LinkedIn Applications: I just added my blog and slideshare content! Wow!:
[Via Beth's Blog: How Nonprofits Can Use Social Media]

LinkedIn is a professional network for business and (and nonprofit professionals.) It is often described as an online social network for job seekers. Perhaps because initially your profile was structured like an online version of your resume. Let me tell you, LinkedIn can be a terrific place to develop professional contacts, grow your business, and promote your work and opportunities. There are many good reasons why nonprofit professionals use online professional networking sites liked LinkedIn.

Earlier this week LinkedIn announced its applications platform that includes a small number of well-chosen apps that can enhance your professional networking profile. You can add your blog content, slide shows, reading lists, files, business travel, and more. (Chris Brogan calls the addition of adding your business travel schedule “dog clever.” Since LinkedIn is primarily a professional networking site that can help you find job prospects, works prospects, and

For my profile, I added BlogLink (it posts my blog posts to my profile automatically) and SlideShare’s Application. (In the video above SlideShare’s CEO Rashmi Sinha demonstrates the application.)

Technorati Tags: Social media, Web 2.0

by dalbera
Is Science Being Distorted?:
[Via The Scholarly Kitchen]

A recent PLoS Medicine article claims that information economics distort science. But maybe it’s an obsession with journals distorting the views of the authors.
[More]

As I said earlier, I thought there would be some interesting discussions. I guess one way of looking at it is that all the ‘good’ data gets published in the prestigious journals and there is nowhere for the ‘bad’ data to be published until after a clinical trial fails. Whether this is a real bias problem is difficult to assess.

I think any problem is due more to the complexity of human health studies than any bias but we have to keep moving forward as best as we can.

Technorati Tags: Science

by tanakawho
Have a problem: Build a web resource:
[Via business|bytes|genes|molecules]

Via a post on Hacker News I ran into the Tulane School of Medicine Student Portal.

As one of the developers writes on Hacker News

Our goal is ‘making med school easier, one less click at a time’. We have no business model, just trying to make our own lives easier.

There is further description on the site

Hello, and welcome to the Tulane University School of Medicine’s Student Portal! This website came into existence over the course of the latter part of the 2007-2008 school year through the hard and volunteered work of a group of students concerned with making the lives of TUSOM medical students a bit easier. Our university community is a dynamic place with much do, and many resources to use on a daily basis. In an effort to reduce the amount of time and energy required to accomplish these activities, we developed this site. Our work has been led, and graciously supported by the Medical Student Government, the Office of Medical education, and the Deans.

This site was developed by students, and for students. As such, if there is a feature that you feel would benefit the community as a whole, please feel free to drop us a line at tmedweb@tulane.edu. We’ll take your suggestion into serious consideration, and see if it within our abilities to accomplish.

That’s the kind of initiative that one loves to see. With hosting cheap, good web frameworks and people increasingly looking to the web for information, not the last time you’ll see something like this either. The key is realizing that often, if you have a problem, you can solve it yourself, and relatively inexpensively. Sometimes you can build a business out of it, a la 37signals

They (or at least Niels Olson) have some pretty ambitious future plans as well.

Online tools are not only cheap, they are also mature enough that it no longer requires a CS degree and years of experience to put something together. Coupled with Open Source, an individual can create pretty complex sites.

A similar attitude is beginning to invade other areas, such as Biotech. So many of the support functions are now available from standalone companies (such as DNA synthesis, sequencing, etc.) that we are almost at the point of ‘garage biotech’, where a very substantial amount of work can be done through contract for much less cost that having to create the infrastructure yourself.

This will never be at the same level as IT sorts of processes but it can have a profound effect on the cost of doing the biotech business. Add in IT tools to facilitate rapid information dispersal and a small lab can accomplish things that required a much larger facility just 5 years ago.

Technorati Tags: Open Access, Web 2.0

by Marcin Wichary
An experiment in open access publishing:
[Via Bench Marks]

The new edition of Essentials of Glycobiology, ” the largest, most authoritative volume available on the structure, synthesis, and biology of glycans (sugar chains), molecules that coat cell surfaces and proteins and play important roles in many normal and disease processes” came out yesterday. What’s particularly interesting about this edition is that it is simultaneously being released online in a freely accessible version, which will hopefully allow the textbook to reach a wider audience.

The theory often espoused is that online release of books leads to higher sales of the print edition, and for us, this is a good test case. Quoting from the press release, John Inglis, Executive Director and Publisher of CSHL Press notes that,

“We will be tracking its usage and how readers of the site respond to the availability of a print version, for both research and teaching purposes.”

“This is an innovative development in the distribution of an established textbook that we hope will benefit readers, authors and editors, and the publisher,” says Ajit Varki, M.D., the book’s executive editor and a leader of the Consortium of Glycobiology Editors, which initiated the project. Varki is Professor at the University of California, San Diego. The Consortium also includes Professors Richard Cummings, Emory University; Jeffrey Esko, UC San Diego; Hudson Freeze, Burnham Institute for Medical Research; Pamela Stanley, Albert Einstein College of Medicine, New York; Carolyn Bertozzi, UC Berkeley; Gerald Hart, Johns Hopkins University School of Medicine; and Marilynn Etzler, UC Davis.

The online edition of Essentials of Glycobiology can be found here, and the print version can be ordered here.

This is a very interesting experiment. I knw that there are books I want to have to be able to access important data when I am not online, usually when I am writing. Being online can be distracting then.

But sometimes when I am online, I want a quick fact. Then finding them in an authoritative source is really important. I personally think that this sort of dual use could be very productive. It has been successful for some fiction works.

I too will be looking to see how well this works.

Technorati Tags: Open Access, Science, Web 2.0

by Corey Leopold
Knowledge wants to be connected:
[Via Science Commons]

That was the core message of a speech by Science Commons’ John Wilbanks at the Open Access and Research Conference 2008 a few weeks ago in Brisbane, Australia. The conference was an opportunity both to celebrate Australia’s burgeoning leadership in harnessing open approaches for advancing science and scholarship, and to talk about where the global open access (OA) movement is headed.

Thanks to the Web, we can gain knowledge about a meeting happening thousands of miles away. Then we can read what others thought of the meeting.

Here’s an excerpt from an article by the Australian Broadcasting Corporation’s Anna Sellah on the speech, which provides a succinct summary of the reasons why open approaches are vital for deriving value from the vast amounts of scientific data being produced:

“The value of any individual piece of knowledge is about the value of any individual piece of lego,” Wilbanks said in a keynote address to the Open Access and Research Conference held in Brisbane last week.

“It’s not that much until you put it together with other legos.”

He says the ability to connect knowledge brings scientific revolutions. For example Watson and Crick’s breakthrough on the structure of DNA involved them reading all the scientific papers on nucleotide bonding and encoding it in the form of a physical model, says Wilbanks.

But this kind of “human scale” analysis is no longer feasible in an age when automated laboratory processes generate vast amounts of information faster than the human mind can process it.

“For example, we have 45,000 papers about one protein or one gene,” says Wilbanks.

He says a scientist might once have analysed the impact of one drug on one gene, but now pipetting robots are capable of analysing 25,000 genes at a time.

“Most of the research says the smartest of us can handle five or six independent variables at once - not 25,000,” he says

You can read the full piece at the ABC website.

Those of you following news of the conference and developments in Australia may also be interested in Open Oz and Doing things with data, two posts by OA leader Dr. Alma Swan, who was also a keynote speaker at the event.

Social netowwrks evolved to deal wit large problems containing many variables (i.e. “what signs are present indicating that its save to plant?”) If we can have large groups examine the problem, many more variables can be looked at. A question would be “Does the number of variables increase linearly with network size or exponentially?”

Technorati Tags: Social media, Web 2.0

Many Eyes = Many Brains:
[Via The Scholarly Kitchen]

Socially networked data visualization becomes a reality with Many Eyes.
[More]

I’ve seen this before and it is a great idea. Lets make data visualization open and allow social networking approaches help come up with new ways to look at data.

Visit and have some fun.

Technorati Tags: Social media, Web 2.0

by Snap®
Current Biomedical Publication System: A Distorted View of the Reality of Scientific Data?:
[Via Scholarship 2.0: An Idea Whose Time Has Come]

Why Current Publication Practices May Distort Science

Young NS, Ioannidis JPA, Al-Ubaydli O

PLoS Medicine Vol. 5, No. 10, e201 / October 7 2008

[doi:10.1371/journal.pmed.0050201]

Summary

The current system of publication in biomedical research provides a distorted view of the reality of scientific data that are generated in the laboratory and clinic. This system can be studied by applying principles from the field of economics. The “winner’s curse,” a more general statement of publication bias, suggests that the small proportion of results chosen for publication are unrepresentative of scientists’ repeated samplings of the real world.

The self-correcting mechanism in science is retarded by the extreme imbalance between the abundance of supply (the output of basic science laboratories and clinical investigations) and the increasingly limited venues for publication (journals with sufficiently high impact). This system would be expected intrinsically to lead to the misallocation of resources. The scarcity of available outlets is artificial, based on the costs of printing in an electronic age and a belief that selectivity is equivalent to quality.

Science is subject to great uncertainty: we cannot be confident now which efforts will ultimately yield worthwhile achievements. However, the current system abdicates to a small number of intermediates an authoritative prescience to anticipate a highly unpredictable future. In considering society’s expectations and our own goals as scientists, we believe that there is a moral imperative to reconsider how scientific data are judged and disseminated.

Full Text Available At:

[http://medicine.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pmed.0050201]
[More]

There are also several other article links at Scholarship 2.0 that are important to read. In particular, there is a discussion of the Winner’s Curse This is an observation that the winner of an auction in which all the bidders have similar information will usually overbid. The idea of the Winner’s Curse was first observed by oil companies bidding on offshore leases.

I expect this work to produce some interesting discussions. I would be surprised if it is entirely true but it does propose some changes that might be worth implementing.

Technorati Tags: Open Access, Science

by *Micky
Zotero facing a lawsuit:
[Via Bench Marks]

I’ve written about Zotero before, it’s an intriguing tool, essentially a Firefox plug-in for managing your reference list and other pieces of information. It’s a bit of a hybrid between online management tools like Connotea and things like Papers which you store on your own computer.

The bad news is that Thomson Reuters, the manufacturers of EndNote, are suing George Mason University and the Commonwealth of Virginia because a new version of Zotero lets you take your EndNote reference lists and convert them for use in Zotero. Yes, this is the same Thomson of Thomson ISI, secret gatekeepers of journal impact factors. They really seem to be going out of their way to lose what little goodwill they have left with the scientific community. It will be interesting to see if this reverse engineering for interoperability holds up in court as something that should be prevented.

This is sadly typical. I loved EndNote back in the 90s because it was a great Mac product. Much better for my needs than its competition, Reference Manager, which was much more of a Windows product. Niles Software really listened to what people wanted and added some very useful features, such as linkage of the library to a Word document. Then you could put the citation directly into Word.

Because the database really belongs to the user not to Thomson. But they try to obscure that by using a proprietary format. This hurts the enduser. Say I have an 10 year old EndNote library I forgot to convert. With say 8000 entries. And an old version of EndNote that no longer works in OS X. How am I supposed to move it to what I currently use without having to purchase EndNote simply for this one use? My favorite example of this horrendous process is the Mac cookbook program Mangia!

Mangia is no longer produced by anyone. The database created was proprietary and undocumented. The program had no export feature. Now it no longer even runs on any computer. So every user now has a database that they created that is unusable. There are workarounds to try and get to the data but they are not satisfactory. They also require the user to be able to run Mangia, which is really impossible for virtually everyone using a Mac today (I think my mother kept an old Mac around just so she could still use this one program. She has a huge library of recipes).

More from Bench Marks:

More importantly, it’s yet again, a lesson in tying yourself to one locked-down proprietary format for your data and your work tools. If you’ve put a huge amount of time and effort into maintaining your EndNote list and a better tool comes along and becomes the standard, all that work may go to waste and you’ll have to start over again. A similar lesson was learned last week from anyone who purchased music downloads from WalMart. Richard Stallman recently gave a warning along the same lines about the much-hyped concept of “cloud computing”.
As you experiment with new online tools for your research, heed these lessons well. Demand tools that support open standards and open formats, tools where if you put in an effort (and most of these tools demand a lot of effort), you can get that work out again so you don’t have to repeat it for the next tool you try. Further discussion here and here.

This gets at the same topic. Who owns the data? There are some very important and useful aspects to having data in the cloud. It makes it very easy for people to access their data from everywhere. Small groups can have a slew of Web 2.0 applications up and running for their group with little cost for maintenance or upkeep. This has some very real benefits.

So, echoing David, stay away from anything that ties you into a specific, closed format. It can come back to bite you big time.

Technorati Tags: Open Access, Web 2.0

I’ve mentioned some of the work by Everett Rogers on technology adoption. The bell curve seen refers to the adoption of innovations by a community. But what about individuals? Is there a process whereby they adopt new technology?

Turns out there is. You can read the work by George Beal and Joe Bohlen in 1957. There is a five step path that each individual appears to go through, although some people are slower to transition between steps.

1. Awareness. The individual is simply aware the innovation exists.
2. Interest. The individual wants more information. They begin to wonder if the innovation can help them.
3. Evaluation. The individual mentally examines the innovation using the information gathered, trying to determine whether it will really impact their work.
4. Trial. The individual actually tests the innovation to see if reality matches expectations.
5. Adoption. The individual likes the innovation and adopts it wholeheartedly.

Beal and Bohlen also described what sources of information were used at each stage. Through the first two, mass media and government agencies were most important.

This was really an attempt to get an ‘unbiased’ viewpoint since friends and salesmen (saesmen always came in last) were the next two sources. But for the last 3 stages, neighbors and friends were the largest source of information, moreso than any other group.

So, early in the diffusion process, unbiased experts are sought. But when the evaluation process is started, the experiences of close ties within a local social network become the most important. For most people, the opinions and personal experiences of their friends are most important for adoption of a new innovation than any external source.

Now the innovators in a community race through these steps. They often are connected to outside groups and use social interactions unavailable to others in the community to more rapidly move through the last 3 steps.

The early adopters take information from the innovators and use their own connections to move through the stages, not as fast as the innovators, but with reasonable speed.

But it is the majority of the community that relies on the early adopters and innovators within the community to inform themselves. Research has shown that they require much more information from trusted sources within the community than innovators and early adopters. Without this information from peers, they will not progress rapidly through the last 3 stages.

The laggards are the slowest to move through the 5 stages. They do not trust most outside sources, so the awareness and interest stages are slowed. Plus they will only listen to certain trusted sources within the community. Until those trusted sources make their own way through the 5 stages, the laggards will not progress.

So, to alter the rate of diffusion of innovation in a community, increased lines of communication must be available, increasing the information that can be provided to individuals.This helps with the first 2 steps. but mostly only for the 16% of the community at the left side of the curve.

However, of greatest importance are the connections between members within the community, particularly the thought-leaders found in the early adopters. About 70% of a community will not adopt new innovations unless they hear clear reasons why, from trusted individuals within the community.

No amount of salesmanship or external proof will easily move them. But, tgiven he right opinion from a community thought-leader and they will rapidly make the transition.

This is an area that Web 2.0 technologies can be of real value. Not only do they make it easier for members of a community to disburse information, they also help the community more accurately identify who is in each group, permitting more focused, explicit approaches to be used to move individuals through the 5 steps.

The thought-leaders can more rapidly progress through the stages and can extend their opinions much more rapidly to the majority because they are not required to be in the same place at the same time as the others in the group. Thus there will be more opportunities for their viewpoints to be assimilated by the majority.

Increasing the rate of diffusion of innovation in a community really means increasing the speed with which each individual progresses through the 5 step.

Technorati Tags: Knowledge Creation, Open Access, Science, Web 2.0

by freeparking
London Science Blogging Conference on Friendfeed:
[Via Confessions of a Science Librarian]

Boy, do I ever love Friendfeed.

You can follow what’s going on at today’s London Science Blogging Conference in its very own Friendfeed room. Each session has it’s own thread with multiple people commenting on the proceedings. It actually gives a very good and surprisingly understandable impression of what’s going on in the sessions. Most of the sessions have dozens of comments. Check it out.

You can also check me out on Friendfeed (join, you won’t regret it). Michael Nielsen has also created a room for the upcoming Science in the 21st Century conference.

As a sort of aggregator of one’s life, FriendFeed can be especially useful for all sorts of ad hoc social meetings, such as conferences. I wonder what the ‘room’ looks like for a really large conference, the 10,000 attending ones? I’ll be sure and check out the Science in the 21st Century room.

Technorati Tags: Open Access, Science, Web 2.0