by tanakawho
Crawling the Internet to track infectious disease outbreaks:
[Via EurekAlert! - Infectious and Emerging Diseases]

(Public Library of Science) Could Internet discussion forums, listservs and online news outlets be an informative source of information on disease outbreaks? A team of researchers from Children’s Hospital Boston and Harvard Medical School thinks so, and it has launched a real-time, automated data-gathering system called HealthMap to gather, organize and disseminate this online intelligence. They describe their project in this week’s PLoS Medicine.
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The site itself is an interesting mashup of online news sites with Google Maps. It does demonstrate how a clever mind kind use the internet to gain useful information. While there may be some bias in the types of diseases being reported, this sort of bottoms-up approach could have some real uses.

Healthmap.org: It Will Make You More Paranoid Than the Weather Channel [Mike the Mad Biologist]:
[Via ScienceBlogs : Combined Feed]

One of the things I find fascinating about the Weather Channel is that after watching it for a while, you actually start to worry about that cold front moving through some other part of the country. You become quite paranoid about things that won’t affect you. Well, I’ve got an even better way to drive yourself nuts about scary things that won’t affect you: HealthMap.org.
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This is done by monitoring published reports from around the world so it is not really a substitute for hard epidemiology (which can take some time) but it is a nice adjunct. Following the Salmonella outbreak, for instance, really permits the rapid gathering of a lot of information.
New tool anyone can use to track disease outbreaks:
[Via Effect Measure]

While CDC and FDA struggle to figure out where the Salmonella saintpaul in a large multistate outbreak is coming from they are not being forthcoming about where it has gone. We know the case total but not much about who is getting sick, where and when. There is no good scientific or privacy reason not to release more information. It’s just the usual tendency to keep control. But some of the information is “out there” anyway, in news reports and other sources of information. People interested in disease outbreaks discovered years ago that this information could be harvested and disseminated to the public health community and in 2003 this informal system provided the first evidence of the SARS outbreak in Guangdong, China, weeks before there was any official confirmation. Many of us subscribe and use the no-cost ProMed Mail service, a pioneering effort by volunteer experts to collect information on disease outbreaks in people and animals worldwide, using official and unofficial sources. The ProMed concept has now been taken several steps further by a team of disease of surveillance experts at Boston’s Childrens Hospital. They use automated internet data-mining with some additional curating by human experts to provide a web-based breaking-news disease reporting system organized by disease agent, time and geographic location, all displayed on a map of the world. The system is free and without registration or subscription barriers. It started in prototype in 2006 and now gets about 20,000 unique visits a month, mainly from the public health community (for comparison, this blog gets 30,000 to 40,000 visits a month). The system, called HealthMap, is pretty impressive. It was just highlighted on the Wired Blog so its traffic is going to increase.
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It will be interesting to see how organizations such as the CDC or FDA respond to this sort of analysis. As a news aggregator, though, this is pretty useful.
Infectious disease surveillance 2.0: Crawling the Net to detect outbreaks:
[Via LISNews - Librarian And Information Science News]

“July 8, 2008 (Computerworld) While recent outbreaks of salmonella in the U.S. have made headlines, an automated real-time system that scours the Web for information about disease outbreaks spied early reports in New Mexico about suspicious gastrointestinal illnesses days before the U.S. Centers for Diseases Control and Prevention (CDC) issued an official report on the problem.
The system, called HealthMap, is a free data-mining tool that extracts, categorizes, filters and links 20,000 Web-based data sources such as news sites, blogs, e-mail lists and chat rooms to monitor emerging public health issues. HealthMap, which is profiled in the July issue of the journal Public Library of Science Medicine and is open to anyone, was developed in late 2006 by John Brownstein and Clark Freifeld. Both men work in the informatics program at Children’s Hospital Boston.”
Read the full article in Computerworld at:
Infectious disease surveillance 2.0: Crawling the Net to detect outbreaks

It is kind of fun to check out what is happening around the world. There are nice pop-ups that can provide further information. I will have to play with this some more.

Technorati Tags: Environment, Health, Web 2.0

by b_d_solis
Reputation Matters:
[Via The Scholarly Kitchen]

A new (and flawed) study reveals that reputation matters. In fact, it’s core to scientific expression.
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While the study may not be definitive, the ability to have a conversation on it helps tremendously. Research usually does not progress in a straight, ascending line. It switches back and forth, sometimes having to retrace its steps in order to find the right path.

Being able to discuss the results of a paper, what it did right and what it did wrong, is not something that usually has occurred in public. Now it can. I expect there to be more and more such discussions as time goes on.

Technorati Tags: Science, Web 2.0

Commentary: Summarizing papers as word clouds:
[Via Buried Treasure]

For use in presentations on literature mining, I did a back-of-the-envelope calculation of how much time I would be able to spend on each new biomedical paper that is published. Assuming that all papers were indexed in PubMed (which they are not) and that I could read papers 24 hours per day all year around (which I cannot), the result is that I could allocate approximately 50 seconds per paper. This nicely illustrates the point that no one can keep up with the complete biomedical literature.

When I discovered Wordle, which can turn any text into a beautiful word cloud, I thus wondered if this visualization method would be useful for summarizing a complete paper as a single figure. To test this, I extracted the complete text of three papers that I coauthored in the NAR database issue 2008. Submitting these to Wordle resulted in the three figures below (click for larger versions):

…I think a large part of the problem is the splitting of multiwords; for example, “cell cycle” becomes two separate terms “cell” and “cycle”. Another problem is that words from different sections of the paper are mixed, which blurs the messages. These two issues could be solved by 1) detecting multiwords and considering them as single tokens, and 2) sorting the terms according to where in the paper they are mainly used.

Technorati Tags: Social media, Web 2.0

by txd
What Social Media Does Best:
[Via chrisbrogan.com]
Before Chris starts his list he has this to say:

If you’re still looking for the best ways to explain to senior management or your team or your coworkers or your spouse what it is that social media does, why it’s different than the old way people used to use computers and the web, why people are giving two hoots about it, here are some thoughts to start out the conversation. I look at this mostly from a business perspective, but I suspect you’ll find these apply to nonprofits and other organizations as well. Further, as I’m fond of saying, social media isn’t relegated to the marketing and PR teams. It’s a bunch of tools that can be used throughout businesses, in different forms. Think on this.

I’m not going to list all of Chris’ points but here are a few to whet your appetite.

Blogs allow chronological organization of thoughts, status, ideas. This means more permanence than emails.

The organizational aspects of blogs are one of their most overlooked features.

Social networks encourage collaboration, can replace intranets and corporate directories, and can promote non-email conversation channels.

Email is not optimized for the sorts information transfer that it is used for. It also makes it impossible to really know just who should see the information. Social networks open this up and make it highly likely that the right information to get to the right people.

Social networks can amass like-minded people around shared interests with little external force, no organizational center, and a group sense of what is important and what comes next.

Ad hoc group creation is one of the best aspects of social networks. Rapid dispersal of information amongst a small, focussed group can occur independent of the need for everyone occupy similar space at the same time, as is done in meetings.

Blogs and wikis encourage conversations, sharing, creation.

Facilitating conversations increases information flow, speeding up the creativity cycle

Social networks are full of prospecting and lead generation information for sales and marketing.

This applies to a much wider group than just sales and marketing because at some level, everyone at an innovative organization needs to look for leads.

Blogs allow you to speak your mind, and let the rest of the world know your thought processes and mindsets.

The personal nature of many social media tools helps enhance the ability of a group to innovate rapidly, without the feeling of a restricting hierarchy that can diminish creativity.

Tagging and sharing and all the other activities common on the social Web mean that information gets passed around much faster.

Web 2.0 approaches make it much easier to find information, even though there is more of it.

Innovation works much faster in a social software environment, open source or otherwise.

The diffusion of innovation throughout an organization is really dependent on the social network of that group, how well connected it is, how people communicate, etc. Social media allows innovation to spread much more rapidly, decreasing the rate of diffusion and allowing the creativity cycle to crank much faster.

People feel heard.

This is a big one. Studies have shown that if people feel that their viewpoint is not heard and do not understand the rationale for a decision they become the most upset. Having a chance to be a part of the discussion can make a big difference, even if they do not agree with the final decision.

Technorati Tags: Social media, Web 2.0

by luisvilla*
I will participate in the Elsevier Article 2.0 Contest:
[Via Gobbledygook]

We have been talking a lot about Web 2.0 approaches for scientific papers. Now Elsevier announced an Article 2.0 Contest:

Demonstrate your best ideas for how scientific research articles should be presented on the web and compete to win great prizes!

The contest runs from September 1st until December 31st. Elsevier will provide 7.500 full text articles in XML format (through a REST API). The contestants that creates the best article presentation (creativity, value-add, ease of use and quality) will win prizes.

This is a very interesting contest, and I plan to participate. I do know enough about programming web pages that I can create something useful in four months. My development platform of choice is Ruby on Rails and Rails has great REST support. I will use the next two months before the contest starts to think about the features I want to implement.

I’m sure that other people are also considering to participate in this contest or would like to make suggestions for features. Please contact me by commenting or via Email or FriendFeed. A great opportunity to not only talk about Science 2.0, but actually do something about it.

While there are not any real rules up yet, this is intriguing. Reformatting a science paper for the Internet. All the information should be there to demonstrate how this new medium can change the way we read articles and disperse information.

We have already seen a little of this in the way journals published by Highwire Press are able to also contain links to papers published more recently, that cite the relevant paper. Take for example this paper by a friend of mine ULBPs, human ligands of the NKG2D receptor, stimulate tumor immunity with enhancement by IL-15.
Scroll to the bottom and there are not only links in the references, which look backwards from the paper, but also citations that look forward, to relevant papers published after this one.

So Elsevier has an interesting idea. Just a couple of hang-ups, as brought out in the comments to Martin’s post. Who owns the application afterwards? What sorts of rights do the creators have? This could be a case where Elsevier only has to pay $2500 but gets the equivalent of hundreds if not thousands of hours of development work done by a large group of people.

*I also wonder what the title of the book actually translates to in Japanese?

Technorati Tags: Bioinformatics, Science, Social media, Web 2.0

It is often hard to really see how things change when you are in the middle of it. We take for granted so much that was simply unattainable just a short while ago.

Web 2.0 tools allow the rapid prototyping of an idea for low cost. We can then work towards perfection by easily making modifications. An example.

Youtube allows us to easily access video created by other people. Great video can be done by almost anyone with a great idea and a strong vision. Matt Harding is a great example. He took some video he made while traveling and created something special. It has been watched about a million times at youtube.

Simple idea. Dance the same dance around the world. The familiar mixed with the exotic. All in less than 3 minutes.

He expanded this, using some corporate sponsorship, to become a 6 month trip though 39 countries, resulting in this video with an incredible opening. It was better.

It was not a big marketing agency that created this but a guy with a camera and an idea. The prototype demonstrated what would work, permitting another effort to enlarge the scope. This video has had over 10 million views since it came out 2 years ago.

Now he has a new one. It came from another idea. In the previous videos, he was the only one dancing. He wanted to include other people. So he went back to the corporate sponsors, pitched the idea to them and here is the result, in high definition.

Where the Hell is Matt? (2008) from Matthew Harding on Vimeo.

It has had almost 5 million views at Youtube since it was uploaded June 20. It does not have the spectacular opening of the second video but it has so much more humanity. From the opening, similar to the first video, to the people from around the world.

Seeing children and adults from every continent dancing ‘together’ is incredible. Simple yet so evocative.

Creativity can come from anywhere. The tools of innovation are so simple and cheap today that a much larger pool of talent can be accessed. Smart companies will access them.

Successful companies will help foster an environment where ideas can be seen, examined and modified as we work towards perfection.

Technorati Tags: Social media, Web 2.0

by …†∆†¡∆µ∆ 
Building scientific communities:
[Via business|bytes|genes|molecules]
Here is an interesting point that should be discussed more, especially with scientific community building (my bolding).

I will start with something I have quoted all too often

Data finds data, then people find people

That quote by Jon Udell, channeling Jeff Jonas is one that, to me at least, defines what the modern web is all about. Too many people tend to put the people first, but in the end without common data to commune around, there can be no communities.

A community needs a purpose to exist, a reason to come together. Some communities arise because of similar political or gardening interests. Most research communities come together for one major reason - to deal with data.

However, standard approaches are too slow and cumbersome. When one group can add 45 billion bases of DNA sequence to the databases a week, the solution cycle has to be shortened.

Science is an intellectual pursuit, whether it is formal academic science or just casual common interest. That’s where all the tools available today come into the picture. The data has always been there. Whether at the backend, or at the front end, we can think about how to get everything together, but being able to discovery and find some utility is very important. One of the reasons the informatics community seems to thrive online, apart from inherent curiosity and interest in such matters, is that we have a general set of interests to talk about, from programming languages, to tools to methods, to just whining about the fact that we spend too much time data munging. Successful life science communities need that common ground. In a blog post, Egon talks about JMOL and CDK. Why would I participate in the CDK community, or the JMOL one? Cause I have some interest in using or modifying JMOL, or finding out more about the CDK toolkit and perhaps using it. Successful communities are the ones that can take this mutual interest around the data and bring together the people.

Part of what is being discussed here is a common language and interest that allows rapid interactions amongst a group. In some ways, this is not different than a bunch of people coalescing around a cult TV show and forming a community. A difference is that the latter is a way to transform information that has purely entertainment value.

The size and depth of these ad hoc communities, as well as their longevity, will depend on the size of the beach, just how much data must be examined. But I guarantee that there will always be more data to examine, even after publication.

So my advice to anyone building a scientific community (the one that jumped out at me during the workshop was the EcoliHub) is to think about what the underlying data that could bring together people is first. Data here is used in a general sense. Not just scientific raw data, but information and interests as well. Then trying and figure out what the goals are that will make these people come together around the data and then figure out what the best mechanism for that might be. Don’t put the cart before the horse. In most such cases, you need a critical mass to make a community successful, to truly benefit from the wealth of networks. In science that’s often hard, so any misstep in step 1, will usually end up in a community that has little or no traction.

EcoliHub is a great example of a website in the wild that is supported almost entirely in an Open Source fashion. This is a nice way to create a very strong community focussed on a single, rich topic. On the wide open Internet, though, it may be harder for smaller communities to come into existence, simply because of how hard it might be for the individual members of the community to find one another.

A grant deadline for example.

Technorati Tags: Social media, Web 2.0

by *L*u*z*a*
How Do I Add FriendFeed Comments to My Blog:
[Via chrisbrogan.com]

Hey, smarter people: how do I add a FriendFeed comments module under my blog comments? I want to see all these great comments. Just found these several days later:

Man, so many great people saying great things, and I didn’t engage at all. : (

Not only is this blog entry a great example of how to start a conversation (i.e. ask your community), the comments are a great example of how the conversation progresses. They provide a solution, naturally, but there is also extensive debugging help to get it to work. Eventually, the creator of the needed plug-in arrives to help and ends up making his own software better.

So by asking for help, the community not only provided an answer to Chris, it helped troubleshoot and make the product even better. All in less than 24 hours. How is that for a development cycle!

Technorati Tags: Social media, Web 2.0

by jeffpearce
Socialtext is Growing Up:
[Via Enterprise 2.0 Blog]

I had a great chat with Socialtext’s co-founder Ross Mayfield this week, and he highlighted a few interesting facts about wiki implementations. Notably, he says that wikis fail in the enterprise if they are imposed by IT, rather than by business groups. This is not surprising, but it’s required the company to think hard about
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Ross is a smart guy. I met him several years ago at an AlwaysOn meeting at Stanford in 2003. Socialtext has been doing wiki’s from the beginning so they know some of the barriers that have to be surmounted.

And what he says applies not only to wikis but also to any Web 2.0 approach. The individuals have to see why it is worth their time to change their workflow. And the tools had better help them to that or the tools will languish.

Technorati Tags: Web 2.0

Life Sciences likes this: Friendfeed:
[Via OpenWetWare]

I’m going to assume that only those currently using FriendFeed will understand the self reference in the title but if you didn’t that’s OK. Just keep on reading, you’ll get it, eventually.

If you happen to be interested or work in the life sciences area I’d recommend you take a few minutes to read Cameron Neylon’s great post about FriendFeed and how it’s been embraced by the life sciences community.

I won’t go into the details of how FriendFeed works, but it’s been rapidly gaining momentum as a medium for groups of users to network and discuss each other’s shared content.

FriendFeed’s about page states:

FriendFeed enables you to keep up-to-date on the web pages, photos, videos and music that your friends and family are sharing. It offers a unique way to discover and discuss information among friends

The life sciences community has picked up on this great website like wildfire. A recently created room called The Life Scientists grew in a very short period (a week?) from just a few active online colleagues to a whooping 100+ users.

FriendFeed rooms offer a way to share on-topic content and further discussion via comments. Commenting can be done on any shared items (yours or others). This has proven to be useful for rapid input and idea sharing amongst the room’s users.

Amongst the 100+ users of the Life Scientists room, both Cameron from Science in the Open and Pedro from Public Rambling have found FriendFeed to be useful and explain why it works. Both great reads.

This is the sort of tool that can very rapidly connect researchers, in ways that Twitter or Facebook do not. Not only can links be put up rapidly but comments are there very fast. It allows one to ask questions, post answers. It is a lot like how the Bionet newsgroup, which you can still access, used to be back in the old days (i.e. 1993-95) when Usenet ruled the Internet.

This is the online equivalent of the water cooler where you can run into someone and strike up a conversation that could lead to innovative thinking. Only instead of two people having to occupy the same space at the same time, this approach decouples both, permitting a much wider circle of people to be involved.

Technorati Tags: Knowledge Creation, Social media, Web 2.0