by hendriko
All the details have been finalized for a three hour seminar SpreadingScience is sponsoring entitled

Transformed! Information, Bioscience and Web 2.0

October 7, 2008 6-9 PM
Lake Washington Rowing Club
910 N. Northlake Way
Seattle WA

The seminar will be given by Richard Gayle, Ph.D. and Mark Minie, Ph.D. It is geared for a general audience that includes researchers, lawyers, clinicians and anyone else interested in using modern technology to solve today’s problems. It will have three segments:

1. The Transformation of Information into Knowledge
   Knowledge is the ability to make a decision, to perform an action. The knowledge creation cycle begins with data. Human social interactions transform data into knowledge. Social networks evolved to provide primates with diverse solutions to complex problems. However, there appear to be hardwired barriers to the size of these social networks, limiting the scope and complexities of the problems that can be solved. The huge amount of information being generated overwhelms these barriers. The difficult problems facing us today are too complex to be solved only the tools we evolved. We must use new digital tools to amplify our inherent abilities.
2. The Transformation of Bioscience by Information
   Biology is now a branch of Information Science, and important new research, discovery and invention is taking place on the World Wide Web. From computer gaming/education to personal genomics, biological engineering and robotics, bioscience is undergoing a true renaissance with previously unexpected impact and dividends. This segment will explore bioscience’s new life on the Internet. It will focus on specific examples and new tools with potential practical uses for both scientists and non-scientists alike.
3. The Web 2.0 Transformation
   Web 2.0 is about online conversations. These tools often remove the need for people to occupy the same space at the same time in order to transform information into knowledge. They permit the examination and understanding of human social networks many times larger than our hardwired limits. This enhances the ability to create knowledge and to increase the rate of diffusion of information in an organization. Communities that can use Web 2.0 tools to leverage human social networks will solve complex problems more rapidly than those that do not.

There is a glut of data in the world today. Our normal processes to deal with this glut – the interactions in a human social network – are overwhelmed. However, the same technologies that are permitting such huge amount of data to be created can also help us enhance our social network interactions, providing organizations with the possibility of solving much more complex problems than before.

Please join us on October 7 as we provide a foundation for understanding how Bioscience is being transformed by information and how we can use novel tools to leverage this transformation into critical solutions .

Until September 23, the cost is $175. After that date it rises to $225. So register early!

Technorati Tags: Science, Web 2.0

by nordique
The independent research institute will drive biomedical innovation:
[Via business|bytes|genes|molecules]

The Broad Institute just got a donation of $400 million from Eli and Edyth Broad. The donation is the formal start of an endowment, making the Broad Institute a permanent, standalone biomedical institution.

I have bemoaned the death of such bastions of innovation like Bell Labs in the past. But there is a trend in the biomedical sciences that is encouraging. Non-profit institutes and research centers like the Broad, The Wellcome Trust Sanger Institute, Janelia Farms, The Institute for Systems Biology, etc, with funding from powerhouse funders like the Wellcome Trust and the Bill and Melinda Gates Foundation are leading a trend towards independent research centers. Given the requirements for focussed cross-disciplinary research, I have a strong feeling that many of the innovations of the next quarter century are going to come from such institutions, funded by non-profits, private enterprises, and non-profit arms of companies like Google.

There will always be place for such federally funded institutes, especially those that fit the model of the ones described above, e.g. the Joint Bioenergy Institute. I wonder, in this changing environment, what the role of the traditional research university will be? In the life sciences, I see a continuum of research and collaboration, between universities, well-funding research institutes, and private enterprise. If we can harness the best of all three arms of research, I think we will be successful at innovation and not get in the kinds of rut we often do today, with too much overlap, little focus, and attempts at trying to leverage a somewhat broken federal funding system.

Is this a growing trend? Are we at risk of diluting the research pool by having too many institutes? We’ll just have to wait and see, but I am quite optimistic.

I think Deepak has hit on a very important trend. Independent, non-profit research centers are a real hotbed now, not only because of the large amount of money from large funders. There is also a lot of Federal money heading towards them.

But non-profits fit right in the sweet spot. They HAVE to solve difficult problems, with deadlines much like small startups but with the freedom of endeavor and choice of research direction seen in universities. Since few are big enough to do everything themselves, collaboration is really required. This drives them to find the best solution to solve their problem, even if that requires collaboration.

It could well be that many universities simply return to undergraduate education and that large-scale research will move to these independent non-profit research institutes. What do you think?

Technorati Tags: Science, Social media, Web 2.0

by Avoir Chaud
Bioinformatics as mashup:
[Via business|bytes|genes|molecules]

bioinformatics: acquiring, collating and rearranging information already available elsewhere?

That is from a Tweet by Neil. My reaction was somthing along the lines of “boy that sounds like the definition of a mashup”.

Bioinformatics is a broad field, but part of it, a good part of what a bioinformatician does is exactly what Neil describes. The work of a bioinformatician is built on data collected by many people around the world and deposited in a variety of data bases. A lot of what we do is take information from one and try and match it up to information from a second source, presumably with the goal of getting additional insights. It might sound crude to call it that, but I think if we start thinking of bioinformatics as a mashup, we could start thinking about making those mashups available to others, and perhaps even new ways to present the information.

Disclaimer: This post was written early in the morning before any intake of caffeine

This is exactly right. Data just exists. It requires human interaction to provide context. Sitting in a database does nothing.

Mashups, as described here, take explicit information and transform it into knowledge. The key is to provide the right tools so that appropriate mashups can be performed. Perhaps Ubiquity will provide an avenue for such mashups.

by jurvetson
How academic health research centers can foster data sharing:
[Via Science Commons]

PLoS Medicine today published a new paper that provides useful guidelines for people at academic health centers seeking to support scientific data sharing. The paper, Towards a Data Sharing Culture: Recommendations for Leadership from Academic Health Centers, discusses both the enormous benefits and the obstacles to forging a research culture that fosters data sharing, and outlines practical steps people can take to set the process in motion.
[More]

There are some very useful recommendations in the paper. It will really take some changes in scientific culture for some of them to be undertaken. But the faster these changes are made, the sooner the benefits can be seen.

Technorati Tags: Science, Web 2.0

The ‘Ubiquitous’ web:
[Via business|bytes|genes|molecules]

Image via Wikipedia
All of you know about it already, but I shall happily add to the noise. Last evening I had one of those “Holy S**t” moments. Was sitting in a coffee shop, catching up with the days news, when I saw a flurry of activity on Friendfeed around Ubiquity. Turns out Ubiquity is a new project by Mozilla Labs, which for want of a better description is like Quicksilver for the browser, a mini command line available with an Alt-space.

[More]

Ubiquity looks to be very interesting and useful. It will be nice to use this for various science mashups. One more reason to use Firefox.

Technorati Tags: Science, Web 2.0

by fdecomite
More on bloggers and OA:
[Via Open Access News]
Bora Zivkovic, ResearchBlogging.org, v.2.0, A Blog Around the Clock, August 29, 2008.

… [W]e took a little look [at the new release of ResearchBlogging.org] at the PLoS HQ and noticed that out of 87 pages of ‘all results’ there are 8 pages of ‘PLoS’ results - implying that about 10% of all the [ResearchBlogging.org] posts are on PLoS papers from all seven journals - and of those, 4 pages are just on PLOS ONE papers - which is about 5%. All I can say is w00t! for Open Access - when bloggers can read, bloggers will write.

ResearchBlogging demonstrates how blogging can be used to disburse information. The individual writers serve as excellent filters. It is like a journal club online, providing a way to cut through some of the jargon in a paper and see what its real relevance is.

It is one step above “Hey, did you see the paper in the latest Blood about X?” Now when an interesting paper is found, a short synopsis, with the proper attribution is available to a large network.

Technorati Tags: Science, Social media, Web 2.0

by cadmanof50s
Science blogging is the new email:
[Via Gobbledygook]

The just finished conference Science Blogging 2008: London was a wonderful chance for real-life socialising networking. I started to upload some fotos to Flickr (e.g. Scott Keir explaining sign language, see all fotos tagged sciblog here), some of them are too embarrassing and I will keep them for bribes reference later on.

The meeting was also a great opportunity to think about where we are today with scienceblogging. Having a conference is a good sign that the field is evolving1, and you can see several subdisciplines evolving:

• conference blogging (also includes event blogging)
• edublogging
• metablogging (blogging about blogging, by far the largest discipline)
• research blogging (blogging about scientific experiments, the smallest discipline)
• investigational blogging (the keynote lecture by Ben Goldacre described this very well)
• evolution blogging (a large subdiscipline)
• news blogging (blogging about science news)
• watercooler blogging (small pieces of interesting or funny thoughts/pictures)
• summary blogging (summarizing other blog posts and linking to them)
• diary blogging (blogging as a personal diary of self-expression)
• hoax blogging (see this example by Jonathan Eisen)

[More]

This is a pretty interesting framing of the use of blogs for research. A lot of useful scientific inquiry is informal in nature, occurring around a coffee machine or at a pub. Blogs just allow people who do not share the same time or place to participate. And in a more useful fashion than email.

Technorati Tags: 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

by Vik Nanda
Royalties for journal article authors:
[Via Bench Marks]

I’m happy to say that this week we sent out our first round of royalty payments to authors of original articles in CSH Protocols. Because we’re doing some reprinting of material from our already-published laboratory manuals, we built in a system to pay royalties to the editors of those manuals. We chose at the time to extend those royalties to authors of new material as well. The idea of writing up methods isn’t something that immediately occurs to most laboratories–they’re usually more interested in publishing data, so we’re hoping that these royalty payments will at least serve as something of a motivation for publishing (and continuing to publish) protocols with us. We’re not talking about huge sums of money, but as I recall from my graduate student days, every little bit helps. It also addresses one of the complaints one hears about us greedy science publishers–that we fail to compensate scientists for the work they’ve put into the publication and keep all the cash for ourselves. While CSHL Press is part of a not-for-profit research institute, and any money we make from our publications goes to fund research at Cold Spring Harbor Laboratory, we’re very curious to see what happens from this experiment in revenue-sharing. Does this make a difference to you as an author?

This set of royalties covers the calendar year 2007. A portion of our subscription revenue is set aside and divided among all authors/editors based on the usage of their individual articles during that calendar year. Those who published articles late in the year may not see much in terms of revenue given the relatively small time scale that their articles were available, but hopefully their articles will see a little more use in 2008.

This is a really interesting experiment. Many researchers will need a little extra incentive to write up a protocol paper, but they can be very useful to have. CSH Protocols has been leading on many ways from their free access articles each month to, now, the use of royalties.

Finding the right niche in an online/offline world is what keeps everyone on their toes. CSH Protocols looks to be making a nice place for itself. I’d imagine there will be some other tweaks to the publishing industry before it is all said and done.

Technorati Tags: Science

by mandj98
Mendeley = Mekentosj Papers + Web 2.0 ?:
[Via bioCS]

Via Ricardo Vidal: Mendeley seems to be a Windows (plus Mac/Linux) equivalent of Mekentosj Papers (which is Mac OS X only, and has been described as “iTunes for your papers”). In addition to handling your PDFs, it has an online component that allows sharing your papers and other Web 2.0 features (billing itself as “Last.fm for papers”).

Here, I’m reviewing the Mac beta version (0.5.6). I am focusing most on the desktop side and compare it to Papers, because I have a working solution in place and I would only switch to Mendeley if the experience is as good as with Papers. (I.e., my main problem is off-line papers management, Web 2.0 features are icing on the cake.)

By Mac standards, the app is quite ugly. Both Mendeley and Papers allow full-text PDF searches, which is important if you want to avoid tagging/categorizing all your papers. Papers can show PDFs in the main window, copy the reference of the paper and email papers. Mendeley in principle can also copy the reference, but special characters are transformed to gibberish in this beta version. Papers allows you to match papers against PubMed, Web of Science etc., while Mendeley only offers to auto-extract often incomplete meta-data. This matching feature is extremely useful as you get all the authorative data from the source, and most often Papers can use the DOI in the PDF to immeadiately give you the correct reference. Update: Mendeley also uses DOIs to retrieve the correct metadata, if available. (Thanks, Victor for your comment.)
[More]

Well, this is a beta being compared to a product on the market (and Papers is quite a good application). I would expect some of the rough edges to come off as it progresses. What will be interesting to see is how the Web 2.0 aspects turn out. They could provide a route for useful filtering of information as people’s paper databases build up. By having these accessible, it will be much easier to see which papers are really being read and used.

The links between literature libraries, online profiles and readership are potentially very interesting. Something to keep an eye on, particularly as the edges are evened out.

Technorati Tags: Science, Social media, Web 2.0