your superb material and DeepDyve can help you get it to us. In the age of Twitter where viral marketing and microcontent rules, DeepDyve is the best of friend of multiple actors. I wish I were as smart as these boys and as someone who loves finding just the right abstract of just that key article to send to a patron and alert him or her to the existence of a journal neither of us had heard of before, I am fondly hoping that publishers will pounce on the marketing savvy of DeepDyve to spread the news of their treasure troves of scholarly material that is lamentably under-disseminated at this point.

Got me on all that? It is hard to write about all of this succinctly and pithily because there is so much to discuss here given the fact that I want to discuss DeepDyve both as a search engine and as an innovator in information discovery and marketing.

Let’s start with the search engine aspects. In a word, superb. The interface is attractive and sleek. Pretty even. (Okay, men — it is okay that a search engine is pretty — if I am going to spend hour after hour in a search environment, I want it to be beautiful. DeepDyve and I are going to get to know each other well and I like the looks of it both aesthetically and technologically.)

And there are gobs of powerful features. I have just been trying them out with my usual favored search term, amyotrophic lateral sclerosis. Loved the excellent results I could call up with “More Like This” and loved being able to highlight certain phrases and drill down incredibly quickly and with dream-like effortlessness.

Read Hope’s entire review here.

Forget keywords, forget ontologies … I’ve seen the future of online search and it’s called Content Intelligence.

Mountain View, California based NetBase launched its Content Intelligence platform today, which is powering a new generation of consumer and B2B content-rich applications. I had the opportunity to attend a briefing last week where they showed off their technology and I have to tell you, as someone who searches Google and PubMed daily, and is well versed in constructing complex search queries to try and return the most relevant results using keyword search, I was extremely impressed with their technology.

How many times have you run a web search and paged through tens, if not hundreds of pages of results? Research firm IDC (Interactive Data Corporation) estimates that in 2006 the world produced 161 Exabytes (trillion Megabytes) of digital data encompassing 70 million blogs and 150 million Web sites. That’s almost 5 terabytes per second. By 2010, it’s estimated that number will grow tenfold. Yet traditional search by keyword fails to address this explosion of information because it returns too many documents with too many irrelevant results and lacks actionable insights and answers.

NetBase’s Content Intelligence platform uses state-of-the-art analytics technology to search, parse and summarize information from any number of industry sectors. Content Intelligence addresses search in a new way by reading every sentence inside documents on an ongoing basis, linguistically analyzing them and identifying relationships between entities and attributes. The information is then stored in structured semantic indexes. NetBase CEO and co-founder Jonathan Spier and Jens Tellefsen, VP of Marketing and Product Strategy, talk more about what makes NetBase and the Content Intelligence platform different from traditional search engines in the video below.

The evolution of search

Keyword search using statistics such as number of incoming links to calculate relevancy and popularity is context independent, and that’s a problem as the amount of information on the web continues to grow.

Linguistic search is different, relying on pre-defined lexicons to extract domain-specific entities from documents. While this is more useful than keyword statistics, lexicons require a lot of time and resources to construct and maintain. Further, linguistic search is often unable to deliver actionable insights and answers from large amounts of data across multiple domains.

In contrast, Content Intelligence focuses on understanding the meaning of sentences — independent of lexicons — by identifying the connection between entities. The relationship between keywords is crucial to the understanding of sentences and that’s where Content Intelligence shines.

NetBase believes that Content Intelligence will solve the problem of information overload, enriching existing content and surfacing high quality, meaningful, contextually aware insights. NetBase’s sematic index can be deployed to access any content and is highly scaleable. The Content Intellegence platform doesn’t rely on hard-wired or human-edited data to identify relevant relationships within content.

Elsevier’s illumin8

Last month, NetBase announced that it’s continuing its customer relationship with science and health information publisher Elsevier. Elsevier has been using NetBase’s Content Intelligence platform to power illumin8 since early last year. illumin8 is a web-based research tool that integrates natural language search technology with content from Elsevier’s full-text scientific articles, millions of scientific abstracts, patents and billions of web sources to give users actionable solutions for research initiatives. The agreeement extends its commitment to NetBase for another three years. To see illumin8 in action click here to view an illumin8 search on “chip cooling”. The interface is designed to return results organized in categories including organizations, products, people, approaches, benefits and related results.

NetBase for Healthcare

NetBase has also announced that it is expanding it focus and marketing to other industries, in particular healthcare. At a time when healthcare professionals and biomedical researchers are looking to collaboratively leverage research, intelligence and new technologies, cutting time to finding relevant information has become all the more important. NetBase for Healthcare enables researchers, doctors and patients to quickly and efficiently search a vast and rapidly expanding number of books, medical journals, databases, Web sites and patient records, creating a new way to discover and use medical content. For example doctors and nurses can look up a symptom like hypertension and instantly see an organized, up-to-the-minute summary of the causes, effects, symptoms, complications, side effects and treatments of the condition. Additionally, consumers and patients could do their own research for alternative treatments, suggested lifestyle changes, or less expensive medications or treatments to cut down on increasing healthcare costs.


As the amount of digital data on the web continues to increase, more sophisticated solutions are necessary to find the actionable insights and answers we need without sifting through thousands of documents. NetBase’s Content Intelligence platform is unique in its ability to understand every sentence of every document without lexicons or human editing and extends search by an order of magnitude over previous approaches. illumin8 was designed specifically for corporate R&D knowledge workers. With NetBase’s expansion into healthcare, we should soon begin to see their search platform become more widely available.

Now, if only I could use this search technology on PubMed directly (PubMed currently uses keyword search). One has to wonder why scientists are using antiquated technology based on keyword statistics to search through cutting-edge biomedical research literature. National Library of Medicine, are you listening?

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Hope attended the Web 2.0 Expo last week in San Francisco, California, covering it for AltSearchEngines. The Web 2.0 Expo features some of the most innovative and successful individuals in the industry from companies such as Google, Twitter, Microsoft, Amazon, Electronic Arts, PBwiki, Nokia, Six Apart and Adobe.

The conference’s theme this year was The Power of Less:

We do some of our best work when we’re constrained: by budgets, by headcount, by technology, by the economy. These are the times when bureaucracy and waste die by necessity. What’s left are ideas, and the muscle to make them real.

2009 will be a tough year in many ways, but now more than ever, the core concepts of Web 2.0 provide an advantage. Lightweight tools, user interfaces, and development models will help streamline productivity and focus resources; new business models will emerge out of the environment of change. Transparency and openness will help avoid disasters and extend our influence, as we learn to trust users as co-developers. Marketers can’t afford to ignore the value of social media, communities, and a new set of analytics. On an individual, team, company, and global level, this is the year we will choose to work on what matters.

And while the fundamentals of Web 2.0 become increasingly relevant and urgent, this is also the time to look ahead. The landscape today enables interactions that were not possible even two years ago, as the devices around us and the data they generate evolve rapidly. Tomorrow’s big ideas are quietly percolating now, in the aisles of major retailers, the back office of enterprises, and in the labs of passionate, independent-minded hackers. We’ll explore the future potential of Web 2.0, so when this storm passes, you’ll be ready.

Over the course of four days, the expo spotlights experts, leaders and under-the-radar innovations, and provides attendees the opportunity to attend lectures, workshops and exhibitions. You can read more about Hope’s thoughts and experiences at the conference in these articles posted over at AltSearchEngines:

• The Leman Report – Web 2.0 Expo Day One

  Hope’s first report — a late night recap of impressions from the first day — includes a narrative on a session focused on Web monitoring and Web analytics.

• The Leman Report – Christina Wodtke of LinkedIn

  An even later late night recap of day one: Hope describes a session she attended on social website design by Christina Wodtke of LinkedIn.

• The Leman Report – Observations from the Web 2.0 Expo

  On day two of the Expo, Hope attended sessions on Web design for the disabled, IT transformation with cloud computing and leveraging Twitter.

• The Leman Report – Larry Chiang and the happy accident

  Hope recounts a session by Larry Chiang titled Peek Into a Secret Society of Entrepreneurs.

• The Leman Report – An Inside Look at Web 2.0 Expo

  Hope provides a sampling of sessions held on day three of the Expo and highlights several technology exhibits.

• The Leman Report – the final day of the Web 2.0 Expo

  Hope reflects on her final day at the Expo and discusses whether Web 2.0 has separated into subgroups, precipitating less need for a large-scale conference such as the Web 2.0 Expo.

Last week, Hope also took the time to guest post over at Nextbio, discussing how FriendFeed and Twitter are part of a larger revolution in scientific communication. Widespread academic use of email began roughly fifteen years ago. Today, researchers can’t imagine not using email to communicate. It will be interesting to see if and when microblogging and feed aggregation become indispensable tools for researchers and scientists to communicate and share information.

DId you attend the Web 2.0 Expo? Leave us a comment below on your experience and impressions of the conference.

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According to the web analytics company Complete, in January 2009 Twitter, the social networking and micro-blogging service that enables users to send and read other users’ updates, received just over 54 million visits and ranked third in social networks behind Facebook and MySpace. Not bad for a company that launched just 3 years ago (March 2006).

Evan Williams is the co-founder of Twitter. He spoke recently at the annual TED conference in Long Beach, California. TED stands for Technology, Entertainment, Design, and provides some of the world’s most fascinating thinkers and doers the opportunity to talk about science, business, the arts and global issues facing our world.

One of the things I found interesting about Twitter is that it was launched as a side project. In his TED talk, Williams shares that he’s learned to follow his intuition:

Now, it’s hard to justify doing a side-project at a startup where focus is so critical, but I had actually launched Blogger as a side-project at my previous company thinking is was just a little thing we’d do on the side, and it ended up taking over not only the company but my life for the next five or six years, so I learned to follow hunches even though you can’t necessarily justify them or know where they’re going to go. And that’s what’s happened with Twitter time after time.

He goes on to explain how many of the ideas driving Twitter’s growth have come from the users themselves. Check out his short 8 minute talk below.

Last month, Nash over at The Daily Nash-on came up with a list of reasons Why Scientists Won’t Use Twitter. He points out that the reasons he came up with are also applicable to other “Web 2.0″ Science resources. Perhaps it’s no surprise then that someone like me who embraces Web 2.0 Science resources would be using Twitter. I’ve found Twitter to be a valuable networking and communication tool, especially for one-on-one conversation/messaging.

The problem with Twitter

The problem with Twitter is that it can be a “noisy” social media platform. The way to manage the noise is to only follow high-value Twitterers. That is, only follow people who closely share your interests and post relevant content. That way you maintain a high signal-to-noise ratio. You can determine high-value Twitterers by screening new followers before you start following them back. Here’s some tips:

• Check out recent tweets and take a look at who they follow — their network will reflect their interests and the conversations they may participate in.
• How many people are they following? The ratio of people followed to followers can give you an idea if they also screen new followers.
• Check out the link provided on their profile. If it links to a blog, read some of the recent posts. Look for an “About” page to learn more.
• Check and see if they have a FriendFeed or LinkedIn profile.

David Bradley at Sciencebase has been compiling a list of Twitter users that are connected to science in some way. Review his list of 252 Scientific Twitter Friends. In addition, WeFollow, a user powered Twitter Directory, currently has a list of 164 users that have tagged themselves with the term “science”.

Do you use Twitter? If so, let us know in the comments below!

… and don’t forget to follow us @NextGenScience

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