ICSTI 2009 Conference: Managing Data for Science

A very interesting conference coming up this June in Ottawa. I'm almost certain that I'll be there.

ICSTI's 2009 Public conference will take place on June 9 and 10, 2009 at Library and Archives Canada, 395 Wellington Street, Ottawa, Ontario, Canada.

Speakers from Canada, the United States and Europe will address:

• How eScience affects the way libraries, publishers and scientists relate to each other.
  
• How the era of "big data" will enable enhanced experimentation and collaboration in science.

The conference program will inform researchers, scientific, technical and medical (STM) publishers, IM/IT professionals, chief information officers, and librarians about specific data initiatives of experts from Microsoft, the San Diego Super-Computing Center, Indiana University, Carleton University (ODESI Project), the British Library, and other institutions.

The program looks great!

ICSTI is the International Council for Scientific and Technical Information. Canada's national science library, CISTI, is organizing the conference.

Computing Surveys on cheminformatics, online community success and web page classification

From the latest issue, v41i2:

• Chemoinformatics—an introduction for computer scientists by Nathan Brown
  
  
• Web page classification: Features and algorithms by Xiaoguang Qi, Brian D. Davison (OA version)
  
  
• A life-cycle perspective on online community success by Alicia Iriberri, Gondy Leroy (OA version)

OLA2009: My session on Science 2.0 & community building

My presentation was this morning and I thought it went very well. The attendance was around 30-35, which is pretty good for a niche topic in a conference with so many parallel sessions. There were some good questions, the timing worked out ok (which is good for me as I can tend to run longer that planned), the audience seemed to be following and nodding in the appropriate ways at the appropriate time. Also, at the end a few people came up to the front and had some very kind things to say.

So, a success.

Here are the slides:



The non-embedded version is here.

For those that are interested, I'll include the references I read but didn't link in the presentation here:

http://del.icio.us/jdupuis/science2.0
http://del.icio.us/jdupuis/escience
http://jdupuis.blogspot.com/2008/09/science-in-21st-century-reading-list.html

Finally, I'd like to thank Alison Stirling for convening my session and for her very kind and generous introduction.

Li, Charlene and Josh Bernoff. Groundswell: Winning in a world transformed by social media. Boston: Harvard Business Press, 2008. 286pp.

The first wave of social media books, like Wikinomics or even Here Comes Everybody, were of the "what the heck is this all about" variety. They focused on getting people up to speed on what social media is and what it could be used for, not so much on concrete strategies for implementing social media for a particular organization or community. The second wave of social media books is starting to hit now, books about the nuts and bolts of online community building, and Charlene Li and Josh Bernoff's Groundswell: Winning in a world transformed by social media is an excellent example.

I wouldn't hesitate to recommend this book to anyone who actaully wants to implement social networking or media software in their organization or for their community. Yes, library and science 2.0 communities, this means you. Want to engage your patrons in online library spaces? Want to build a "Facebook for scientists" that will actually be more than a barren windswept wasteland? This book is for you.

Trying to summarize or explain all the lists of suggestions and strategies the authors give us is probably not that practical, especially since their top to bottom, beginning to end treatment of implementing social media will mean that some chapters are more relevant to some people and other chapters to other people.

A brief outline of the sections will probably give a better feeling for what the book is about. The first part explains what the social media groundswell is and why it's suddenly become important for organizations to engage their communities directly. Part two is about tapping into the groundswell: listening, talking, energizing, helping and embracing. Part three is about transforming your organization internally so that it can embrace the customer groundswell.

One like I did like, at the very end of the book, does give us an idea of how the authors see organizations transforming their attitudes to allow them to embrace the groundswell.

So, we'll finish with some advice, not on what to do, but on how to be. This is the essence of groundswell thinking we've been describing...developing the right attitude. Here are some lessons we learned from groundswell thinkers, lessons that will help you make this amazing transition.

First, never forget that the groundswell is about person-to-person activity...

Second, be a good listener...

Third, be patient...

Fourth, be opportunistic....

Fifth, be flexible...

Sixth, be collaborative...

Seventh, and last, be humble...

These are the principles of groundswell thinking. Aspire t these qualities, and you can use the strategies we've laid out to your advantage -- or invent your own. You'll be able to build on you successes, both with customers and within you company. And then, as the groundswell rises and becomes ubiquitous, you will be ready.

I'm often critical of business hype books and their shallowness and repetition. This book just isn't like those others. It's actually pretty down to earth and practical. It has certainly changed the way I think about library web presences and how we can work to engage our patron communities. It also shapes my thinking and research directions every day.

This book is suitable and recommended for any collection that supports entrepreneurship and online community building, be it in a business, social science, technology or industrial setting. As well, public libraries that reach out to local business communities could do with this book, both for their patrons and for figuring out how to reach out to their communities.

And has there ever been a better time in recent memory to be a community organizer?

Interview with Michael Nielsen

No, not me interviewing Michael Nielsen (although I'll probably get around to it one of these days).

It's my older son Sam who is in grade 10. It's for a Career Studies assignment because he's thinking that theoretical physicist is a possible career path. Check out the interview here.

Recently, I had to do an interview of someone who was on, or had been on, a similar career path to the one we want to pursue (being in grade 10, there's some growing up left to do, but it doesn't feel right to say 'when we grow up'). I've been thinking theoretical physicist as of late (have I mentioned that before?) and I was hoping to interview someone who's... in theoretical physics. At first, it seemed like a hopeless journey; how could I reach someone who's in physics and actually convince them to do an interview? I didn't even know where to start to find a physicist, unless one counts asking my dad. Of course, he said something along the lines of 'Michael Nielsen! He was a physicist and is now writing on the future of science as a whole. He's famous and his career path is extremely relevant.' My curiosity was piqued.

Science Education in Computational Thinking

Just like last year, Eugene Wallingford (CoaSL interview here) of the blog Knowing and Doing has written up some pretty detailed workshop session reports from the 2008 NSF Workshop on Science Education in Computational Thinking. Here's his Table of Contents post, which I'll be reproducing below along with some excerpts from each post.

Primary entries:

• Workshop 1: A Course in Computational Thinking -- SECANT a year later
  

  Teaching CS principles to non-CS students required the CS faculty to take an approach unlike what they are used to. They took advantage of Python's strengths as a high-level, dynamic scripting language to use powerful primitives, plentiful libraries, and existing tools for visualizing results. (They also had to deal with its weaknesses, not the least of which for them was the delayed feedback about program correctness that students encounter in a dynamically-typed language.) They delayed teaching the sort of software engineering principles that we CS guys love to teach early. Instead, they tried to introduce abstractions only on a need-to-know basis.

  
  
  
• Workshop 2: Computational Thinking in the Health Sciences -- big data is changing the research method of science
  

  In addition to technical skills and domain knowledge, scientists of the future need the elusive "problem-solving skills" we all talk about and hope to develop in our courses. Haixu Tang, from the Informatics program at Indiana contrasted the mentality of what he called information technology and scientific computing:

  • technique-driven versus problem-driven
    
  • general models versus specific, even novel, models
    
  • robust, scalable, and modular software versus accurate, efficient programs

  
  These distinctions reflect a cultural divide that makes integrating CS into science disciplines tough. In Tang's experience, domain knowledge is not the primary hurdle, but he has found it easier to teach computer scientists biology than to teach biologists computer science.

  
  
  
• Workshop 3: Computational Thinking in Physics -- bringing computation to the undergrad physics curriculum
  

  ...Further, many students do not think that computational physics is "real" physics. To them, physics == equations.
  
  This is a cultural expectation across the sciences, a product of the few centuries of practice. Nor is it limited to students; people out in the world think of science as equations. Perhaps they pick this notion up in their high-school courses, or even in their college courses. I think that faculty in and out of the sciences share this misperception as well. The one exception is probably biology, which may account for part of its popularity as a major -- no math! no equations! I couldn't help but think of Bernard Chazelle's efforts to popularize the notion that the algorithm is the idiom of modern science.

  
  
  
• Workshop 4: Computer Scientists on CS Education Issues -- bringing science awareness to computer science departments
  

  Next, Tom Cortina talked about Teaching Key Principles of Computer Science Without Programming. In many ways, Cortina was swimming against the tide of this workshop, as he argued that non-majors could (should?) learn CS minus the programming. There certainly is a lot of cool stuff that students can learn using canned tools, talking about history, and doing some light math and logic. Cortina's course in particular covers a lot of neat material about algorithms. But still I think students miss out on something useful -- even central to computing -- when they bypass programming altogether. However, if the choice is between this course and a majors-style course that leaves non-majors confused, frustrated, or hating CS, well, then, I'll take this!

  
  
  
• Workshop 5: Curriculum Development -- some miscellaneous projects in the trenches
  

  Bruce Sherwood reported a physics student comment of his own: "I don't like computers." Sherwood responded, "That's okay. You're a physicist. I don't like them either." But physics students and professors need to realize that saying they don't like computers is like saying, "I don't like voltmeters." If you can't work with a voltmeter or a computer, you are in the wrong business. That's just the way the world is.
  
  My favorite line of Landau's is one that applies as well to computer science as to physics:
  
  We need a curriculum for doers, not monks.

  
  
  
• Workshop 6: The Next Generation of Scientists in the Workforce -- computational thinking as competitive advantage
  

  How does computational thinking help the company do more better and faster? By...

  • ... letting scientists spend more time doing what they love.
    
  • ... eliminating low-value-add transactional activities in the business process.
    
  • ... boosting the speed and scalability of their systems.

  
  Notice that these advantages range from the scientific to business process to the technical. It's not only about techies sitting in front of monitors.

  
  

Ancillary entries:

• This and That -- the inevitable miscellaneous thoughts
  

  The buzzword of this year's workshop: infiltration. Frontal curricular assaults often fail, so people here are looking for ways to sneak new ideas into courses and programs. An incremental approach creates problems of its own, but agile software proponents understand its value.

  
  
  
• No One Programs Any More -- a timely conversation the week before the workshop
  

  In the time since I joined the faculty here, many departments have dropped the computer programming requirement from their majors. Part of the reason is probably that the intro programming courses were not meeting their students' needs, and our department needs to take responsibility for that. But a big part of the reason is that many faculty across campus believe as the Math faculty do, that their students don't need to learn computer programming anymore. Not too surprisingly, I disagree.

E-Science, Science 2.0, Open Science -- So what's a librarian to do?

Thinking about the science 2.0 part of that.

A couple of not-quite-so-recent posts here have gotten me thinking about some of the interesting stuff going on in the web 2.0/science 2.0 space. The first post dealt with some definitional issues and sparked a nice discussion on FriendFeed. The second was some impressions I had from the Science in the 21st Century conference and how what's going on in science may affect libraries.

I thought it might be nice to bring some of those themes around to some more concrete ideas about what I might be able to do in my library to engage students (graduate and undergraduate), faculty and researchers in that science 2.0 space.

Here's some ideas, some fairly widely implemented already, mostly pretty easy to get started, some of which I've tried and some I haven't, some I probably never will. Some of them will be good ideas, some will be bad, some will work in some places but not others.

• Institutional FriendFeed Room. The idea here would to create something like a "York University Faculty of Science & Engineering Room" and post interesting stuff to it, both about science and engineering in general and about York's contributions. Furthering the idea, members of the York Science & Engineering community would also participate, post and comment.
  
  
  
  
• Nature Network. The idea here is to encourage some forward thinking faculty and grad students to jump in and join Nature Network. We could create groups and forums, some of us could blog and comment in other blogs and groups. The interest and excitement sparked by this core would attract others and maybe the groups would be viable and some faculty or grads would find that blogging suits them.
  
  
  
  
• Institutional Blogs. I think that there are two kinds of focus here, one internally focused and one externally focused. An inwardly focused blog would be all about library and general science news focused on the community. A lot of institutions have these kinds of blogs, with the York Libraries having a lot of them. An outward focused library blog would try to bring the institution's story to a broader audience. My CSE blog had some elements of that and I'm not sure what others have done in this vein. The problem with an externally focused blog is that it might step on toes of faculty or institutional communications people. But, if they aren't blogging, maybe the library should just do it; it's easier to apologize than to ask permission.
  
  Overall, blogging is an established activity and a good way to build community. This could be a good way to start, but definitely with a strong commitment and with keeping expectations is check as these types of things can take a while to build momentum.
  
  
  
  
• FaceBook Group and/or Page. This is the lamest option. They mostly don't work at creating community but I feel that I do have to mention them here. Easy to create and maintain, so it's not a bad idea to create one but expectations have to be low. We have one with a fair number of fans but not a lot of activity
  
  
  
• Citation Management. An interesting idea would be to make a big push promoting a citation tool that really emphasizes sharing and collaboration, like Connotea or Mendeley or that is really cool and user friendly like Zotero. These are all free and very cool looking so they'll attract grad students. On the other hand, they're also not quite as functional as a boring old standby like RefWorks. But, since these types of tools are very popular and necessary, they can be a way to get people involved.
  
  
  
• Leverage what's already happening. If there are social spaces that faculties or departments are setting up, find a way to get the library some real estate in those spaces. When I look at something like what MST Visions is doing, I always think that there's got to be a way to take advantage of that, to get the library involved and providing content. It's not always possible, but it's worth trying. If some departments, faculties or schools already have blogs or whatever, find a way worm our way in. The worst that can happen is they say no. Be persistent and persuasive. Often the people that run the sites are looking for content and contributors.

Just throwing these out there.

In many of the above scenarios, the real challenge is first, creating something that's useful, fun and compelling. The second challenge is to interest people in joining and contributing. The two challenges are related, of course. The degree to which these kinds of initiatives and useful, fun and compelling is directly related to who's involved and how much they contribute. The chicken-and-egg factor is quite high here and there's only so much that the library people involved can function as pump-primers. There's nothing sadder than an empty social network.

What I'm really hoping for from you out there is some input on all this. What are some other ideas that are worth exploring? Which of the above have the best chance of working? What are some strategies to get the buy-in and participation that are

If you're a scientist or faculty member out there reading this -- what would work for you? How could your library facilitate a discussion around scholarly communications issues in your institution. How could your library help you to connect and share information both locally and with scientists nationally and internationally. Any librarians or Research/Communications Officers out there with any ideas? Grad and undergrad students are also welcome to pitch in.

If you think the answer is that I'm delusional and that libraries don't really have a role in those areas, you can feel free to just be blunt about that too.

(Escience and open science are a couple of whole other cans of worms and maybe I'll come up with some ideas about libraries nosing their way into those a bit later on.)

(This post has been percolating for quite a while, so sorry if it seems disconnected to my recent posting. I'm doing an OLA presentation more-or-less on this topic in the new year, so this is also part of those ruminations.)

Workshop: Web 2.0 for Scientists

This is a kind of follow up to a couple of posts from last year about the Cool Tools for Scholars workshop I did for my librarian colleagues here at York.

Since that workshop was relatively well received, I'm reprising it this year in two parts for the larger science faculty and grad student community: one part being Web 2.0 for Scientists and the second, Cool Tools for Scholars. I'm hosting the presentation notes on my IL blog here. My intention is to see what the audience of a particular session wants to cover and go from there, roughly dividing the two sessions by stages in the research process. As you can see from the notes, there's a lot of things to talk about!

I'm hoping that hosting fairly bare-bones presentation notes on the blog will make the sessions more flexible and interactive as well as making the notes easier to find and share with a broader audience. I'm also hoping that they would be reusable by others doing similar presentation.

So, my request for the librarians and scientists out there: What do you think? Are there things that aren't there that should be? Would you organize the sessions differently? The descriptive text for the individual tools will continue to evolve, but what would you do differently there as well?

And for the scientists (ie. faculty, researchers, grad students, post docs, etc.), what could I do marketing-wise to get you interested in actually coming to the library so such a session?

(That last bit reminds me of a short I had with conversation with Timo Hannay at the Science in the 21st Century conference: as a librarian I'm definitely interested in helping them get uptake for tools like Connotea but I'm not sure, short of wandering around departments waving my arms yelling "Connotea!" how to get the time and attention of the scientists to show them the tools. He agreed that it's a problem.)

Science in the 21st Century reading list

I spent the past week at the Science in the 21st Century conference at the Perimeter Institute in Waterloo, ON. It was a heck of a conference, an intense five days of workshops, discussions and social events. I'm still digesting what went on and trying to make a bit of sense of it, especially how it all relates to libraries. However, I'm not quite up to the task of getting all that down on pixels yet. I thought I'd first start by arranging some of my "to be read" list that I gleaned from various of the discussions.

As you can imagine, lots of books, articles and web sites were mentioned at the conference, which is no surprise, of course. A lot of the web sites and articles that were mentioned are listed in the various FriendFeed threads in the Science21 room. A bunch of books were also mentioned in a thread that Mark Tovey started. I thought it would be interesting to take Mark's thread as well as some notes that I made during the conference and make a nice list here. (Thanks to everyone who contributed to Mark's thread!)

You could do a lot worse job of preparing for the present and future of science and scientific communication than reading these books:

• The Dream Machine : J.C.R. Licklider and the Revolution That Made Computing Personal by M. Mitchell Waldrop
  
  
• Libraries of the Future by J.C.R. Licklider
  
  
• Rethinking Expertise by Harry Collins and Robert Evans
  
  
• Gravity's Shadow: The Search for Gravitational Waves by Harry Collins
  
  
• American Physics and the Cold War Bubble by David Kaiser
  
  
• Pedagogy and the Practice of Science: Historical and Contemporary Perspectives edited by David Kaiser
  
  
• The Ghost of the Executed Engineer: Technology and the Fall of the Soviet Union by Loren Graham
  
  
• Scientists in the Classroom: The Cold War Reconstruction of American Science Education by John L. Rudolph
  
  
• The Sputnik Challenge by Robert A. Divine
  
  
• Brainpower for the Cold War The Sputnik Crisis and National Defense Education Act of 1958 by Barbara Barksdale Clowse
  
  
• Image and Logic: A Material Culture of Microphysics by Peter Louis Galison
  
  
• QED and the Men Who Made It by Silvan S. Schweber
  
  
• The Cold War and American Science: The Military-Industrial Complex at MIT and Stanford by Stuart W. Leslie
  
  
• Towards 2020 Science
  
  
• Bury the Chains: Prophets and Rebels in the Fight to Free an Empire's Slaves by Adam Hochschild
  
  
• Sixty Days and Counting by Kim Stanley Robinson
  
  
• Rainbow's End by Vernor Vinge
  
  
• Here Comes Everybody by Clay Shirky
  
  
• The Victorian Internet: The Remarkable Story of the Telegraph and the Nineteenth Century's On-Line Pioneers by Tom Standage
  
  
• Collective Intelligence: Creating a Prosperous World at Peace edited by Mark Tovey
  
  
• Anything by Lawrence Lessig
  
  
• The Wealth of Networks by Yochai Benkler
  
  
• Crowdsourcing by Jeff Howe
  
  
• The access principle: The case for open access to research and scholarship by John Willinsky
  
  
• Ambient Findabillity by Peter Morville
  
  
• Everything Is Miscellaneous: The Power of the New Digital Disorder by David Weinberger
  
  
• The Future of Reputation: Gossip, Rumor, and Privacy on the Internet by Daniel J. Solove
  
  
• The Big Switch: Rewiring the World, from Edison to Google by Nicholas Carr
  
  
• Community: The Structure of Belonging by Peter Block
  
  
• The Cathedral & the Bazaar: Musings on Linux and Open Source by an Accidental Revolutionary by Eric S. Raymond
  
  
• Dreaming in Code: Two Dozen Programmers, Three Years, 4,732 Bugs, and One Quest for Transcendent Software by Scott Rosenberg
  
  
• The Logic of Collective Action: Public Goods and the Theory of Groups by Mancur Olson
  
  
• Wikinomics: How Mass Collaboration Changes Everything by Don Tapscott and Anthony D. Williams
  
  
• Scholarship in the Digital Age: Information, Infrastructure, and the Internet by Christine L. Borgman

Of course, a similar list or lists could be compiled for articles, web sites, videos, etc, but I'll leave that task to some one else. Books lists seem to be more my thing.

In any case, feel free to suggest more books either here or in the FriendFeed thread, especially if there were items from the conference, the FriendFeed or the video that I've forgotten.

Nature Network panel discussion & pub night

The Toronto Nature Network mafia are organizing another event this coming Sunday evening:

Science 2.0: the future of online tools for scientists
A pub night and panel with Timo Hannay, Cameron Neylon, and Michael Nielsen, hosted by Nature Network Toronto

What does the future hold for the way we do science? Are online repositories such as GenBank and the physics preprint ArXiv, or social tools such as Nature Network, about to change science profoundly? To find out, join Nature Network Toronto for an interactive panel discussion over drinks at the pub.

Date: Sunday September 7 at 7:30pm
Place: Fionn MacCool's (181 University Avenue, near corner with Adelaide)
Map: http://maps.google.com/maps?f=q&hl=en&geocode=&q=181+university+ave+toronto&sll=46.55886,-95.712891&sspn=34.760328,92.8125&ie=UTF8&z=16&iwloc=addr

About the panelists:

Timo Hannay is Publishing Director of Nature.com at the Nature Publishing Group, publishers of Nature and over seventy other scientific journals, plus numerous online resources for scientists. He is responsible for new online initiatives in social software, databases and audio-visual content. Timo trained as a neurophysiologist at the University of Oxford and worked as a journalist and a management consultant before becoming a publisher.

Cameron Neylon is a biophysicist working in molecular biology, biophysics, and high throughput methods. He has a joint appointment as a Lecturer in Combinatorial Chemistry at the University of Southampton and as a Senior Scientist in Biomolecular Sciences at the ISIS Pulsed Neutron and Muon Facility. He is developing an electronic notebook for biochemistry labs which has lead to his involvement in the Open Research movement and to his group moving to an Open Notebook.

Michael Nielsen is a writer living just outside Toronto, Canada. He is currently working on a book about The Future of Science. One of the pioneers of quantum computation, he coauthored the standard text on quantum computation that is the most highly cited physics publication of the last 25 years. He is the author of more than fifty scientific papers, including invited contributions to Nature and Scientific American.

For more information visit Nature Network Toronto (http://network.nature.com/group/toronto), or contact Eva Amsen (eva.amsen@gmail.com) or Jen Dodd (jen@jendodd.com)

It looks like a fun event, coinciding with the two of the panelists appearing at the Science in the 21st Century conference starting the next day. I'll be there, of course.

There is, of course, the obligatory Facebook event.

E-Science, Science 2.0, Open Science

Some recent posts that got me thinking about various escience/science 2.0/open science issues:

First, Christina gets us rolling with some definitions:

So I'm asking and proposing that e-science is

• grid computing - using distributed computing power to do new computational methods in other areas of science (not in CS but in Astro, in bio, etc.)
  
• data curation - using computing power and information science to store, discribe, and provide access to scientific information for reuse while taking security and policy issues into account
  
• supporting scientists work using social computing technologies (SCTs) to support collaboration around data and equipment (as in collaboratories) as well as collaboration to find new research partners and to discuss science
  
• maybe some sort of support for benchtop computational methods or support for workflow or electronic lab notebooks?

What do you think? Is it just one of these or all or some subset?

More or less, as I said on FriendFeed, I see the terms e-science, science 2.0 and open science bandied about quite a bit these days. I tend to thing of e-science as comprising grid computing and data curation issues. Science 2.0 I think of more as social software applications in science, including lab notebooks and the like.

Open science is a newer term, I think, and a little more nebulous to me. It's more an overarching attitude and approach rather than a set of tools. Certainly, open science includes aspects of grid computing, data curation and web 2.0 tools but all of the above don't necessarily have to be "open." It's possible to curate large data sets that are private, for example, or for a wiki lab notebook to be for the lab members only; e-science and and science 2.0 don't have to be fully open although, of course, it's infinitely preferable that they are.

So, I'm a little uncomfortable with using open science as a catch-all term for all the four items that Christina mentions, just as I'm a little uncomfortable with e-science as the catch-all. If I had to choose, though, I'd probably go with Christina and pick e-science.

And speaking of getting more openness into science, check out this article, Era of Scientific Secrecy Near End by Robin Lloyd.

Beyond email, teleconferencing and search engines, there are many examples: blogs where scientists can correspond casually about their work long before it is published in a journal; social networks that are scientist friendly such as Laboratree and Ologeez; GoogleDocs and wikis which make it easy for people to collaborate via the Web on single documents; a site called Connotea that allows scientists to share bookmarks for research papers; sites like Arxiv, where physicists post their "pre-print" research papers before they are published in a print journal; OpenWetWare which allows scientists to post and share new innovations in lab techniques; the Journal of Visualized Experiments, an open-access site where you can see videos of how research teams do their work; GenBank, an online searchable database for DNA sequences; Science Commons, a non-profit project at MIT to make research more efficient via the Web, such as enabling easy online ordering of lab materials referenced in journal articles; virtual conferences; online open-access (and free) journals like Public Library of Science (PLoS); and open-source software that can often be downloaded free off Web sites.

The upshot: Science is no longer under lock and key, trickling out as it used to at the discretion of laconic professors and tense PR offices. For some scientists, secrets no longer serve them.

The article is basically about using web 2.0 tools (blogs, wikis, mashups, collaborative document creation) to create a more open scientific culture. In other words, what I've called science 2.0 above. It's a very well-written article, particularly for an audience that might not be that familiar with the topic.

Of course it's great to have all these sharing and collaborative tools available for scientists to use, but how to you actually get more than a handful of them to use them? What's the killer app for science 2.0, in other words. Eva Amsen has some ideas!

Many, if not most, scientists are not in the habit of putting things online. The ones that are might be tempted by the concept of sharing the papers they read, letting everyone look at their lab notebook, joining a forum or writing a blog. If you’re reading this in your RSS feed or clicked through from FriendFeed , you’re probably one of those people. But think about your friends and colleagues who only turn on their computer for work and e-mail. They’re not going to tag their favourite papers or discuss the process of research with total strangers on the internet. It’s an extra thing to do that’s not already part of their lives, and no matter how appealing they might find the concept of open data or sharing information, they won’t join these sites or movements because it’s not something they are already doing.

*snip*

Imagine if there was a bibliography reference manager that keeps a record of papers read, and allows users to cite papers with one click of the mouse, but does all this in a simpler way than EndNote, and perhaps has one extra feature that people really need but that EndNote doesn’t have. For example: if you’re cowriting a paper with someone else, the EndNote library needs to be on two computers. You can export it, but it’s kind of unwieldy. It would be easier to have a common shared library that both computers could use to cite in their word processing software....

Now imagine if this utopian tool they all switched to because it was so simple and fast and useful just happened to come with the default setting to share your entire collection of papers and prompted to quickly tag everything once you added it. People would leave the public setting on, and they would tag....

Please, read the whole post. It's wonderful. Eva's idea is that the killer app for science 2.0 is combining citation management with document preparation and making it social. A great idea, because it takes what scientists have to do already (ie. write papers) and blows it up into the miscellaneous universe.

But, are we there yet? First of all, take a look at these two conversations on FriendFeed about how to make Connotea the killer app: here and here. It's great to know that Nature is thinking deeply about transforming what is now Connotea into something that will truly help scientists. At the same time, you have to think that the Zotero project also has great potential to be that killer app with amazing improvements in v1.5 and a social version coming up.

Praxis: A new carnival about the scientific life

The first edition of the new carnival Praxis has just been posted at A Blog around the Clock.

Here's a description of what the carnival is all about:

The carnival is intended to cover all aspects of life as an academic, whether it's the lifestyle, career progress, doing a Ph.D., getting funding, climbing the slippery pole, academic life as a minority, working with colleagues and students, dealing with the peer-review process, publishing, grants, science 2.0, amusing anecdotes, conference experiences, philosophical musings, public engagement, or even historical articles about what life was like in the good (or bad) old days.

Here's a list of the next bunch of editions.

For this first edition, Bora has gathered together a great big triple handful of posts covering a whole bunch of different topics areas: Doing Science, Career Choices and Getting Funded, Presenting Data, Sharing and Networking, Getting Published, The Publishing Business, Science Communication and Education, Academic Atmosphere and Special topic of the month: Animal Research.

There's really way to much here for most of us to get around to reading more than a selection, but on the other hand virtually everyone will be able to find more than a few gems.

Enjoy!

Michael Nielsen on The Future of Science

Michael Nielsen has posted a fantastic essay on the Future of Science over on his blog:

Science is an example par excellence of creative collaboration, yet scientific collaboration still takes place mainly via face-to-face meetings. With the exception of email, few of the new social tools have been broadly adopted by scientists, even though it is these tools which have the greatest potential to improve how science is done.

Why have scientists been so slow to adopt these remarkable tools? Is it simply that they are too conservative in their habits, or that the new tools are no better than what we already have? Both these glib answers are wrong. We’ll resolve this puzzle by looking in detail at two examples where excellent online tools have failed to be adopted by scientists. What we’ll find is that there are major cultural barriers which are preventing scientists from getting involved, and so slowing down the progress of science.

*snip*

We should aim to create an open scientific culture where as much information as possible is moved out of people’s heads and labs, onto the network, and into tools which can help us structure and filter the information. This means everything - data, scientific opinions, questions, ideas, folk knowledge, workflows, and everything else - the works. Information not on the network can’t do any good.

Ideally, we’ll achieve a kind of extreme openness. This means: making many more types of content available than just scientific papers; allowing creative reuse and modification of existing work through more open licensing and community norms; making all information not just human readable but also machine readable; providing open APIs to enable the building of additional services on top of the scientific literature, and possibly even multiple layers of increasingly powerful services. Such extreme openness is the ultimate expression of the idea that others may build upon and extend the work of individual scientists in ways they themselves would never have conceived.

And lots more. The whole essay is well worth reading for it's provocative insights and well-reasoned arguments. Nielsen is writing a book on the future of science and it's pretty likely to me that the themes he explores in this essay of openness, collaboration and networking will form the backbone of that book. I can't wait to see more!

That being said, it seems to me that the core issues that surround a of what he talks about is trust and/or/versus incentives. Trust in the sense of trusting that your own openness won't be abused. Incentives in the sense of incentives to be open and trust others. I think they're really interrelated and the essay kind of dances
around the relationship without really nailing it down.

After all, people need incentives to participate in open peer review, but couldn't a kind of radical trust actually be that incentive? In formal peer review the incentives are pretty obvious. You do peer review for my paper and I'll do peer review for someone else's. It works because everyone knows/trusts that the load is spread around.

With open peer review, people can't trust that the load is spread around so people are hesitant to jump in and be the first to effectively take on both the formal and informal roles. The incentive to review someone else's paper is the knowledge/trust that my paper will be reviewed too; in open peer review, how do I know someone else will reciprocate my contributions.

It's the same with collaboration markets. What's the incentive to trust the other players in the market? Normally, the incentive to trust someone in a collaborative relationship is reciprocity. Basically, the parties in the collaboration help solve each other's problems with the goal of solving a larger problem in the process. How do you maintain those incentives in an open system?

It seems to me that a lot of the issues around open science / science 2.0 are really about incentives and trust. Solving the issues requires a certain leap of faith. The key point in Nielsen's essay is the line: "The danger of free riders who will take advantage for their own benefit (and to Alice’s detriment) is just too high."

The potential for a tragedy of the commons situation is always there in an "unregulated" system where no one is organizing to make sure contributions to the common good (i.e. performing peer review or volunteering to collaborate) are more or less evenly distributed.

Of course, there lies the challenge at the heart of the essay; the challenge to build an open community that somehow maintains and builds on the incentive/trust structures in place for Science 1.0 while at the same time being more open, trusting and collaborative. Neilsen has a lot to say about those and keeping the conversation going is the way to help those structures get built.

FriendFeed

Yes, I've quaffed the Kool-Aid. I set up a FriendFeed account for myself a bit earlier this afternoon.

You can find me here: http://friendfeed.com/johndupuis

I only have a few subscriptions set up so far, only some science-y types. No librarians as yet. Of course, Bora was the first person to subscribe to me, about 47 seconds after I set up my account. Feel free to subscribe to my feed or to suggest some feeds for me to subscribe to. I'm not sure what the FF protocol is on these things, but I'll certainly be happy to subscribe to anyone who subscribes to me. In particular, a couple of librarian feeds would be nice to get started.

What is FriendFeed, you ask? According to Wikipedia:

FriendFeed is a social aggregator that consolidates the updates from social websites such as blog entries, social bookmarking websites, and social networks among others. This allows individuals using multiple social websites to have a consolidated stream of details on all their activities across these websites.

Bloggers writing about FriendFeed have said that this service addresses the shortcomings of social media services which exclusively facilitate tracking of their own members' social media activities on that particular social media service, whereas FriendFeed provides the facility to track these activities (such as posting on blogs, Twitter and Flickr) across a broad range of different social networks.

In other words, I get to stalk some people.

Why did I join? First of all, it looks cool and interesting and it's been a while since I signed up for a new cool and interesting service. Most importantly, it seems to be emerging as a very interesting and powerful tool for sharing and collaboration, something people are already thinking about. A lot of science types who are using it heavily to share information and I think it's worth seeing what all the fuss is about. We as librarians need to be in the same spaces as our users.

I'll be giving my Cool Tools for Scholars presentation again in the near future, and FriendFeed will definitely be part of the story this time around.

Nature vs. PLoS

So, it seems that Declan Butler of Nature has taken a potshot at the business model and publishing practices of the Open Access publisher Public Library of Science.

Now, I'm not going to comment on the truth and accuracy of Butler's claims about PLoS in particular or OA in general. Not surprisingly, Bora does a great job of summarizing that. Of course, I am a staunch OA supporter but I also recognize that there's a wide variety of publisher business models that are valid and that we have to deal with. As most science librarians, I am somewhat critical of Nature's tendency to charge boatloads of money for their journals and journal backfiles, but I do accept that what they do costs money and that they have a right to run their company as they see fit. I don't have a problem paying for stuff that has real value.

However, I do have to say I am very disappointed with this turn of events. Notwithstanding their journal business, I have always been very impressed by the web group at Nature and the fine work they have done on products like Scintilla, PostGenomic, Precedings, Connotea, Nature Network and others. Those are, for the most part, fine products that are really pushing the edges and trying new and exciting things. They are of of the few commercial publishers that really seems to get doing science on the web and I've been happy to promote those products and services in my community here and to present about them to a wider audience. Of course, OA is a very important piece of the puzzle of doing science on the web and PLoS is also trying new and exciting things and really seems to get it. There's a real conflict there. Perhaps Nature's left hand should be telling it's right hand what's really going on out here.

On a side note, related to the previous post on science blogging communities, there's a bit of an exchange in the comments between Hank of ScientificBlogging and GrrlScientist of Scienceblogs, mostly around who owns what and "political litmus tests" for science bloggers. It's worth noting that as far as I can tell, no one on Nature Network Blogs has blogged or commented on the Nature vs. PLoS controversy. Make of that what you will.

Update 2008.07.08: Two very reasonable and sensible posts providing a bit of clarification from the Nature point of view by Timo Hannay and John Wilbanks. Both the posts also have a lot of interesting conversation in the comments.

Journal of Science Communication

Thanks to A Blog Around the Clock for pointing me to the latest issue of the Journal of Science Communication, volume 7, issue 2.

This is a journal that I wasn't really aware of but I think I'll be paying a lot more attention to it from now on. The back issues are also a treasure trove of interesting stuff.

Here's some of the current issue's TOC:

• Collaborative Web between open and closed science by Alessandro Delfanti
  
  
• The future of the scientific paper by Bora Zivkovic
  
  
• Grid computing and e-science: a view from inside by Stefano Cozzini
  
  
• Public domain, copyright licenses and the freedom to integrate science by John Wilbanks
  
  
• To blog or not to blog, not a real choice there... by Elisabetta Tola
  
  
• The other books – A journey through science books by Juan Nepote

IEEE Annals of the History of Computing

Lots of interesting stuff from v30i2:

• The Technical Development of Internet Email by Partridge, Craig
  
  
• Netlib and NA-Net: Building a Scientific Computing Community by Dongarra, Jack; Golub, Gene H.; Grosse, Eric; Moler, Cleve; Moore, Keith
  
  
• Defining the Computer: Herbert Simon and the Bureaucratic Mind -- Part 1 & Part 2 by Heyck, Hunter
  
  
• Biographies: Jack Dongarra, Supercomputing Expert and Mathematical Computing Specialist by Haigh, Thomas

JCDL/DL: International Conference on Digital Libraries

This is a conference I have to get to one of these days. This year's edition is actually going on right now in Pittsburgh -- ironically, since I'll be in Pittsburgh next week for ASEE. Had I been sufficiently foresightful, it would have made a great two week visit!

You can see the program on the Conference web site here.

The ACM also has the proceedings online already! Here's some very brief excerpts from the TOC:

• Seeking information in realistic books: a user study by Veronica Liesaputra, Witten H. Ian
  
  
• The myth of find: user behaviour and attitudes towards the basic search feature by Fernando Loizides, George R. Buchanan
  
  
• A longitudinal study of exploratory and keyword search by Max L. Wilson, m.c. schraefel
  
  
• From nsdl 1.0 to nsdl 2.0: towards a comprehensive cyberinfrastructure for teaching and learning by David J. McArthur, Lee L. Zia
  
  
• Cross-disciplinary molecular science education in introductory science courses: an nsdl matdl collection by David J. Yaron, Jodi L. Davenport, et al.
  
  
• Curriculum overlay model for embedding digital resources by Huda Khan, Keith Maull, Tamara Sumner
  
  
• Semi automated metadata extraction for preprints archives by Emma Tonkin, Henk L. Muller
  
  
• A metadata generation system for scanned scientific volumes by Xiaonan Lu, Brewster Kahle, James Z. Wang, C. Lee Giles
  
  
• Math information retrieval: user requirements and prototype implementation by Jin Zhao, Min-Yen Kan, Yin Leng Theng
  
  
• From writing and analysis to the repository: taking the scholars' perspective on scholarly archiving by Catherine C. Marshall
  
  
• A simple method for citation metadata extraction using hidden markov models by Erik Hetzner
  
  
• Portable digital libraries on an ipod by David Bainbridge, Steve Jones, Sam McIntosh, Matt Jones, Ian H. Witten

Science in the 21st Century

I've been remiss in blogging about this conference that's happening at the Perimeter Institute for Theoretical Physics in Waterloo, ON this coming September 8-12.

However, Michael Nielson informs us that there are only a few spots left for registrants!

Well, I'm registered and it would be great if a few more librarians were there as well to fly the flags for our place in 21st Century Science!

Science in the 21st Century: Science, Society and Information Technology

Times are changing. In the earlier days, we used to go to the library, today we search and archive our papers online. We have collaborations per email, hold telephone seminars, organize virtual networks, write blogs, and make our seminars available on the internet. Without any doubt, these technological developments influence the way science is done, and they also redefine our relation to the society we live in. Information exchange and management, the scientific community, and the society as a whole can be thought of as a triangle of relationships, the mutual interactions in which are becoming increasingly important.

Here's the list of topics, most of which are naturals for librarians too:

• Web/Web 2.0.
  Communication, Social and Information Networks, Wikis, Blogs, Information Overflow, and the Illusion of Knowledge
  
  
• Globalization
  Collaboration and Competition in the scientific community, The Global Village, the Limits of Growth, Science and Democracy
  
  
• Open Access
  Scientific Publishing, Science Journalism, Framing, and the 'Marketplace of Ideas'
  
  
• Sociology
  Ethics, Morals, Trends, and their impact on scientific directions, organization of our communities, fragmentation, feedback, selection, and the ivory tower.
  
  
• Miscellaneous and Other
  Teaching, Information storage, Resilience and the next Generation

There's also a skeletal program and list of participants.

Oh yeah, the Perimeter Institute has been in the news the last few days!

Here & There

A bunch of items from around the web:

• BoingBoing points us to Vanity Fair's How the Web Was Won: An Oral History of the Internet.
  

  This year marks the 50th anniversary of an extraordinary moment. In 1958 the United States government set up a special unit, the Advanced Research Projects Agency (arpa), to help jump-start new efforts in science and technology. This was the agency that would nurture the Internet.
  
  This year also marks the 15th anniversary of the launch of Mosaic, the first widely used browser, which brought the Internet into the hands of ordinary people.

  
  This one jumps right to the front of my reading list!
  
  
• One again, thanks to BoingBoing we see that there's a new book on the future of music: SOUND UNBOUND: Sampling Digital Music and Culture Edited by Paul D. Miller aka DJ Spooky that Subliminal Kid, Foreword by Cory Doctorow, Introduction by Steve Reich. Oddly, and ironically, you can't download all the articles for free off the internet. You actually have to buy the book.
  
  
• Sustainability and Revenue Models for Online Academic Resources by Kevin Guthrie, Rebecca Griffiths, and Nancy Maron looks very interesting and important. There aren't too many more important questions in academic librarianship these days than, "What's worth paying for?" Finding sustainable business models for those resources in a world of Free is going to be a challenge in the medium to long term. This report looks very interesting and will merit a close examination.
  
  I'll excerpt the same bit as Open Access News.

  ...We define ‘sustainability’ as having a mechanism in place for generating, or gaining access to, the economic resources necessary to keep the intellectual property or the service available on an ongoing basis. This does not...presuppose any particular method for revenue generation: an Open Access resource, for example, will have a different set of revenue options available to it than a project that is willing to charge a subscription fee, but both should be expected to develop a sustainable economic model....
  
  It does not matter if a resource is subscription-based, Open Access, or supported by budgets of a host institution. For any site, users have a choice in what they pay for, where they spend their time online, or whether to volunteer their time to help support a project. Each project must build sources of advantage that make it valuable and attractive to users, and find ways to sustain these advantages over time....

  
  
  
• Cool article on SciBarCamp by Jim Thomas!
  

  ‘It’s a huge improvement on the regular science conference format – those usually suck the life and joy out of these things,’ says SciBarCamper Paul Bloore, a local software entrepreuner. His friend Melina Strathopoulos concurs. ‘Its a literal “confer-ence” where people are actually conferring,’ she points out, ‘rather than just an “attend-ance”.

  
  Thanks to Jim for bringing it to our attention on the SciBarCamp group on Nature Network.
  
  
• What is the Ecological Footprint of Disneyland?
  

  Having just returned from a visit to the magic kingdom, the above was a question that continually haunted my consciousness. Disneyland was remarkably pristine in that cookie cutter, artificial, yet aesthetically pleasing way, but it must be a major sink in terms of waste, energy consumption, carbon emissions, etc.
  
  Or is it? Maybe in terms of footprint, by applying its incredible density (>15 million visitors each year!), it comes out not looking so bad?
  
  It should be noted that Disney appears to be viewing environmental issues in a relatively serious manner, with a number of programs in place. Here are a few factoids I can provide that would support this notion.