Archive for the 'scio12' category

From the Archives: Confessions of a Science Librarian (and #IAmScience)

Jan 27 2012 Published by under librarianship, personal, scio12, scio13

A repost from February 9, 2006 from the old blog. it tells the story of how I became a science librarian. It's my small contribution to the #IAmScience meme on Twitter right now.

Basically it's about unconventional career paths in science. And this is mine.


Inspired by Adventures in Ethics and Science and Stranger Fruit...

So, how does a person go from being a software developer to being a science librarian?

  • From a very young age, always read a lot of books, magazines, comic books and whatever else is lying around, mostly science fiction and fantasy but a lot of other stuff too.
  • Also from a young age, related to an interest in science fiction, also read a lot and exhibit a lot of interest in science and math. Math is always the best subject at school, by far.
  • Source of much pocket money during college and university -- tutoring math (especially geometry, always loved geometry) and other subjects at former high school.
  • At middle of college career (college in Quebec where I grew up is a two year pre-university institution, equivalent to grades 12 and 13) in 1982 get a tour of a computing centre where a cousin worked and think, "hey, this is kinda cool."
  • Take Fortran course in second year. Life is changed. Even do bonus extra assignment on matrix multiplications. Using computers to solve mathematical problems is a revelation (although this thread is sorta never followed up on).
  • Apply to Computer Science at Concordia University. Pursue General Business Option and end up taking a lot of accounting, finance, marketing, etc, along with Fortran, Pascal, data structures, operating systems and all the rest. Do really well in stats and numerical analysis courses. Except for this one stats course we won't really talk about.
  • Along with tutoring, get a job as Programmer on Duty at Concordia Computer Centre. Involves sitting at desk or roving around helping students debug their programs or get the systems to work. Challenging but lots of fun. Remarkably like reference desk, but never make the connection.
  • After graduation (1986), get job at multinational insurance broker doing database development in FoxPro, later in Wang Pace and Powerbuilder. Work there for 12+ years. Best part about the job? Working mostly with the finance and accounting functions, helping people find the information they need to get their job done. Remarkably like research consultations, never make the connection. Like working with people and crunching premium and commission numbers.
  • Eventually tire of the constant retraining to new technologies, fed up of unstable mergers/acquisitions situation at company for several years, contemplate leaving job and getting a new one. However, since in the middle of a large, multi-year project, don't want to leave until that is mostly put to bed.
  • Have lots of time to think, "Do I want a new job or a new career?" Examples of librarians among friends and family. Research indicates that libraries seem to be rather computer-oriented these days. This is about 1996-97. Start to make some of those connections. Start to make plans.
  • Quit job and go to Library School full time at McGill. This is fall 1998.
  • Figure I'll end up working at a library vendor until, at the end of the first year, a student in the second year (Thanks, Larry!) recruits me to do a practicum placement at the Physical Sciences and Engineering Library. End up doing some volunteer reference work in the fall of the second year, 144 hour practicum in the winter and 3 week contract in the spring.
  • Get acquainted with serving a scitech clientele as a science librarian and think, "Hey, this is great! I wouldn't mind doing this!" (Thanks, Darlene, Marika and Liz).
  • Coincidentally, while looking for a job during the spring of second year, see a posting on notice board for a science librarian job at York University. Even though it's in Toronto and I'm in Montreal and we don't really want to move, apply anyway.
  • Get job. Start in August 2000. Rest is history.
  • Much sadness about old place of work.
  • Really like buying books on numerical analysis and scientific computing.

You wouldn't believe how often I get asked why I switched from a techie career to librarianship. Now we all know. I encourage more stories.

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Science Online 2012 feedback -- and ideas for #scio13!

Well, I survived.

Science Online 2012 took place this past weekend and it was a blast. There's already been quite a bit of discussion in blogs and on Twitter about how it went.

A very small selection of the them bits are:

But there's way more that I've missed, I'm sure.

One of the things the stellar organizing committee of Bora Zivkovic, Anton Zuiker and Karyn Traphagen are very good at is learning and evolving.

Hence, the feedback form goes out only a couple of days after the event!

So, I've listed below my answers to some of the questions on the form along with some other musings about the #scio12 experience.

  • The decision to allow only two moderators per session worked out very well. It definitely reduced the amount of sageing on the stage and promoted a lot more discussion and dialogue.
  • The session I co-moderated with my York colleague Tanya Noel went very well. It was on Undergraduate Education: Collaborating to Create the Next Generation of Open Scientists. We had a small but engaged crowd who were really interested in how to turn all the cool stuff we talk about at Science Online into action in the undergrad classroom.
  • It's hard to pick one session as the most memorable, but I'll go with What to do when you're the go-to online outreach person at your institution, moderated by Miriam Goldstein and Jai Ranganathan. I'm choosing it mostly because it's what I find myself more and more involved in -- outreach for my institution, both to students but increasingly to internal stakeholders. This session had a lot of nuts and bolts talk about using online tools to raise your profile and your institutions. And there were a lot of people at the session in the same situation as I am, where they are some sort of accidental expert.
  • There was one session I very consciously avoided, Making Book on e-Books, by Tabitha Powledge & Carl Zimmer. I avoided it mostly because I don't want to become some sort of professional ebook wet blanket guy, the role I sort of performed last year and at Science Online NYC this past September. This year, the panel was aimed at practical strategies, so I figured that should be the focus. Ironically, when I spoke to Carl about the panel later on he said he'd actually ended up being the voice of caution, raising the kinds of concerns that I've raised in the past. Life is strange sometimes.
  • How could the conference get better? One idea that's traveled around Twitter is to have a hackathon, probably at the end of the conference. I think that would be a great idea.

    Another thing that I really think is needed is to have some "pure unconference" slots in the programming, sessions that are proposed and organized at the conference itself. Perhaps a slot or two on Friday could be pitched & voted on Thursday. With the conference program wiki starting to take shape so far in advance every year, there's a danger that we'll just rehash the same few topics every year. This year an obvious topic that should have obsessed us on the program but somehow didn't was the whole Research Works Act/SOPA/PIPA controversy. The conference started the day after Wikipedia went black for day, after all. We should have had a chance to pitch a session on The Politics of Open Access or something like that. This also allows first-timers a chance to get in on the fun.

  • What sessions, topics or activities would you like to propose for next year's conference? Yes, the #scio13 program wiki is already up.

    I'm not sure if I have concrete ideas yet, but there are a few things that continue to interest me and that I might want to develop a bit more fully in collaboration with the Science Online community.

    • Institutional & personal social media outreach are topics that are certainly obsessing me -- how to get more faculty and others blogging, on Twitter and engaged with telling their stories to the world. The Goldstein/Ranganathan session above could certainly be expanded in different directions and I think that would be a lot of fun.
    • How to translate all the cool stuff we talk about at scio12, 13, etc, into the undergrad classroom is another topic that obsesses me. Obviously Tanya and I already touched on this but I think there's a lot more room to develop these ideas.
    • The new media landscape as it affects core values of sharing, openness and preservation. This is somewhat about ebooks but is also about data, lab info, journals and other stuff. It's hard to know now what will make sense for a session in 2013 but I can certainly see wanting to do something on ebooks & the cultural commons again. This is the session that I didn't want Carl Zimmer's ebook session to become because I kept butting in as the ebook bad cop. This may be my uber-obsession and possibly the most worthwhile to develop into a session.
    • The politics of openness is another idea, exploring where politics, publishing and money crash together. It's not pretty, but it needs to be explored. It makes me wish that there were more commercial and society publishers that sent people to Science Online.

    As for what maybe we could talk a little bit less about? Maybe we can move beyond having so many sessions about blogging. And the blogger vs. journalist strain of that is getting particularly old.

  • Random thoughts? I think it's really important to get people from the broader higher education world to Science Online. It would be great if reporters from places like The Chronicle of Higher Education or Inside Higher Ed added a conference like Science Online to their beat. Science Online is an amazing model for conferences in higher ed and beyond and I think the broader community could learn a lot from what we're doing. I think it would be valuable and useful for both sides Digital humanities THATCamps get a lot of press, but not Science Online? I think it's time.

Once again, a huge thanks to Bora Zivkovic, Anton Zuiker, Karyn Traphagen and all the other volunteers for yet another stellar conference.

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Michael Nielsen: SPARC Innovator

Sometimes good things happen to good people and this is certainly the case.

Michael Nielsen has been named a SPARC Innovator for 2012.

I don't usually do awards announcements here but I've made exceptions in the past for friends and I'm doing that again today.

The Scholarly Publishing and Academic Resources Coalition has a program called the SPARC Innovators that twice a year recognizes innovations in the field.

The SPARC Innovator program is a new initiative that recognizes an individual, institution, or group that exemplifies SPARC principles by working to challenge the status quo in scholarly communication for the benefit of researchers, libraries, universities, and the public. SPARC Innovators are featured on the SPARC Web site semi-annually.

SPARC Innovators are named by the SPARC staff in consultation with the SPARC Steering Committee. Individuals can nominate their colleagues as potential SPARC Innovators at Criteria include but are not limited to a commitment to:

  • Reducing barriers to access, sharing, and use of scholarship, particularly in the scientific research field;
  • Advancing the understanding and implementation of open access to research results;
  • Working to create a balanced scholarly communication system;
  • Use of technology to develop alternative publishing and communication solutions;
  • Refusing to be constrained by the status quo and implementing new and creative ideas that are backed by research;
  • Vision of the library as a focus for and/or supporter of change;
  • The belief that individual actions can have a profound and positive impact in the scholarly communication field.

A SPARC Innovator can be an individual, a group of people, an institution, or another group that has been active in the areas listed above. Their actions may be broadly defined and may include online activity (i.e., postings on listservs and Web sites); on-campus programs and conferences; writing and editing (i.e., articles and books); promoting awareness and activism among others; and creating technologies and/or programs. There is no monetary award for SPARC Innovators.

For further information, please see the SPARC Web site at

I can't imagine a more fitting exemplar for the open science movement from the second half of 2011 and the beginning of 2012 that Michael Nielsen. With the publication of his book Reinventing Discovery: The New Era of Networked Science and his long and arduous Open Science World Tour/Book Promotional Tour, it's a great way to recognize his contributions.

The SPARC site has a great profile, which I was delighted to contribute to. It's well worth checking out the whole thing.

Michael Nielsen tours like a rock star.

But the 37-year-old, Australian quantum physicist rejects the notion that he is a rock star of Open Science. "There are many, many people who are doing this, as it should be," says Nielsen, listing other thinkers in the field. "It's not a concept that anybody owns. It goes back to the 17th century." For real change to happen in the culture of science, he says, it will take more than one or a few people; it will take thousands working together.

While Nielsen is not alone in promoting the open sharing of data and research to advance science, he has been in the spotlight this fall as an advocate for the cause. The Open Society Foundations supported sending him on an awareness-raising tour on Open Science. In three months, Nielsen did 33 talks in 17 cities - from small gatherings of high school students in Lithuania to a 1,000-plus audience in Canada. (The recording on of his presentation at TEDxWaterloo has received more than 150,000 hits.)


"What Michael has done is taken the time to think deeply and really sort out what the major issues are that need to be considered - and what are the sidetracks," says Cameron Neylon, a biochemist at the Rutherford Appleton Laboratory in Didcot, England, whose path has crossed with Nielsen in open-access advocacy. "He's very much a synthesizer and integrator of ideas and concepts. He can identify trends and understand the larger context that they fit into."

Nielsen is able to describe and articulate complex issues through stories in a way that opens people's minds and leads important discussions, says Neylon. "He's provided a level of intellectual rigor and framework that has allowed the community to move rapidly from a disparate group of individuals and institutions through to where there is a clear understanding of what the position are," he says. "He's really sharpened the message."

I interviewed Michael about his new book a little while back.

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Science Online 2012: Library and librarian sessions

With the final countdown underway and the conference less than a week away, this post follows my post on library people in attendance at Science Online 2012 from a few weeks ago.

And I'd like to start off with another best-tweet-ever, this time Marieclaire Shanahan retweeting Colin Schutze:

+ they'll be fascinating! RT @_ColinS_: #Scio12 Newbie Tips: You will meet more librarians in one day than you thought existed in the world.

And that's long been one of my goals, to promote the integration of librarians into faculty and researcher conferences and social networks. And Science Online has always been a great example of how librarians and other library people could successfully integrate themselves into our patron community. My reflections on the success of last year's libraryish sessions lead me to propose some ideas for this year and ultimately to issue a kind of manifesto.

Related to that, I have an idle thought. Or question, rather.

Is there any other non-librarian conference out there with as much librarian presence and involvement as Science Online? I suspect it might be something in the Digital Humanities, but would love to hear about people's experiences.

Anyways, here's a list of all the librar* sessions at Science Online 2010:

Thursday, 4:00-5:00pm
D1S4c: Room 4. Undergraduate Education: Collaborating to Create the Next Generation of Open Scientists (discussion) - John Dupuis and Tanya Noel

Science faculty and librarians can collaborate on many aspects of undergraduate education - two ideas are the focus of this discussion. First: How can we best help undergrads understand and explore the scholarly information landscape? In addition to formal sources like journal articles, informal sources (e.g., blogs) are of increasing importance/relevance, which raises a question: How do we get students to think about what formal and informal really mean? How do we - faculty, librarians and others - work together to teach students to navigate the disciplinary landscape and become productive and critical consumers of - and contributors to - the disciplinary conversation? Second: How do we introduce students to the great big wide world of open science? How do the various players in higher education communicate to the next generation the incredible depth and complexity of what going on out there? How do we raise (inspire? support?) the next generation of Cameron Neylons, Steve Koches and Jean-Claude Bradleys (not to mention the next generation of Dorothea Salos and Christina Pikases)?

Friday, 10:45-11:45am
D2S2b: Room 3. Teaching Core Competencies in Science: Solving Algebraic and Word Problems (discussion) - Kiyomi Deards and Khadijah M. Britton

Math skills are necessary to the successful pursuit of science. Unfortunately, many students have not been given the tools to understand crucial core math concepts, or how they fit into the scientific process, by the time they enter a biology, physics, chemistry, or other science class. Co-moderated by a numeric dyslexic and a librarian, this session will be an adventure in communicating what we really mean by words like "logarithms," "meta-analysis," "distribution" or even "zero." We'll work through some word problems and analyze some graphs as a group, and try our hand at finding the shortest distance between a concept and a eureka. Bring your expertise, questions and creativity, and come out with new ways to communicate math simply, clearly and effectively.

Friday, 10:45-11:45am
D2S2d: Room 5. The Semantic Web (discussion) - Kristi Holmes and Antony Williams

Semantic Web-based projects are becoming increasingly more popular across a wide variety of disciplines. The session will provide a basic introduction to the topic and highlight different perspectives from people working in this space. We'll show *why* this technology is being used in so many areas - and demonstrate the benefits of linked data (especially in areas related to data reuse for visualizations, research discovery, and more). Open PHACTS, VIVO, and a number of the open government initiatives are good examples and there are many others. This session can serve as an introduction to the concept and highlight interesting and different ways that this technology is being used successfully.

Saturday, 9:30-10:30am
D3S1d: Room 5. Digital Preservation and Science Online (discussion) - Trevor Owens and Bonnie Swoger

Preserving Science Online? What should we be keeping for posterity? Science is now a largely digital affair. A lot of resources are being invested in ensuring that scientific datasets and digital incarnations of traditional scholarly journals will be around for the future. However, little effort has been spent on the preservation of new modes of science communication; like blogging and podcasting, or on things like citizen science projects. After a brief introduction to digital preservation, this session will serve to brainstorm and identify critical at-risk digital content and articulate why that content is important. Time permitting, we will kick around ideas for how we might go about putting partnerships together to collect and preserve this content. Come prepared to discuss what science is happening online that you think is important and why? How should we go about selecting what to preserve? Lastly, who should go about ensuring long term access to this content?

Saturday, 1:00-2:00pm
D3S3e: Room 6. Genomic Medicine: From Bench to Bedside (discussion) - Kristi Holmes and Sandra Porter

This session will serve as an introduction to the topic of personalized medicine from the perspective of major stakeholders including: scientists, physicians, patients and their advocates, community groups and media professionals. We'll begin with an introduction to the basic concepts and efforts in this area, followed by a discussion of information resources to serve stakeholder groups including relevant clinical, consumer health, and advocacy and policy resources. Various initiatives by government agencies, the commercial sector and academia will be discussed, including: Genetics Home Reference, 23andMe, PatientsLikeMe, and more

The Friday Blitz Talks & Demos also have some mini-sessions by library people or which are of interest from library perspective.

2:15-2:30pm - Writing for Robots: Getting your research noticed in the algorithmic era - William Gunn, Mendeley
With the volume of research output always rising, it's very hard to stay on top of what you need to read. Practically no one finds research articles anymore by going to the journal first and reading the table of contents. We all depend to some degree on algorithms to help us find what we should know. I'd like to talk a little about how some of the major algorithms work, how knowledge of the algorithms can make you a better writer, and how search and recommendation work together to bring you just the right paper at the right time. I'll present some specific examples of situations where these principles can be applied in three phases of research - starting a project, actively doing research, and writing up your results.

3:00-3:15pm - Research Discovery: Finding Networking Nirvana on the Semantic Web - Kristi Holmes
VIVO is an open source, open ontology research discovery platform for hosting information about scientists and their interests, activities, and accomplishments. The rich data in VIVO can be repurposed and shared to highlight expertise and facilitate discovery at many levels. Across implementations, VIVO provides a uniform semantic structure to enable a new class of tools which can use the rich data to advance science. There are currently over 50 VIVO implementations in the United States and over 20 international VIVO projects. This presentation will provide a brief description of VIVO and will demonstrate how diverse groups are not only using VIVO, but are also developing apps to consume the semantically-rich data for visualizations, enhanced multi-site search, discovery, and more. Learn more at

3:45-4:00pm - PaperCritic - Jason Priem (on behalf of Martin Bachwerk)
In a world where our lives are broadcast by Facebook and Twitter, our news consumption is dominated by blogs and our knowledge is defined by Wikipedia articles, science somehow remains 20 years behind in terms of communicating about its advances. PaperCritic aims to improve the situation by offering researchers a way of monitoring all types of feedback about their scientific work, as well as allowing everyone to easily review the work of others, in a fully open and transparent environment. The demo will give an overview of the site's main functions as well as discuss some plans for the future. Feel welcome to visit in the meantime to check it out for yourself.

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The Toronto Star: Science Ink FTW, Science Books FTL

First the good news.

Saturday's Toronto Star had a really nice little piece on the trend among some Toronto-area science grad students to get a sign of their scientific passion tattooed onto their bodies.

T.D. MacDonald fact-checked the design five times before he let one drop of ink penetrate his skin.

"I didn't want to have an incorrect chemical structure on my body," he says, recounting the long hours he spent creating his tattoo. "The way it is oriented in space had to be right."

That his ink is accurate matters to him, of course.

But few of us would know the strangely beautiful tattoo that encircles MacDonald's upper right arm is composed of amino acids -- let alone whether they were in the correct configuration.

Tattoos, traditionally proclamations of passion, are no less so for scientists like MacDonald who, beneath lab coats and t-shirts, are baring their skin to get a permanent emblem of their infatuations, whether mathematical equation or phylogenetic tree.

The article is accompanied online by a gallery of some additional tattooed scientists and an interview with Science Ink
author Carl Zimmer.

Q. What tattoos have you seen most often?

A. A lot of DNA tattoos. A lot of people have the number pi. Those are the two most common ones. If someone sends me a tattoo and says, 'Look! I've got pi on my arm!' I have to say, I'm not particularly impressed. Now, on the other hand, if that person has the first 200 digits of pi written out on their arm -- that's nice.

A very cool article, very cool gallery (and a special shout out to York U tweep Jesse Rogerson) and very cool interview. It's also worth noting that Science Online 2012 looks to have an interesting sideline emphasis on science tattoos, mostly due to the perennial presence of Carl Zimmer as an attendee.

And now for the not-so-good news.

As you may know, this time of year I post a whole bunch of Best Science Books 2011 lists here on the blog. They aggregate the sciencey books from all the "Year's Best" lists I can find.

Well, also on Saturday The Star posted its list of the 100 best books of the year, as chosen by their crew of reviewers.

And guess how many science books are on that list?

Zero. Not one single science book. Out of a hundred.

A pathetically limited choice by reviewers with strangely limited tastes.

The list of reviewers, for those that are interested:

  • Sarah Murdoch
  • Michel Basiliere
  • Nancy Wigston
  • Laura Eggertson
  • Christine Sismondo
  • James Macgowan
  • James Grainger
  • Emily Donaldson
  • Barbara Carey
  • Jennifer Hunter

(Jack Batten's top 10 mystery novels was also included in the list.)

The closest thing to a science book was Tropic of Chaos: Climate Change and the New Geography of Violence by Michael Parenti which is about human migrations caused by climate change.

I'll admit to being very disappointed with The Star. Their science coverage hasn't been fantastic lately, in any part of the paper. But here, within the very same issue, they are trying to capitalize on a young, hip, sexy "image" for science people while at the same time totally ignoring terrific reporting on the vast amounts of actual science going on in the world. I'm at a loss for words. They should be embarrassed.

For what it's worth, The Globe and Mail did a much better job.

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Best. Tweet. Ever. Or, library people at Science Online 2012

It all started with this innocent little tweet from @seelix:

In going through the twitter list, I believe that half the #scio12 people are either a librarian, a marine scientist or named Emily.

To which I responded:

@seelix is there a marine science librarian named Emily? #scio12

@BoraZ had to chime in as well:

The holotype #scio12-er RT @dupuisj: @seelix is there a marine science librarian named Emily? #scio12

With @seelix getting the last word:

Found my new career path! RT @BoraZ The holotype #scio12-er RT @dupuisj: @seelix is there a marine science librarian named Emily? #scio12

Over the years, there have been few Twitter exchanges that have made me as happy as that one. And not because it's funny in its own right.

It's because it reflects the significant presence at Science Online over the years of librarians and other library people. It reflects our efforts to establish ourselves within the community, to get it know what roles we can play and what we have to offer.

Librarians are making a place for themselves in science online by being part of Science Online.

Anyways, the webpage is here, the preliminary program is here and the full public registration list is here.

And from that public registration list, here is the list of library people I was able to find:

I note that a few of the librarians listed above are not on Twitter or G+. The rest of us shall have to do something about that ­čśë

And of course, please let me know if I missed anyone!

It's a good showing this year for sure, even with a couple of regulars are missing this year. Molly Keener has a speaking engagement elsewhere and Christina Pikas seems to have other things on her schedule as well. (Congrats, Christina!)

I'll have a post a bit later on that will profile the sessions that have librarians, library people or libraryish content.

And finally, the previous library people at Science Online lists: 2008, 2010, 2011.

Update 2012.01.11. Added Abigail Potter.

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ScienceOnline 2011 Debrief Part 3: Some session ideas for #scio12

A few days ago I posted some thoughts on the programming of the recent ScienceOnline 2011 conference and yesterday I posted some thoughts about the more social and fun aspects of the event.

In this post I like to look forward to next year's conference and start thinking about some of the sessions I might like to organize. My very early thoughts are coalescing around undergraduate education around. I have a couple of ideas which I think might be interesting to pursue.

First of all, I'm interested in collaborations around teaching undergrads about the scholarly information landscape. On the one hand, this is about making sure students can find the information they need for their school work, both formal sources like journals and informal sources like blogs. And this brings up the problem of how do we get them to think about what formal and informal really means? Students don't just arrive at university with that knowledge built in. We might like to think they do, we might hope they do, and certainly the ones we like to hang around with at conferences already do. But, trust me, most of them don't know much about scholarly communications in their fields when they arrive on campus for the first time.

So, how do we work together to teach students to navigate the disciplinary landscape and become productive and critical consumers of and contributors to their disciplinary conversation. Not surprisingly, this seems like an opportunity to practice some stealth librarianship.

My second idea is related to the first (and perhaps really it's just one great big idea): how do we teach students about the great big wide world of open science? How do all the various players in higher education make sure that the incredible depth and complexity of what going on out there is communicated to the next generation? How do we raise the next generation of Cameron Neylons, Steve Kochs and Jean-Claude Bradleys (not to mention the next generation of Dorothea Salos or Christina Pikases)?

There's a lot to cover here: blogs, blog networks, blog aggregators, open access, open data, open notebooks, citizen science, alt-metrics and all the rest. I guess the central tenet of stealth librarianship in the ScienceOnline world is to demonstrate that libraries and librarians are researchers' most natural collaborators in advancing and promoting open science. I've done some things along these lines myself already, but it would be interesting to see what others have done. And it would be valuable to talk about what we can do together to advance the open science agenda.

These thoughts are, of course, very preliminary but I'd definitely like to hear feedback both in terms of the ideas themselves and if there's anyone out there who'd like to join me.

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