That's awesome! (the shirt and the weight loss)
- Katy S
I eat less, not because I'm trying to, but because school keeps me so damn busy. I did make a concerted effort to stop eating fast food and to cook at home; I bet that's a factor too. And thanks, Katy!
- Derrick
I love it! My daughter is a tattoo artist. I am working on a new website for her ...
- Patricia F. Anderson
"On newsstands, December's cover of Wired magazine is a little hard to miss. Accompanying a piece on tissue engineering is a shot of a woman's cleavage. Slapped with the cover line, “100% Natural,” it's a visual (sexual) assault. In a struggling publishing industry, highly sexualized images of women have become so common that we've become suspect to otherwise respectable images. But thankfully, we're hardly subjected to those pesky decent images of women in American media… Two days ago, Cindy Royal scolded Wired in a blog post that's been cheered around the Web many times over. An assistant professor at Texas State University, Royal rebuked the magazine for its depiction of women as faceless, person-less beings. “A pair of breasts, no head, no rest of body… just boobs,” she wrote. “Sure it accompanied a story on tissue re-engineering, so what other possible way might you visually represent that, but with a pair of breasts? No other possible way?”"
- Derrick
from Bookmarklet
I got news for ya - women aren't only objectified in tech.
- Spidra Webster
The interview with Chris Anderson that included discussion of the cover was interesting. I'll see if I can find the link. It's all about whether magazines will sell or not. UPDATE: http://tech.cindyroyal.net/... discussion is in the comments. Again, $ trumps sense and sensitivity.
- Tinfoil 2.0
The whole discussion quite rightly focuses on the point of the impact on recruiting diverse views and abilities into the profession. Basically, act like a chauvinist, and no one new will want to play with you.
- Patricia F. Anderson
public symposium on The Value of Shared Access and Reuse of Publicly Funded Scientific Data. The event is being organized by the National Research Council's Board on Research Data and Information, and will be held on the afternoon of December 1 in Washington, DC...
Wednesday, December 1, 2010, 2:00-4:15 p.m. 20 F Street Conference Center Conference Room B, 20 F Street, NW, Washington, DC
- Christina Pikas
This symposium will examine some of the research, economic, and social benefits that can be derived from providing online access to publicly-funded scientific data, as well as how such benefits can be evaluated. The event will include presentations on the scientific data sharing and reuse policies of the federal government; compelling examples of the value of free online access and...
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- Christina Pikas
Moderator: Michael Lesk, Rutgers University and Board Chair Speakers: Interagency Working Group on Digital Data, OSTP (invited) Rod Atkinson and Jan Johansson, Congressional Research Service Neil S. Buckholtz, National Institute on Aging, NIH Carl Shapiro, U.S. Geological Survey Heather Joseph, SPARC Michael Carroll, Washington School of Law, American University Paul David, Stanford Institute for Economic Policy Research, Stanford University
- Christina Pikas
it will be webcast, check that page for details
- Christina Pikas
I'm waiting for the "download full understanding of presentation concept as understood by the presenter into my brain in 5-10 seconds" feature of webinars. There are so many that sound intersting, for which I do not have or cannot make time to watch in real-time / recorded
- awd
abstract: Increased public and private investments in large-scale team science initiatives over the past two decades have underscored the need to better understand how contextual factors influence the effectiveness of transdisciplinary scientific collaboration. Toward that goal, the findings from four distinct areas of research on team performance and collaboration are reviewed: (1) social psychological and management research on the effectiveness of teams in organizational and institutional settings; (2) studies of cyber-infrastructures (i.e., computer-based infrastructures) designed to support transdisciplinary collaboration across remote research sites; (3) investigations of community-based coalitions for health promotion; and (4) studies focusing directly on the antecedents, processes, and outcomes of scientific collaboration within transdisciplinary research centers and training programs. The empirical literature within these four domains reveals several contextual circumstances...
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- Mickey Schafer
I've written a post as an introduction to my open lab notebook, explaining how I view it and how it's organized and integrated with my github, flickr, and mendeley accounts. Still figuring things out, but think I've learned a lot about notebook workflow over the past 6 months. Feedback welcome!
- Carl Boettiger
from Bookmarklet
sweet, just what I was looking for. Think modifying the color a bit to match my site break the consistency?
- Carl Boettiger
Carl - sure feel free to modify and add your logos to the pool of images on the ONSclaims wiki. The key thing is that if someone clicks on the image on your site it takes you to the wiki for the full description.
- Jean-Claude Bradley
A place for information that isn't necessarily bound by books or texts, although they can obviously be books or texts.
- Derrick
I bet a lot of it is just lack of education or understanding by those people. Until fairly recently, I had no idea that I could get information from librarians other "where in this place can I find a book on whatever topic?" I guess no one ever really told me or explained what all libraries and librarians can offer.
- Rochelle
I call shenanigans. Libraries are nothing but big boxes with lots of dusty books. Stop trying to dispel the truth. They never have tapes, cd's, dvd's, magazines, micro-fiche, photographic archives, computer databases... wait, what?
- SAM
Actually, LogEx, the library where I'm interning doesn't have many books at all; they were all destroyed by the flood. We're in the process of A) Moving to a more permanent structure (we're still in trailers), and B), rebuilding our collection of books.
- Derrick
it's because you're biased, D. and libraries (overall) don't do the best job of marketing themselves as anything else outside of academia. I remember when a coworker first told me she rented audio books from the library online. seriously, I don't think most people know that.
- jbrotherlove
I don't think Libraries are doing a good job of marketing themselves then. Honestly, I am not aware of what services a library could offer me besides finding physical media that may or may not be current (and, unless I am looking for history or literature probably won't be.... I mean, printed stuff is old once it is printed). Would they offer help if i am researching something? Can they point me to resources online? Can they hap me find things I couldn't find on my own?
- Lindsay
Lindsay, they can do all of that and more. I certainly don't know how to fix how libraries market themselves, but there's much more to libraries than just books, and physical media. Where I am interning, we have very few books. The bulk of our work is utilizing digital texts and searching for work that Google doesn't access. But again, I'm biased, so there's that.
- Derrick
I'll second RepoRat's latest comment... with the note that, if you want public support, an even wronger thing is running away from books as though they have cooties. "Books+lots more" is a good message. "Oh, no, we don't care about books any more"...not so much, at least for public libraries/librarians.
- Walt Crawford
on a more serious note, since libraries (overall) have not been able to update their image to a large mass of people, how does that image perception get changed? public monies for a marketing campaign? local involvement with neighboring businesses? a kick ass website? who are the people that would most benefit from what the library offers (currently vs. historically) and how do you reach them? this will be on my mind for the rest of the night.
- jbrotherlove
Mine too, J. That's kind of half-heartedly why I asked it. I need to figure out, at least partially, while I'm in school what it is that people use libraries for, and what they can be. At least for me. Public libraries are suffering from huge cuts, as are academic libraries (particularly in state funded public university libraries), but it's not as easy (I don't think) as a new campaign or website. People need to know that there's a lot that can be done, learned, accomplished, and executed in a library.
- Derrick
Bookstores are another 'place with books', that provide other products and services as well. They seem to make more money off of coffee than books. And yet, they mostly seem to do just fine marketing themselves largely as outlets for physical media. You need to take a look at how they market additional products and services to people *once they are in the door*: http://en.wikipedia.org/wiki... and http://en.wikipedia.org/wiki...
- Michael R. Bernstein
I'm sorta' annoyed by people who dislike that "place for books" perception but INSIST on retaining the misleading, archaic names of "library" and "librarian." http://en.wiktionary.org/wiki...
- David Rothman (☤)
I think of MPOW as a community technology center and a place for lifelong education.
- Julian
I work in a public library and our big push right now is appealing to "young professionals" - those folks between school research and bringing their kids for story time. It's one reason why we are so heavily involved in social networking. Well, that and the fact that I work there and I'm heavily involved in social networks...
- WebGoddess
In the sense that most inventions are based on prior inventions? I suppose. But invention can also mean creating something that has never existed before, whereas the definition of innovation is dependent on existing processes and ideas.
- Victor Ganata
You have to love the English language that there's a complete disconnect in the definition of "innovate" vs "innovation" and "innovative" This would also explain my dislike of the words altogether.
- Scoble, Alex Scoble
Yes, but the root word is "to innovate" "make changes in something establishe" seems straight forward
- Victor Ganata
There isn't a disconnect. Related words are related. That people use words in looser senses is a feature, not a bug. But if Apple is using it in the strict sense, it doesn't make sense to criticize them using the looser sense.
- Victor Ganata
so what you guys are inventing innovations ?
- Peter Dawson
Don't you think that if Steve Jobs had actually invented something, he'd straight up say he invented it?
- Victor Ganata
To Alex, innovation only exists where the Whole is something we've never seen before. A flibbertygidget that does things we didn't even know needed doing.
- Tinfoil 2.0
Innovative decisions like ditching the SSD enclosure, integrating all top-of-the-line components, overcoming unique design and manufacturing challenges to fit components to millimeter tolerances to minimize size and weight, creating new software elements and usage paradigms for better UX and efficiency. Nope, none of that is innovation, it's just a regular day at the office.
- Tinfoil 2.0
The disconnect is in the dictionary...we can't use the dictionary as the ultimate arbiter of meaning in one case and then turn around in another and say "well, it ought to say it means this". Yeah, it's pedantic, but it is there.
- Scoble, Alex Scoble
Wikipedia has a section on the difference between the two words. http://en.wikipedia.org/wiki... . As to the meaning of a word being what OED says the root word means, well... You know how people use the word "sick" to mean "good" these days. ?!?! Sometimes it's more important to focus on there being two distinct ideas, that need to be disinguished in some way or another, than...
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- Sue - Friendfeed is best
I would never use a dictionary as the ultimate arbiter of meaning--I think that ultimately meaning is determined by usage. But it still provides a useful starting point. And I do think "innovate", "innovation", and "innovative" are generally used in similar senses, although, yeah, there are verb forms, noun forms, and adjectival forms of other words that are wildly disparate in meaning....
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- Victor Ganata
David Crotty, over at Scholarly Kitchen as an interesting piece on metrics, arguing that many of these have not been thought through because they don’t provide concrete motivation to researchers to care about them. Really he’s focused mainly on exchange mechanisms, means of persuading people that doing high quality review is worth their while by giving them something in exchange, but the argument extends to all sorts of metrics. Why would you care about any given measure if achieving on it doesn’t translate into more resources, time, or glory? You might expect me to disagree with a lot of this but for the most part I don’t.
- Cameron Neylon
I'm only reading when someone else's summary makes it seem relevant and interesting enough I have to admit. But I'm more inclined to go for David Crotty than most of the rest.
- Cameron Neylon
David is definitely worth the time -- the other authors over there, not so much. (I like how D says "try not to read SK"... there is definitely an element of morbid fascination.)
- Bill Hooker
I'm probably not the most objective person for this topic because it's our proposal that David Crotty is mainly going after in the article that you've linked to. I actually agree completely about the need for incentives and that metrics need to matter/linked to said incentives. I just disagree with his statement that our proposal doesn't actually provide (these) incentives. And given...
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- Wobbler
But we're not on paper ;-) Seriously tho I think we'd robably both agree with him on the general and disagree on the specific. I haven't actually caught up with the to and fro that followed on from this (which is why I didn't talk about it) but what I didn't really get from your proposal was a way in which the value/currency/incentives can spread wider. I don't think barter is enough - we need something more sophisticated and transferable. But if I'm missing something then am happy to discuss deeper.
- Cameron Neylon
from twhirl
I'm not entirely sure how it can even spread "wider"? The metric/incentives that we have in mind increase the odds of the peer reviewers' own eprints (preprints mainly, though) being noticed, read, reviewed and cited. And it has OA (pr)eprint repositories as its platform. It can be accessed by anyone. And how many scholars wouldn't access free, reviewed articles? How much more publicly accessible/noticeable do you want it to be?
- Wobbler
general comments without specific detail is one of the most frustrating things about TSK, back when I used to read it, anyways.
- Mr. Gunn
@Wobbler My points was that as I understood it it dealt purely with review and publications and then only publications in IR. So in a sense it was a barter, similar to some other simpler proposed systems where the idea is simply that you "pay" to be able to submit by doing a certain number of reviews. Its not about accessibility, its about whether I can trade off doing review vs paying...
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- Cameron Neylon
@Cameron: It’s more of an independent system feeding on OA preprint repositories (IR or CR) mainly because of the easy access to manuscripts eligible for peer review. Anyone can submit manuscripts to IR/CR, and it has nothing to do with what we propose. We have no limitations on submitting or accessing manuscripts. What you actually get out of the system we propose are, if you peer...
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- Wobbler
I think I agree right up to the last point. At the moment people don't much care about the visibility of their papers _in institutional repositories_. I think we can agree we'd like to see that change but at the moment I think that's a gap, which is part of the general gap we have between IRs and people's hard core motivations. Now if there's a strong case that it would lead to more...
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- Cameron Neylon
I think you’re right that most people (traditionally) don’t really care about the visibility of their papers in (their) IRs. I think that’s partly because the majority of people don’t care about 1. Papers in IR in general and 2. Searching for those IRs in the first place. CRs are more popular because they’re easier to find, submit and keep track of. In that sense, an independent, one...
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- Wobbler
Proving that our proposed system can work at the same efficiency (its effectiveness is probably easier to reason for) is going to be a major issue, indeed. And you’re right about there being a chicken and egg problem: without users, peer reviewing for visibility doesn’t really take off. It’s going to be difficult to (initially) get enough scholars, who are qualified to peer review, for...
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- Wobbler
I "liked" this reflexively without even reading (that is the power of my experience with D's writing). Then I read it. Wish I could "like" it again. Well done D.
- MoTO #TeamMonique
I'm not wearing purple today for Spirit Day, though my thoughts are clearly connected to the issue. Thought this was a little more my speed. Thanks for reading, y'all.
- Derrick
I cried the entire time I was writing it. Brings up a lot of old memories that despite that, need not to ever be forgotten.
- Derrick
Derrick, I am glad you are able to share your story with others. And let youth know that if you are different in High School, you are usually successful in life.
- ♫410 I Coach 'em Up♫
Is that long, ffcode? I'm a writer by nature and have been doing so since I was a kid. I can see now that we live in a short quip, 140 or less character world, but I've always been drawn to telling the story as long as it needs to be in order for it to be told. I just write until my thoughts are more or less complete.
- Derrick
Thanks for reading, ffcode. I appreciate it.
- Derrick
"there's so much more to life than what might seem obvious"
- Clare Dibble
I don't know you, but would also like to hug you through the Web. I have to miss local vigil tonight in support of It Gets Better, but will think of your post while doing other things. Many thanks.
- Louise "Weezy" Alcorn
Thanks everyone. I'm genuinely touched. I wasn't expecting to get so personal, but recent events led me to scribble this out this morning before starting my day, and I'm glad I did. I hope it does someone out there some good.
- Derrick
I said it there and I will say it here, your writing is as beautiful as your heart & soul, compadre. Much love...
- JA Castillo
books on shelves. I haven't been to a library in probably 20 years. Did high school research there but even in college and beyond I never went in the library. I should go and start checking out books again but for research i can survive with Mr Google
- SteVe C
Books, to be honest...we sometimes go to them to buy children's books on sale for Cassie's classroom, but neither of us are big book readers and we use other services to get the various other media that you'd get at a library, but I think that libraries are a necessary institution in our society and that we should be doing more to support them
- Scoble, Alex Scoble
Public libraries? books and dvds on shelves, public computer/internet access, literacy programs. Oh yes, and librarians.
- Michael R. Bernstein
I love libraries. A library is like a sanctuary
- Shevonne
I have a slightly different picture in mind when thinking of university libraries, if that was what you meant.
- Michael R. Bernstein
No discrimination, Michael. University libraries apply as well.
- Derrick
Note: I really REALLY miss the public library system in Las Vegas. Albuquerque's is a pale shadow by comparison. We used to go to the library every one or two weeks in LV, here in ABQ we've gone a half-dozen times in the last two years.
- Michael R. Bernstein
University libraries: books on shelves, journal access, institutional repositories, special collections. And librarians.
- Michael R. Bernstein
books, quiet, newspapers, study rooms, writing. We go quite regularly, especially in the summer. Waif's book habit was going to break a brother until she got a library card. Waif and Wife go to Mother/Daughter book club once a month. I often pick up graphic novels there. And I'm slowly making my way through their non-fiction section (have a translation of the Koran out now). Edit: Oh and my local liberry has a smokin' Jazz CD collection.
- MoTO #TeamMonique
Books on shelves. I haven't been in years. I don't think I really have a need right now. If I ever have the time to read a book (which is extremely rare these days), I have a ton of books here at home that I haven't read yet. And if I need to research something, the Internet is right here. Plus, I don't think library patrons or employees would be impressed by me bringing two screaming babies into a library.
- Rochelle
I usually think of libraries as those places that never have the actual book I want, forcing me to go track it down online, but where I can also browse around and find something random that I wasn't actually looking for.
- Alex Scrivener
This is obviously an informal poll, but consistent in what I've been reading and learning about. Libraries are going to continue to be in trouble. The internet search is killing them, even though the databases and resources available to libraries far supersedes what most people use (and perhaps what most people need). It's a dilemma for sure and I'm just trying to keep my eyes on the prize in lieu of my frustration with library school right now. Thanks for responding.
- Derrick
My first thought: ZOMG FREE STUFF. because I am a complete bookwhore, and they are my personal amazon.com. I use my public library very heavily for my leisure reading (and did even before I became a librarian). I think of my public library as community programming, leisure reading, work skills training. I'm a similarly heavy user of my academic library for my more academic work and research.
- ωαřмaiden ❤Marrit Woman❤
I'm with the Warmaiden on this one - I use my local PL for the trashy romance novels I don't want to buy, books I hear about (often at the bookstore), and craft books to "try before I buy"....I also borrow heavily from the popular CD collection
- ~Courtney F
Courtney and Warmaiden, you're both librarians. Do you feel you are biased?
- Derrick
home. (I mean, that's not like my considered opinion, or anything else, but it's gods honest truth the first thing that comes to mind.) and I think the 'home' feeling is why I work in a library, not the other way around.
- Marianne
Biased how, Derrick? Biased in that I think of the library before the bookstore? (that's really more because I am cheap.) Or biased because I think of my library at all? I use MPOW for my research, since they have all the databases my PL has (and then some)....
- ~Courtney F
Courtney, just in the sense that those of us with a relationship tend to think of libraries first, and, as noted in this thread, people who don't haven't been in one in twenty years. That discrepancy is huge. I'm just thinking out loud.
- Derrick
@Derrick - not really, I dont think I'm biased by being a librarian. I became a librarian largely because I was already a heavy library user - both public (I practically grew up in my publib) and academic, once I learned how to use it in college and my pre-MLS grad school days. Like Marianne, I became a librarian because to me it has a sense of home. Becoming a librarian introduced me...
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- ωαřмaiden ❤Marrit Woman❤
Understaffed. I work in the same building as the library & constantly get questions, even though I don't work there. Also tired of trying to explain the difference between archives & library.
- Anne Graham
I also use the library to borrow what I don't want to buy, and try out craft books before I buy.
- Paulette
Cultural centers, study halls and homeless shelters all in one.
- Rob H.
Rob H., I agree on the homeless shelters part. The library in downtown Seattle was packed with homeless people (and their luggage, carts, etc.) last time I was there. The bathroom was unusable because it was full of homeless people bathing in the sinks.
- Rochelle
Public libraries - places to go to get DVDs and books when I don't want to buy them or Netflix them, or places to go when my wifi at home is broken. University libraries - shrines to knowledge where I can find anything I want about anything I want and I can just stand in awe staring at all the books wishing I had time to READ THEM ALL.
- Jandy
I'm a medical librarian, but I go to my local public library about once a week. I primarily go there to pick up books I want to read, and make good use of holds and interlibrary loan to get the books that maybe aren't there immediately. I also go to see exhibits. I don't really need the classes they offer, and have my own internet access, but that is a privilege. I see libraries as a...
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- Rachel Walden
Books come to mind first and foremost because that's all there was when I started going to the library weekly as a young child. Over the years as their collections have expanded to include other media, I have continued to frequent the library two to three times a month to borrow items, to attend meetings and view exhibits, and to browse in search of new attractions.
- Anne Bouey
Books and community. I use the local public library frequently (the source of most of the books I read), and every time I go in it's bustling, and I'm 99.999% certain very few of those users are librarians. Oh, and their frequent programs are regularly highlighted in the local weekly paper and well-attended. (Lots of other media, too; I just happen to borrow books primarily.)
- Walt Crawford
Thanks everyone. I wasn't planning on ranting that out, but something struck a nerve. Shannon, I have seen that. I have a love/hate thing going on with Dan Savage, but I do applaud and celebrate the It Gets Better Project.
- Derrick
Someone else's failure has never made me smile so much *hugs*
- Nathalie
You don't even have to be a queer teen to appreciate this lesson
- Martha
How about this one, Derrick? Joel Burns tells gay teens ' it gets better' www.youtube.com Sent from a gay classmate to our entire Class of 1962 of Poland Seminary High School in Poland Ohio. And no, I did *not* go to a seminary. Glad you're around.
- Mama Lawson
I thought that would come up as a URL. Sorry. I'm neither a librarian nor technologically educated.
- Mama Lawson
I *was* like that when I was younger. As I've got older there's no peer pressure, and these days I *do* listen to whatever I like as loud as I like - almost anyway.
- Ian May
If I write some code while a graduate student at a university, who owns that code? If they're scripts used for data analysis, but clearly aren't substantial enough to warrant publication or patents, can I safely open-source it and post it online? Will this somehow run me afoul of my school's IP office?
I'm interested in non-lawyer opinions too. If you have experience with doing it and haven't had any problems, that's useful information too.
- Chris Miller
I'd try and find out what the school's IP office's official policy is (without necessarily making it sound more than hypothetical, if you're worried). At MPOW policy is that students and staff own their own creations (and I *think* the IP office will work with you to monetise it if you want, at which point I presume it'd take a cut, but I'm more or less making this whole parenthetical up).
- Deborah Fitchett
it probably also depends on what your PI's contract was. Most employees have to sign something that gives the IP rights first the employer - you don't sign it as a student but I think it still applies to you for work done in the lab paid via the university.
- Jason Stajich
from twhirl
It also depends on what you have signed. It's commonplace in many of the large Australian unis to have grad students now sign an IP deed, that basically says "we own the IP you generate, but we may give you a small slice of the royalties". But then, in practical terms, if there in no money to be made, it seems unlikely to create an issue .. but sometimes these organizations get warped...
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- Andrew Perry
from Android
The position for students is often different to that for staff. It may depend on what you were paid from and for, and will certainly depend on the details of your contract. In practice I'd treat it as tho it were a publication - who would you contact before publishing something that you'd done on your own out of your PhD?
- Cameron Neylon
I had to sign contracts as a grad student that passed ownership of anything created to the university. In practice, though, the unspoken rule seemed to be that the university only noticed what you produced if it made a lot of $$. Small publications, even those garnering a bit of cash, were ignored. We've since had major discussions between creators and the university, largely b/c of the...
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- Mickey Schafer
If still in the lab, I'd ask your advisor whether he or she cares. If not in the lab, but still have good relationship, I'd still consult with old advisor and any collaborators to see if they care. You don't have to worry about the IP office, unless you signed some kind of crazy contract that I've never seen before. If you want friendly relations with IP office, you can always email...
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- Steve Koch
It is worth knowing your institution's policy, but don't be surprised if the acquisition and spread of knowledge for the betterment of humankind is not the primary purpose of that policy. It can be necessary to educate your legal department even if you simply wish to apply standard open source licensing (e.g. the classic story of Steven Brenner's struggles at UC Berkeley: http://bit.ly/ccVgbv)
- Todd Vision
PLoS thinking about requiring authors to write a 'data availability statement'. How to word it to avoid the pitfalls? http://alexholcombe.wordpress.com/2010... Hoping to duplicate some fraction of Cameron's crowdsourcing success
pitfall 1: authors would have to write statement at time of submission. Most won't have tried yet to deposit their data anywhere. So they may write something inconsidered that won't actually be true come publication time. Indeed, many will say the data will be available but then they won't follow through.
- Alex Holcombe
pitfall 2: Policing. PLoS would feel some responsibility to police whether the authors' data is available, an additional burden on PLoS
- Alex Holcombe
pitfall 3: PLoS will look less kindly at authors who don't make their data available and don't have a legitimate excuse like human data privacy issues. But may be impossible to apply a uniform standard- expectations differ across fields, most reviewers still won't expect any data sharing, etc. If data availability is a factor but not completely consistently, is that fair?
- Alex Holcombe
are there expectations that data will be shared locally? I don't think this will be possible for all authors.
- Elizabeth Brown
Thanks much for these pointers and comments. Elizabeth, I'm not sure I know what you mean by 'shared locally'. I was thinking they'd have to share it globally, which includes locally :) but probably I'm misunderstanding
- Alex Holcombe
I think Elizabeth means taking responsibility for hosting the data locally. And I think the answer is no, not necessarily, it could go to Supp Mateials, it could go to BMC Research Notes, or to an appropriate data repo or IR, or some local server. Actually they can just make it available in response to email requests and satisfy existing policy. The aim here is to get people to think a...
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- Cameron Neylon
Yes, I meant hosting locally. Some authors (esp. at small colleges and orgs) may not have a local IR or server space. I agree the email option is a good way to satisfy that though.
- Elizabeth Brown
regarding Policing ... after the authors addressed the reviewers comments but before it is formally accepted and published is around the time where editors have the most leverage. this is when the editor should make sure that the data is available in supplementary info or databases. If it is hard for the editors to evaluate this then include in the feedback you ask from your reviewers to detail if the authors should provide any extra data to comply with your policy
- Pedro Beltrao
re: Elizabeth's suggestion regarding email as a dissemination mechanism. There is quite a lot of evidence in the literature about how poorly sharing-upon-request works in practice that an effective policy should steer clear of that route entirely. PLoS should encourage and enable authors to archive the data before publication so that the article can contain a permanent link to the data, and authors no longer have the burden or responsibility of mediating data reuse once the article is published.
- Todd Vision
You know, I've never even known a case where 1 scientist requested to see another's data. The climate is such that I'd probably feel like to jerk doing so, unless it was a friend. And I never come across data made freely available either. And yet I feel people would devour the data if they had the chance. Definitely one of the difficulties has to be how to decide which data to share -...
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- Jason Snyder
About email distribution, as Todd says it hasn't worked well in the past because most authors don't reply to requests or refuse them (there was a recent PLoS ONE paper showing this). Jason: I've asked for others' data on two or three occasions. I know what you mean though- I would have felt like a jerk doing so if I wasn't used to being such a callous person already :) If I remember...
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- Alex Holcombe
Agree that email is a bad mechanism in general terms and tends to lead to low compliance, but the point is that authors _can_ satisfy the current policy by just replying to an email. On the other hand, if they say, 'available by email' then arguably the editor could request it by email and stick it in a comment...
- Cameron Neylon
I have an nstruction T/Fquestion for students asking them if Zotero is named after a sorcerer in a Disney movie. I think there's a title idea in there somewhere.
- Elizabeth Brown
Google Docs is an easy-to-use online word processor that enables you to create, store, share, and collaborate on documents with your science and math students. You can even import any existing document from Word and Simple Text. You can work from anywhere and with any computer platform to access your documents. Considering the versatility of Google Docs, there are many ingenious ways teachers use this free online program with students.
- David Wetzel
from Bookmarklet
This photo is the most common I have seen on the web when microbiology is concerned. It has been used with a press release on one of my papers as well (http://healthnews.uc.edu/news...). The funny thing is I think this just shows a bunch of contaminants in a particular environment. It's a lousy culture
- Ramy Karam Aziz
Yes, it looks like a contaminated Petri dish that they used just to shoot a few pretty pictures. The photo is available on several stock photo websites such as iStockphoto (http://is.gd/fveN9) or Shutterstock (http://is.gd/fvg4A). The author appears to be a photographer called Alexander Raths. Funny, if you click on the photo at the press release you mentioned...
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- Cesar Sanchez
OT but of relevance. One issue that was discussed at Science Online 2010: London was ye olde subject of the image that the general public have of what a Scientist looks like. The example given by the Prof who raised the subject said http://sharp.sefora.org/wp-cont... was the 1st image that appears when doing a Google search. I checked this for myself whilst he was talking and indeed, this is the one he meant <groans>....
- Graham Steel
"The case of the BRCA genes, which act as a tumour suppressor, illustrates how close we are to the edge. Mutations of the BRCA genes are linked to breast cancer and ovarian cancer, and tests can be carried out to identify mutations. The company Myriad Genetics held two patents for the diagnosis of mutations in the BRCA1 and BRCA2 genes and carries out the genetic screening test, which is very costly. The patent prevented any other laboratory from doing the test for a lesser cost. The American Civil Liberties Union and the Public Patent Foundation filed a lawsuit charging that patents on two human genes associated with breast and ovarian cancer are unconstitutional and invalid. On 29 March 2010 a New York federal court ruled that the patents on the BRCA1 and BRCA2 genes are invalid (BMJ 2010;340:c1870, doi:10.1136/bmj.c1870)."
- Thomas Brox Røst
from Bookmarklet
"Personal View: Why are we copyrighting science? " Indeed, and moreover, why oh why did the Authors stick this behind a ****ing paywall ??
- Graham Steel
Takes a look at a challenge I regularly hand out to undergrads whose blithe acceptance of the RCT borders on faith-based indoctrination, particularly in cases where we DO know something about the biological course of a disease.
- Mickey Schafer
"And doctors say that for them, the new wave of cancer drugs is intensifying the conflict between their responsibility to their patients and their commitment to gathering scientific knowledge for generations of the critically ill."
- Mickey Schafer
"Some melanoma specialists familiar with the drug would have traded the data for faster access to the drug. “I know all that I need to know based on the results we already have,” said Dr. Keith Flaherty of Massachusetts General Hospital, who led the early clinical testing. “My use of this drug is not going to be informed by testing it against a drug we all hate and would rather never give a dose of again in our lives.” "
- Mickey Schafer
Makes me wonder how many people are blogging and thinking and working on these issues, with whom I've never come into contact. E.g. I'd never heard of Mark until science 3.0. This seems like a trite question but to me it's interesting because the whole point of open foo is connections between people.
- Bill Hooker
Bill - I think this is all good - the more services like this evolve the more likely people will find people at some point
- Jean-Claude Bradley
My thoughts here are half baked at best -- there is some connection somewhere in my brain between solving the pressing problems in open foo (buy-in from the community, establishing successful examples, etc) and me having some way to be confident that I know, or at least know of, (nearly) everyone who is interested in open foo. If there were a way for me to do the latter, it might point to solutions to the former... or something.
- Bill Hooker
Bill: Quite apart from what Dorothea sez, I don't think there's any (current) way to get a full list of "everyone who is interested in open foo," or even in a supposedly-well-defined subset such as open access. I could be wrong.
- Walt Crawford
I think interested people are still finding each other, like others have said. I would argue the groups intermingle but not necessarily all at the same events or through the same channels (online attendence vs. in-person).
- Elizabeth Brown
I agree with Walt - there is not a well defined community of openness because it covers so much. But I do think that anyone who wants to find others who have similar interests can find them easily starting from a simple Google search. It will probably require interacting with people that are initially found that way. An excellent case that comes to mind is Hope Leman and how quickly she found the people she was looking for in her specific Open Science interests.
- Jean-Claude Bradley
There are two disparate questions: "Finding others who have similar interests"--which, as Jean-Claude says, shouldn't be too difficult--and "knowing of (nearly) everyone who is interested"--which is somewhere between difficult and impossible. Makes life interesting.
- Walt Crawford
Walt - can someone really be categorized as "interested" if they can't be bothered to participate in even the smallest way?
- Jean-Claude Bradley
Jean-Claude: Yes, I think they can--but, more to the point, there are lots of forms of participation that won't show up in simple Google searches. (Would you even find me as an "open foo person" in a simple Google search? I wonder...but then, one Important OA Advocate regards me as an enemy of OA, so maybe that's appropriate.)
- Walt Crawford
I think you need a LOT more than a Google search to find people interested in these topics. Plus even if you make a connection online, someone may not know who you are until you meet in person. In my experience I've tended to meet someone in-person before establishing the online connection.
- Elizabeth Brown
My point wasn't that you would find all relevant people directly from a Google search - just that you identify enough people to map out the rest of the network after contacting them. That seems to be a strategy that reporters use to quickly learn about a new area.
- Jean-Claude Bradley
Elizabeth - my experience is exactly the opposite - I almost always meet people online before meeting them in person (if I ever do :)
- Jean-Claude Bradley
I want to both agree & disagree with @D0r0th34 's assertion that open-movement people in various groups "never, EVER do they talk to each other, except in very circumscribed, scripted ways." I am thinking back to the early research on "the invisible college" and "technological gatekeepers" and "boundary spanners", having found that the folk who work and function in those roles tend...
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- Patricia F. Anderson
D - I don't know if the isolation is mainly due to scorn or just limited time. I don't closely follow everyone pushing OA or government policy because that's too far removed from my core focus but I certainly respect what proponents of those causes are working hard to do. I think we're mainly all on the same team. I didn't get the feeling that PMR hates librarians :) That would make for an interesting survey though...
- Jean-Claude Bradley
OK D - since you have opened the can of worms - I have to vehemently disagree with the clearinghouse concept. I have absolutely no trust in any specific individuals to tell me who are the "right people" to follow.
- Jean-Claude Bradley
Dipping in to that can of worms: A clearinghouse doesn't necessarily require trust in one or a few people. For the OA piece of Open Foo, I think the Open Access Directory is getting pretty close to being that clearinghouse (cross fingers, don't ask me to define "pretty close"). And I don't think it tries to identify "the right people." For the others, or for some commingling? I haven't a clue, partly because I've ignored most other aspects.
- Walt Crawford
What D and Walt are talking about is close to what I was wiffling on about upthread -- I wish, for instance, that everyone in the whole world who is into open foo would have a FriendFeed account and join the Life Sciences and Science 2.0 rooms. That wouldn't require any trusted filters (other than the ones I use now, the people I follow here). But how to make that, or something equivalent to that, happen...?
- Bill Hooker
What a coincidence... I'm wrapping up (hope to submit next week) a grant on building something like a Directory of Open Foo in Science (including search engine with API, downloadable index and filtering on level of openness whatever it might mean in practice). It's not going to replace FriendFeed-like aggregation, but that's not my goal. The most of the money I'm asking for is going to...
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- Pawel Szczesny
Graham Steel maintains a Google Doc of contact info for all the usual suspects, and seems to be adding suspects at a steady pace. Perhaps one way my wish could come true is if Graham spent all his time on that document...
- Bill Hooker
Following up on Bill - nothing wrong with getting a list of leads from the FF Science2.0 room as a starting point (just as a Google search would be another starting point). But no matter the starting point it is up to the person doing research to contact some of these people to get lists of names to further pursue (as reporters do routinely). Very quickly the same names will keep popping up and you will end up with very similar networks of active individuals
- Jean-Claude Bradley
Jean-Claude I have a different opinion - because of that circular references one can hardly leave the network one had started with. Similarly a search phrase defines the network (while there are some differences between 'openness in science' and 'transparency in science', people talking about the latter often mean the former, but they don't appear that high or at all in search results)....
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- Pawel Szczesny
To what Pawel just said, I would add my original plaint: that I keep finding new people, more or less by accident! It's an unknown-unknown problem: I don't know how many other interesting open foo people are out there whom I haven't found yet. Partly, of course, it's because I don't spend a lot of time actively networking and searching -- being low on the totem pole in...
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- Bill Hooker
I agree with Bill - I find people by accident. I meet them online too, but looking at my contacts the majority are still people I met first in person before I added them to a social network. In fact one of them was you, Jean-Claude. :) If you hadn't suggested ff I wouldn't have started using it more.
- Elizabeth Brown
Fascinating--and the discussion itself helps indicates the extent to which there are different circles: "in science" is not, for example, a great way to pick up most library people involved in OA or, for that matter, humanities people involved in various aspects of Open. (Or Open Source people, for that matter, but that may not be part of Open Foo?)
- Walt Crawford
Elizabeth - yes you are an exception for me of someone I met in person first :)
- Jean-Claude Bradley
I'm like Jean-Claude in this: I met most people online long before I ever met them in real life. I still haven't met the majority of my FF friends in the Big Blue Room, although I'd like to. (Hmmm... a FF Life Scientists meetup?)
- Bill Hooker
It is such a thrill for me to meet people face-to-face who I know only online. I am like Bill and Jean-Claude this way. A meetup would be wonderful, but (knowing me) I probably couldn't come!
- Patricia F. Anderson
The pharma drug development pipeline is broken.
- Ruchira S. Datta
Standards of care are inadequate: people are getting treatments that aren't appropriate for them, with concomitant side effects.
- Ruchira S. Datta
We need to look in the mirror for blame: many of the blocks are in academia.
- Ruchira S. Datta
Oswald Avery found that DNA is the substance of genes, Watson & Crick solved the structure.
- Ruchira S. Datta
We used to focus on single genes. Gene regulation circa 1990: everyone looked at single gene pathways.
- Ruchira S. Datta
1996: See interconnecting pathways in Wnt gene regulatory network.
- Ruchira S. Datta
2002: See very complex system with many different genes. But now very confusing: for therapeutics, which is the correct target?
- Ruchira S. Datta
How is genomic data used to understand biology? GWAS identifies causative DNA variation but provides NO mechanism. Profiling approaches (microarrays) at genome scale provide correlates of disease, but what is cause and effect?
- Ruchira S. Datta
Biological systems are very flexible. They work around single perturbations.
- Ruchira S. Datta
Looking at integrating genetics approaches and clinical data.
- Ruchira S. Datta
Steven Friend started Rosetta Informatics, which was acquired by Merck. Integrate multiple Bayesian models to make predictive models of where to perturb for effective therapeutics.
- Ruchira S. Datta
Computationally intensive: keep updating Bayesian networks.
- Ruchira S. Datta
>60 publications over 5 years substantiating probabilistic causal bionetwork models. Use these to make detailed priority lists of what is important.
- Ruchira S. Datta
Cancer and metabolic diseases are very diverse among patients. Opportunity for individual medicine.
- Ruchira S. Datta
Mission of Sage Bionetworks is to create a Commons where integrative bionetworks are evolved by contributor scientists.
- Ruchira S. Datta
New non-profit, over a year. Lease offices at Fred Hutchinson Cancer Research Center. Now an NIH research center.
- Ruchira S. Datta
Small, plan to stay small. Rather, work with partners including commercial groups.
- Ruchira S. Datta
Many of the commercial groups are actually some of the best partners for open access sharing. E.g., Merck, Lilly have found very early stage research should be open--very difficult to value very early stage research.
- Ruchira S. Datta
See The Sage Commons website. Get highly annotated, globally coherent data with multiple layers of data.
- Ruchira S. Datta
Have datasets stratified in different stages.
- Ruchira S. Datta
Challenges from Sage Commons Congress (scientists, funders, policy experts, publishers): workgroups on Standards (data, annotation), Tools (combining, analyzing), Citation (recognition), Internationalization, Public Engagement
- Ruchira S. Datta
especially, how to engage patient advocacy groups
- Ruchira S. Datta
Many barriers to openness, trying to work through with partners
- Ruchira S. Datta
Checked the scientific social network of attendees at the Congress. Many hubs.
- Ruchira S. Datta
IT experts tended to collaborate w/ everyone; media, policy, funders weren't as interested in talking with them!
- Ruchira S. Datta
Biomedical research developed as a Cottage Industry.
- Ruchira S. Datta
Resulted in current complex ecosystem w/ FACULTY and TENURE.
- Ruchira S. Datta
Have rapid information transfer within labs, very slow between labs. This is costing lives.
- Ruchira S. Datta
Incentive issues. The Federation Experiment: fuse four research labs.
- Ruchira S. Datta
from Android
What about Stanford & The Mission Bay Campus? "New non-profit, over a year. Lease offices at Fred Hutchinson Cancer Research Center. Now an NIH research center"
- Attila Csordas
Attila, are they there too? Got no indication from the talk or their website.
- Ruchira S. Datta
Surprised that among all the meanings of SAGE from which Sage Bionetworks distinguishes themselves, no one mentioned the OSS math system http://www.sagemath.org Slogan similar in spirit: "instead of reinventing the wheel, let's build the car". Founder William Stein also now Seattle-based (fellow Berkeley math PhD).
- Ruchira S. Datta
Well, it's logical to assume that the sage guys want to expand to the Bay Area too :)
- Attila Csordas
this is a big issue because it can be time-consuming. I try to put much of what they need to know on the lab wiki (http://openwetware.org/wiki...). Want to move away from reliance on oral transmission of knowledge (which should have gone out of style 2000 yrs ago). Also the wiki potentially benefits others around the world.
- Alex Holcombe
Important question. There are a few online resources that the people in my lab use, but most of their instruction will be on their topic and hands-on, so it has to be shown. However, for some tasks I have videos, e.g. a JoVE video.
- Björn Brembs
The lab I work in recently created a small induction manual for new students joining the lab - it's a bit like Kathy Barkers "At the Bench: A laboratory navigator", but with specifics that apply to our lab. A copy is kept on our internal wiki (not wiki-fied unfortunately - it's a Word doc), and I think it helps reduce the training load by answering a lot of the common queries about protocols and safety etc.
- Andrew Perry
As Alex says keeping lab notebooks and other info on a wiki helps tremendously
- Jean-Claude Bradley
Thanks so much, everyone! I'm in the position of training new faculty and my supervisor is encouraging me to use the CMS to produce course templates. It also has wiki function that I was planning to use, too.
- Mickey Schafer