Knowledge Creation, Open Access, Web 2.0

Just a taste

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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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Open Access, Science, Web 2.0

Now we have article 2.0

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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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Web 2.0

How things have changed

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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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Knowledge Creation, Web 2.0

Scientific commuity building

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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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Science

Two a day

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hard drive platters by oskay
15 human genomes each week:
[Via Eureka! Science News – Popular science news]

The Wellcome Trust Sanger Institute has sequenced the equivalent of 300 human genomes in just over six months. The Institute has just reached the staggering total of 1,000,000,000,000 letters of genetic code that will be read by researchers worldwide, helping them to understand the role of genes in health and disease. Scientists will be able to answer questions unthinkable even a few years ago and human medical genetics will be transformed.
[More]

Some of this is part of the 1000 Genomes Project, an effort to sequence that many human genomes. This will allow us to gain a tremendous amount of insight into just what it is that makes each of us different or the same.

All this PR really states is that they are now capable of sequencing about 45 billion base pairs of DNA a day. They are not directly applying all of that capability to the human genome. While they, or someone, possibly could, the groups involved with 1000 genomes will take a more statistical approach to speed things up and lower costs.

It starts with in depth sequencing of a couple of nuclear families (about 6 people). This will be high resolution sequencing equivalent to 20 passes of the entire genome of each. This level of redundancy will help edit out any sequencing errors from the techniques themselves. All these approaches will help the researchers get a better handle on the most optimal processes to use.

The second step will look at 180 genomes but with only 2 sequencing passes. The high level sequence from the first step will serve as a template for the next 180. The goal here is to be able to rapidly identify sequence variation, not necessarily to make sure every nucleotide is sequenced. It is hoped that the detail learned from step 1 will allow them to be able to infer similar detail here without having to essentially re-sequence the same DNA another 18 times.

Once they have these approaches worked out, and have an idea of the level of genetic variation expected to be seen, they will examine just the cgene oding regions of about 1000 people. This will inform them of how best to proceed to get a more detailed map of an individual’s genome.

This is because the actual differences expected to be found among any two humans’ DNA sequences is expected to be quite low. So they want to identify processes that will highlight these differences as rapidly and effectively as possible.

They were hoping to be sequencing the equivalent of 2 human genomes a day and they are not too far off of that mark. At the end of this study, they will have sequenced and deposited into databases 6 trillion bases (a 6 followed by 12 zeroes). In December 2007, GenBank, the largest American database had a total of 84 billion bases (84 followed by 9 zeroes) that took 25 years to produce.

So this effort will add over 60 times as much DNA sequence to databases as have already been deposited! It plans to to this in only 2 years. The databases, and the tools to examine them, will have to adapt to this huge influx of data.

And, more importantly, the scientists doing the examining will have to appreciate the sheer size of this. It took 13 years to complete the Human Genome Project. Now, 5 years after that project was completed, we can potentially sequence a single human genome in half a day.

The NIH had projected that technology will support sequencing a single human genome in 1 day for under $1000 in 4 years or so. The members of 1000 genomes are hoping to be able to accomplish their work for $30-50,000 per genome. So, the NIH projection may not be too far off.

But what will the databases look like that store and manipulate this huge amount of data? The Sanger Institute is generating 50 Terabytes of data a week, according to the PR.

Maybe I should invest in data storage companies.

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Open Access

Using other scientific disciplines

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fractal fern by SantaRosa OLD SKOOL
Three Thoughts on Interdisciplinary Research:
[Via Michael Jubb’s blog]
Comments on Michael’s three thoughts following some meetings he has attended recently:

The first was a suggestion, perhaps a hypothesis, that interdisciplinary research will lead (has led?) to an increase in researchers’ interest in open access. The thought here is that researchers in some disciplines (notably some areas of the biosciences) are more inclined to adopt some form of open access in publishing their work; and that as researchers from other disciplines less inclined to open access join with, say, bioscientists in their research, they will be introduced to open access ways of thought. It seems a plausible hypothesis, and one that could fairly easily be tested. Does interdisciplinary research feature particularly prominently in OA journals, or in the contents of repositories?

I think part of this is that working in a interdisciplinary fashion fosters openness. That is, such researchers are often working in and relying on access to scientific disciplines other than the one that the researcher was trained in. If they can not access research from a discipline, they will not really be able to work in that discipline.

It would seem likely that collaborative efforts would most easily flow to those areas that foster open communication with collaborators. Hard to be multidisciplinary it there is not open collaboration with others.Thus open access becomes part of the culture of multidisciplinary research.

The second thought comes from a presentation by Carol Tenopir of the findings of the latest Tenopir and King reader surveys. One of the interesting findings is that interdisciplinary researchers are more likely than other researchers to follow citation links as their means of getting access to journal articles; and that the latest article they have read is more likely to be in digital, as distinct from print, format. Why that should be is perhaps worth some investigation.

Online is all about finding information quickly, incorporating it into the local community and then using it to create knowledge to make decisions. Rapid analysis followed by community synthesis. The collaborative cycle cranks much faster when online tools and Web 2.0 approaches are used. This allows multidisciplinary efforts to be launched that would be virtually impossible without these tools. This pace of collaboration can not be as rapidly sustained using paper means.

The third thought comes from a presentation by Mayur Amin of Elsevier about surveys of usage of journals in Science Direct. One of the interesting findings here is that while for researchers in physics and maths, 70% or more of usage is of journals within the discipline, for researchers in other disciplines, such including chemistry and environmental sciences, usage of journals within the discipline is at less than half that level. This may of course be an effect of the way in which Elsevier classify the journals. But it is at least open to the suggestion that researchers in some disciplines are more inclined to read beyond their own discipline. Is this evidence that some disciplines are more interdisciplinary than others? Is this something worth investigating?

One hypothesis is based on the hierarchy of science and the natural world. Math as a discipline is the most abstract; it can exist without any real need to be part of any other discipline but almost every other discipline needs math. Physics then comes next. It needs math to describe itself but little else other than physics.

Then comes chemistry and biology. Each level down involves lesser abstraction and closer dealings with the natural world. Each requires more and more simple experimentation and observation. Physics has gedanken experiments, which come close to the Greek ideal of not needing to do any experimentation. Math needs no experiments at all and can be done simply in one’s head.

I’m stretching a point but to really understand biology, you need to at least be familiar with chemistry, with physics and with math (not necessarily comfortable since I often think some people go into biology because the math requirements in college are easier than for physics). Physics, though, does not really require a knowledge of chemistry or biology. So, perhaps, this need to understand other fields in order to be trained in biology instills a little more attraction to interdisciplinary approaches, as can be seen in the journal usage seen by Elsevier.

Or maybe it is just sampling error.

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Web 2.0

Ask a question. Fix a problem.

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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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Web 2.0

Ross is right

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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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General

Norms are changing

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columns by TankGirlJones
Column on NIH and Harvard policies:
[Via Open Access News]
Karla Hahn, Two new policies widen the path to balanced copyright management: Developments on author rights, C&RL News, July/August 2008.

A light bulb is going off that is casting the issue of author rights management into new relief. On January 11, 2008, the National Institutes of Health (NIH) announced a revision of its Public Access Policy. Effective April 7, 2008, the agency requires investigators to deposit their articles stemming from NIH funding in the NIH online archive, PubMed Central. Librarians have been looking forward to such an announcement, especially since studies found that the voluntary version of the policy was achieving deposit rates of affected articles on the order of a few percentage points.

Since we as taxpayers pay for this research, it should not be bound up behind access control. Now, because of the NIH’s revision, it won’t.

With the article deposit requirement, researchers can no longer simply sign publication agreements without careful review and, in some cases, modification of the publisher’s proposed terms. While this may be perceived as a minor annoyance, it calls attention to the value of scholarly publications and the necessity to consider carefully whether an appropriate balance between author and publisher rights and needs is on offer.

The norm in science has been to always quickly sign over copyright so that the paper could be published. This sometimes resulted in the absurd prospect that the author of a paper could not use his own data in slides, since he no more owned the copyright of it than any other random scientist. Now there is a little leverage for the author to retain some aspects of copyright.

As institutions, as grantees, become responsible for ensuring that funded authors retain the rights they need to meet the NIH public Access Policy requirements, there is a new incentive for campus leaders to reconsider institutional policies and local practices relating to faculty copyrights as assets. …
The February 2008 vote by the Harvard Faculty of Arts and Sciences to grant Harvard a limited license to make certain uses of their journal articles is another important indicator of an accelerating shift in attitudes about author rights management, and also reveals the value of taking an institutional approach to the issue. …

Academic pressure is coming to bear on these policies and it will be interesting to see how it all plays out. In most instances, providing open access will be the better route but now the individual institutions will be responsible for providing the necessary infrastructure.

Perhaps something like Highwire Press will appear. Here , instead of each scientific association having to develop their own infrastructure, Highwire does it for many of them, greatly simplifying publishing for all. Highwire now has almost 2 million article published with free access. Perhaps something similar for institutional storage would be helpful.

Norms are always more difficult to change than technologies. We are now witnessing a key shift in norms for sharing scholarly work that promises a giant step forward in leveraging the potential of network technologies and digital scholarship to advance research, teaching, policy development, professional practice, and technology transfer. …

What scientists expect when they publish a paper is changing rapidly. What once took 6-9 months from submission to publication can now happen in weeks. Where once all rights had to be assigned to the publisher, now the authors can retain some for their own use.

What will the norms be like in five years?

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