Category Archives: Web 2.0

Browsing clouds, not papers

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

The web provides entirely new avenues for decimating information and for visualizing it. It can be very time consuming to browse throught the literature, even though the most creative research often comes from the intervention of Serendipity (the Wikipedia article lists many examples).

Lars discusses some interesting numbers and comes up with an intriguing solution.

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):


These sorts of rich figures could be very useful in a scientific setting, where being able to rapidly filter a large number of articles is important.

However, he does notice that this approach may not work for all articles, unless there are changes made, either in how the articles are written or in the software that creates the visuals.

…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.

And it would be easy to adapt the visuals to scientific needs and then be able to track if they are actually useful in practice.

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Just a taste

atomium 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.

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Now we have article 2.0

ruby on rails 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.

This works well for Open Source approaches, since the community ‘owns’ the final result. But in this case, it very likely may be Elsevier that owns everything, making the $2500 a very small price to pay indeed.

This could, in fact, spear an Open Source approach to redefining how papers are presented on the Internet. This is because PLoS presents its papers in downloadable XML format where the same sort of process as Elsevier is attempting could be done by a community for the entire communtiy’s enrichment.

And since all of the PLoS papers are Open Access, instead of the limited number that Elsevier decides to chose, we could get a real view of how this medium could boost the transfer of information for scientific papers.

I wonder what an Open Source approach would look like and how it might differ from a commercial approach?

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

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How things have changed

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.

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Scientific commuity building

sand 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.

Now data simply exists, like grains of sand. It requires human interaction to gain context and become information. In social settings, this information can be transformed into the knowledge that allows a decision to be made, decisions such as ‘I need to redo the experiment’ or ‘I can now publish.’

It used to be possible for a single researcher, or a small number, to examine a single handful of sand in order to generate information needed to answer scientific questions. Now we have to examine an entire beach or even an entire coastline. A much larger group of people must now be brought together to provide context for this data in any reasonable timeframe.

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 researchers are actually trying to get their work done. What Web 2.0 approaches do is permit scientists to come together in virtual ad hoc communities to examine large amounts of data and help transform that into knowledge. Instead of one handful at a time, buckets and truckloads of sand can be examined at one time, with a degree of intensity impossible for a small group.

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.

But there are other processes allowing other communities to come together with smaller goals and more focussed needs. The decoupling of time and space seen with Web 2.0 approaches, frees these groups from having to wait until the participants can occupy the same space at the same time. These group can examine a large amount of data rapidly and move on. There is not the need to assure the community that it will be around for a long time.

This is the sort of community that may be more likely to come into existence inside an organization. There are other pressures that drive the creation of these types of groups than simply a desire to talk with people of similar interests about some data.

A grant deadline for example.

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Ask a question. Fix a problem.

drop 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:

FriendFeed

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!

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Ross is right

arches 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
[More]

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.

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Life scientists at Friendfeed

Life Sciences likes this: Friendfeed:
[Via OpenWetWare]

FriendFeed
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.

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Using our social networks

It’s Harvest Time for Networking and Tomatoes by Beth Kanter

This week I am an online mentor on the topic of “Effective Online Networking” as part of the Networking for Success project at the the Women’s Technology Empowerment Centre. The project will teach women how to use Web 2.0 tools and other ICTs to effectively develop and advance their work. Participants are learning how to use these tools to initiate and manage projects; as well as identify networking opportunities with others.

I started with a post with some thoughts about effective online networking. (And posted an invitation to others to participate on my blog). Oreoluwa Somolu, Executive Director of the Women’s Technology Empowerment Centre, left a thoughtful comment.

“I like how you point out that it’s the quality of the relationships that you build online that matters, not just how many people you meet.An analogy is when we attend conferences or other ‘live’ networking events and focus on collecting as many business cards as possible, without taking the time to have proper conversations with people (as well as you can in those settings) and following-up with them afterwards.”

As with face-to-face interactions, there are grooming exercises to be done online. What these new tools do is make it easier for all of us to do a little grooming every so often, without a large expenditure of time.

And finding creative uses of these tools is always important. Such as this:

Chris Brogan shared some excellent post conference networking hacks. I particularly liked this little trick:

“I play “shuffle up and email” often. I take my cards from past events, and then send someone a random email (hopefully with value to what they’re doing, and mindful of what I’d want to do with them). The email is a “ping,” a chance to show them that I’m still out there, and that we might still have business. Further, it might just be the thing that gets someone thinking of me for another opportunity.”

Thinking of email as a ping is a useful idea. Just as salespeople use ticklers to remind them to contact people, this can be used online by anyone. Perhaps we need a little widget in our email that will randomly pick out name, along with some information, and remind us to send an email.

Social grooming is something we all like to do in person. Just think about including it in your online presence. Lots of people love an email out of the blue and it helps maintain a link, as well as further information flow. It is the weak ties that often lead to the most innovative solutions.

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Web 2.0 Behavior

hill by helmet13
Action and Reaction:
[Via A Journey In Social Media]


Conversations are basically what Web 2.0 is all about. It uses new tools but they only accentuate what humans already do naturally – interact and exchange information with a large social network. Many of the same social skills we use in person can be adapted to online use.

Here is a nice discussion of just that at Chuck’s blog as he discusses some of the problems they have seen following a Web 2.0 rollout at his company.

We Want People To Have Conversations

And they are.

Lots of conversations, really. Mostly about work stuff. But not always.

A while back, there was a notable surge in “off topic” discussions — favorite movies, raising rabbits, anime, commute times, etc.

In a pure Web 2.0 idealized world, it’s all good, right?

Well, we’re not exactly in this progressive 2.0 world quite yet. And we have to be mindful of the transition.

There Is A Valid Business Need For Off-Topic Discussions

More and more of our teams are geographically and culturally dispersed. We want people to align and bond around common interests — whatever they might be.

Just like we spend boatloads of money to fly people around for group meetings — and subsequent “team building” events — this sort of idle chatter has a role in “enterprise 2.0”, and we don’t want to be shutting things down.

But, we also want broad adoption in our 1.0 employee base. And if certain 2.0 behaviors hamper that, well — that’s an issue, isn’t it?

So, how to deal with the innovation of a new world to play in as it bumps up against real world situations? First, identify the problems. Here are three.

Problem #1 — Clutter

With our current 1.x Clearspace implementation, we have a “home page” that dutifully records each and every thought someone shares (except blog comments for some reason). That off-topic clutter at a corporate level is downright annoying to many people.

Sure, the user can take action: set up filters, personalize, etc. There’s some of that in Clearspace 1.x, more in 2.x, and then there’s RSS feeds, etc. But all of these are highly dependent on users taking control of their content stream.

And that’s a new 2.0-ish skill that not too many people at our company have. Sure, we could tell them “here’s what you have to do to control the problem”, but we’re trying to drive broader engagement and adoption of the platform, and we’ve had more than a few people new to the environment simply say “I can’t handle this social content stream in addition to my email deluge”.

It’s one thing when they’re exposed to the business-related deluge. It’s another thing entirely when it looks like 40-50% of the stream appears to be purely social in nature.

Doesn’t make it look like a business platform, which is how it was sold to the company.

Problem #2 — Naysayers

In physics, every force results in an opposite force. And in driving corporate change, the same generally holds true. I’m not being negative, just practical.

And, not surprisingly, there are those that look at our internal social media platform with a cold, cynical eye. They don’t understand, they may be threatened, they’re not comfortable, or maybe they’re generally concerned.

Collectively, they have “voice”.

And now they have a bit more evidence for their case.

Problem #3 — The Proficient

We now have upwards of 1,000 people who are truly comfortable and really enjoy the deep end of the pool. They love being exposed to everything. They’re very comfortable controlling the content stream.

And they inherently resist any thought of control, policy, etc. — it just doesn’t work for them. And they’re quite vocal that the rest of the world has to adapt to this 2.0 world, and they better get on with it, now!

And — they have a point. But I’m looking at outcome, and less to make a philisophical statement.

He thought they had a software fix – create a ‘water cooler’ area for the off topic material. But their software made this a problem.

So what he decided to do was use normal social approaches to modify online behavior.

What We’re Doing Short Term

A couple of things, really. First, I went to the more — ahem — prolific threads, and simply reminded people that everything they write is syndicated up to the corporate feed, and that their insightful comments were widely read by several thousand people.

And that while it’s OK to get off topic, please keep in mind that we’ve got a business platform, and you may want to think twice before an extended off-topic discussion for several reasons, e.g. is this what you do all day at work?

The second thing we’re doing is engaging the community. I wrote a blog post outlining the problem and the tradeoffs, and simply asked “what do you all think we should do?”.

People appreciated that we engaged them rather than arbitrarily doing something — good 2.0 behavior. And, somewhere in the dozens of comments, the discussion became pretty clear: we should take no action to limit discussions on the platform, but we should work towards having a “default” home page for newbies that’s a little less intimidating.

He did this with social tools we already possess. For example, he quietly and respectfully told someone, in a non-judgemental way, that their behavior was not really appropriate and to please stop. Then, like a village elder, he directly asked the community what to do. The company can not hire enough annies, tutors, mentors and police to deal with everyone. The community has to use its own members to fill these roles.

It appears that Chuck’s community is doing just that, which indicates to me that it is a rich, well-developed community and that Chuck is far along on the path to success. Because he knows to do this:

So, What Do You Think?

Now that we have a clear “digital divide” in our company with regards to our social productivity platform, what’s the ideal compromise position? Or should there be compromise at all?

And — any proposed solution can’t involve a bunch of custom software, nor can it involve hiring and dedicating people to the task. Nor can it involve having tens of thousands of employees learning to control their content stream as a prerequisite for success.

An interesting challenge, to be sure ….

He checks with the larger outside community, because he also acts as a connector between communities. He engages the groups for answers so that if there are other ideas, he can quickly implement them for his community. This is how creativity and innovation can be so rapidly created with Web 2.0 approaches.

Innovation diffusion rates in a community can be greatly affected by these approaches.

Because the potential number of other communities he can engage is huge. if there is any solution out there, he does not need it to diffuse to him by Web 1.0 or even World 1.0 approaches, which could take years. Web 2.0 greatly decreases the friction of information transfer from other approaches.

The faster a community can deal with change, the more it can deal with innovation, the better decisions it can make because it has access to more information and creativity, the sooner it will gain wisdom.

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