I'm not sure I like the idea of paying, especially on a monthly basis for a subscription, once I have to foot the bill, and also if free cloud-based services exist and can do a half decent job...
- Jason Snyder
I'm more worried about the NIH devoting itself to one provider... people should have the freedom to pick a ELN that suites them, and the organization should be careful not to fall for the Vendor Lockin trap... they should pick a provider that strongly supports Open Standards...
- Egon Willighagen
Personally I would run screaming in the opposite direction at this point. Trying to standardise across the NIH with anything that describes itself as an ELN is very like to be a disaster IMO
- Cameron Neylon
from twhirl
data portability is the keystone for software selection, because however perfectly any program meets today's standards, in the future those requirements are sure to change
- Mike Chelen
I May give ELNs a try, just to see what I'm missing, but you all bring up some key points that make them pretty unattractive. I think the take home message for me is to spend a few hours deciding how exactly to best organize my lab notebook. Currently, it's a mix of lab books, sheets of paper, google calendar, google notebook (which isn't even being maintained by google), and a bunch of files stored remotely via dropbox...all the info's there, just not so cohesive.
- Jason Snyder
I've been working with a small outfit called BioKM to get them to support data portability and open standards, but so far I haven't been able to get much of a committment from them regarding how open data and data portability fits into their roadmap. Hopefully this thread will help them see the importance. (In case anyone's wondering, that's my strategy to get more support for open science - help the service providers get a clue about what customers want in this regard)
- Mr. Gunn
Gunn: what do you recommend for data potability? XML maybe? We just released Samples (scimatic.com/samples) and I'd like to look into doing more in regards to data portability
- Jamie McQuay
from iPhone
I would have said XML some year ago, but now I'd say RDF using Open Specification namespaces, like FOAF, DOAP, Dublin Core, BIBO, ...
- Egon Willighagen
Egon: thanks for the info, will be looking into more exportability in our next point release of Samples.
- Jamie McQuay
+1 Egon, and thanks. RDF FTW I need to turn on comment notification or something.
- Mr. Gunn
Followup the NIH evaluation process, recently the Scientific Directors have decided that each researcher is free to choose the electronic lab notebook that best suites their needs. During the committee evaluation, Sparklix e-Notebook received high praises for its ease of use, reach functionality and the included support. this electronic lab notbook is free, I would give it a try - http://www.sparklix.com/signup
- Roi Paz
Central thesis: "open access means that there will be more potentially harmful papers available to general public". We should get rid of the internet too, perhaps?
- Noel O'Boyle
Noel, that's not central thesis. That's example of reasoning to which Peter's approach leads.
- Pawel Szczesny
from iPhone
Pawel, I agree with your point, but I disagree with your example... allowing people to make mistakes I value more than believing you know better and disallow things... your argument is like disallowing freedoms because some cannot handle them... that makes your argument quite different from those of PMR, even though both anecdotal of shape...
- Egon Willighagen
Egon, I get the difference very well and that example was chosen on purpose (I had some less "nuanced" as well, but didn't decide to use them). However, if a scientist is using unscientific arguments, the remaining nuances don't make a difference anymore. How we can improve the quality of public discourse if we allow for such argumentation?
- Pawel Szczesny
Well, theoretical sciences I guess :) PMR formulated a hypothesis, that is worthy of empirical validation... which effect is larger: that of foolish people, of that of people kept uninformed... (I don't know; I'm not a social scientist...) Where would science be if we cannot hypothesize anymore.... You provided an important alternative hypothesis... null hypothesis, perhaps?
- Egon Willighagen
Ok - I get you now. Central thesis: "Anecdotal evidence is irrelevant to a scientific argument." And other things besides OA can help more.
- Noel O'Boyle
Egon, the problem I see is that PMR's own words: "I don’t think anyone can deny the truth of that conclusion." are not a formulation of hypothesis, but a populist language. This unfortunately has many implications, none of which I like.
- Pawel Szczesny
I agree that PMR's blog posts are often short on links to further detail. I personally prefer linking in my blog to further info to back up my story and improve the 'learnability'... I personally think 'learnability' is the more important aspect, and Open is the means. PMR is an established Cambridge scholar... they can do with bold language, leaving things to be worked out by others....
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- Egon Willighagen
Egon, you've touched a few very important issues. One thing is that if you don't have a leverage, you use the leverage of the community of which you're a member. So, PMR comments might influence position of people relying on the community in certain situation where trust in a discussion depends on the community's 'brand'. The other thing is that from perspective of people in less...
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- Pawel Szczesny
And finally, the biggest win of OA will be when the general public actually cares about open access to knowledge, not when scholarly communication will be open and still nobody cares. That will translate to _rational_ public discourse, because fact checking and hypothesis testing will be a normal mode of coming to conclusions on public issues. Indeed, there's a place for anecdotal evidence, but they serve as a starting points of coming to conclusions, not end points.
- Pawel Szczesny
Steven Pinker on the History and decline of Violence: 'Today we are probably living in the most peaceful moment of our species’ time on Earth' - http://aminotes.tumblr.com/post...
“Drawing on the work of the archaeologist Lawrence Keeley, Steven Pinker recently concluded that the chance of our ancient hunter-gatherer ancestors meeting a bloody end was somewhere between 15% and 60%. In the 20th century, which included two world wars and the mass killers Stalin and Hitler, the likelihood of a European or American dying a violent death was less than 1%. Pinker shows that, with notable exceptions, the long-term trend for murder and violence has been going down since humans first developed agriculture 10,000 years ago. And it has dropped steeply since the Middle Ages. It may come as a surprise to fans of Inspector Morse but Oxford in the 1300s, Pinker tells us, was 110 times more murderous than it is today. (...) Conventional history has long shown that, in many ways, we have been getting kinder and gentler. (...)"
- Amira
from Bookmarklet
"The decline of violence is a fractal phenomenon, visible at the scale of millennia, centuries, decades, and years. It applies over several orders of magnitude of violence, from genocide to war to rioting to homicide to the treatment of children and animals. And it appears to be a worldwide trend, though not a homogeneous one. The leading edge has been in Western societies, especially...
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- Amira
"After the cold war, every part of the world saw a steep drop-off in state-based conflicts, and those that do occur are more likely to end in negotiated settlements rather than being fought to the bitter end. Meanwhile, according to political scientist Barbara Harff, between 1989 and 2005 the number of campaigns of mass killing of civilians decreased by 90 percent. (...) The decline of...
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- Amira
Thanks! I have also uploaded it to http://www.youtube.com/watch... and http://commons.wikimedia.org/wiki... . We have the audio and video files separately, so if anyone would like to go for a translation or other modification, that should be facilitated. Just looking for a good place where to put these additional files.
- Daniel Mietchen
Yeah, right now all I do is work, eat, and sleep... hacking a bit now for relaxing, but gonna pay for that the whole rest of the weekend... :/
- Egon Willighagen
"The Interplanetary Transport Network (ITN) is a collection of gravitationally determined pathways through the solar system that require very little energy for an object to follow. The ITN makes particular use of Lagrange points as locations where trajectories through space can be redirected using little or no energy. These points have the peculiar property of allowing objects to orbit around them, despite the absence of any material object therein. (...) The transfers are so low-energy that they make travel to almost any point in the solar system possible. "
- Amira
from Bookmarklet
I've seen science fiction writers refer to these paths as "chaotic" trajectories, on account of the complexity of the mapping process. I imagine we're now at a place where there's enough affordable computing power to actually map these paths in real-time.
- Slippy
"Caroline Herschel (1750-1848) was the first woman to discover a comet and the first to have her work published by the Royal Society. * Mary Anning (1799-1847) began a long career as a fossil hunter. She found hundreds, possibly thousands, of fossils that helped scientists to draw a picture of the marine world 200 million to 140 million years ago during the Jurassic. (...) * Barbara McClintock (1902-1992) was awarded a Lasker Prize in 1981 and Nobel Prize in 1983. She discovered that genes could move within and between chromosomes. (...)....
- Amira
Ada Lovelace - (1815-1852) English writer chiefly known for her work on Charles Babbage's early mechanical general-purpose computer, the analytical engine. Her notes on the engine include what is recognised as the first algorithm intended to be processed by a machine; as such she is sometimes portrayed as the "World's First Computer Programmer"." http://en.wikipedia.org/wiki...
- Amira
Grace Murray Hopper - (1906-1992) "American computer scientist and United States Navy officer. A pioneer in the field, she was one of the first programmers of the Harvard Mark I computer, and developed the first compiler for a computer programming language. She conceptualized the idea of machine-independent programming languages, which led to the development of COBOL, one of the first modern programming languages." http://en.wikipedia.org/wiki...
- Amira
Jeff Hammerbacher: ‘The best minds of my generation are thinking about how to make people click ads… That sucks.’ - http://www.businessweek.com/magazin...
"After a couple years at Facebook, Hammerbacher grew restless. He figured that much of the groundbreaking computer science had been done. Something else gnawed at him. Hammerbacher looked around Silicon Valley at companies like his own, Google (GOOG), and Twitter, and saw his peers wasting their talents. "The best minds of my generation are thinking about how to make people click ads," he says. "That sucks." (...) "Any generation of smart people will be drawn to where the money is, and right now it's the ad generation," says Steve Perlman, a Silicon Valley entrepreneur who once sold WebTV to Microsoft for $425 million and is now running OnLive, an online video game service. " (...) [Hammerbacher]: "If instead of pointing their incredible infrastructure at making people click on ads," he likes to ask, "they pointed it at great unsolved problems in science, how would the world be different today?" (...) At social networking companies, Wants may sit among the computer scientists and...
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- Amira
from Bookmarklet
"These consumer-targeting operations look a lot like what quants do on Wall Street. A Want system, for example, might watch what someone searches for on Google, what they write about in Gmail, and the websites they visit. "You get all this data and then build very rapid decision-making models based on their history and commercial intent," says Will Price, CEO of Flite, an online ad...
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- Amira
It's all about data mining, data mining, data mining and more data mining. The possibilities are exciting and endless, and I do not feel quite as jaundiced on the subject as Jeff Hammerbacher. One can learn a great deal about the human mind in general by data mining consumer behavior to the absolute limit.
- Sean McBride
Must read for research institutes who use the JIF to rank candidates to positions... Jan Aerts originally shared this post: http://arxiv.org/pdf...
- Egon Willighagen
What's the best way to get data out of FriendFeed? Looks to me like it's gradually coming to an end. I'd love to have a way of archiving all the conversations I've participated in.
Fascinating - though the articles are in the public domain, he might have violated licenses by downloading the public domain documents from a database in numbers and not just for personal use.
- barbara fister
I was trying to sort this in my head as well, Barbara…if they are public domain, I'm very curious if this guy could be held to the click-through license that JSTOR uses before allowing a PDF download.
- Jason Griffey
The internet archive and gutenberg projects work hard to make sure to find print copies actually published prior to 1923 to ensure that the work is clearly in the public domain. I can only think that somebody might try to claim rights to the electronic copies created as a result of scanning, OCRing, and copyediting the text. But then, there's nothing "creative" in any of that, so within the US, with it's "no copyright on databases" rules, the PD stuff might just be PD still. But nobody's tested it yet.
- DJF
DJF, I would think libraries would take a lead role here... are they not?
- Egon Willighagen
Actually, I should say some are. But as a class, there is no plan that I am aware of for libraries to work together to tackle digitizing and hosting scholarly journal literature in any significant way. U Mich digitized 19th century journals as part of Making of America - http://quod.lib.umich.edu/m... - and there are other pockets of things like that. Nothing like JSTOR but public domain that I am aware of.
- barbara fister
They should of course be taking the lead role. They're the institution on this planet with centuries of experience, after all. If not libraries, who else?
- Björn Brembs
These digitization projects are hugely expensive and there's no ROI if you're digitizing stuff that other libraries already have access to like old journals. That's why they usually do unique collections. With that said, Hathi Trust is precisely about universities banding together to make digital copies (obtained through Google or local efforts) available and to preserve them. They are also taking a lead role in pushing the orphan works issues.
- Christina Pikas
I thought about Hathi (in the wee hours of the morning) - it's a premier example of multi-library cooperation. I wonder if in this era these projects will be what we originally created OCLC for - sharing of both our work and of intellectual materials?
- barbara fister
(Though I would hope it would avoid the corporate mentality.)
- barbara fister
Analytical and Bioanalytical Chemistry, Vol. 384, No. 3. (1 February 2006), pp. 620-630. Innovation in the last decade has endowed nanotechnology with an assortment of tools for delivery, imaging, and sensing in cancer research—stealthy nanoparticle vectors circulating in vivo, assembled with exquisite molecular control, capable of selective tumor targeting and potent delivery of therapeutics; intense and photostable quantum dot-based tumor imaging, enabling multicolor detection of cell receptors with a single optical excitation source; arrays of semiconducting nanowire and carbon nanotube sensor elements for selective multiplexed sensing of cancer markers without the need for probe labeling. These rapidly emerging tools are indicative of a burgeoning field ready to expand into medical applications. This review attempts to outline most of the current nanoparticle toolset for therapeutic release by liposomes, dendrimers, smart polymers, and virus-based systems. Advantages of...
- Egon Willighagen
Despite the internet’s dynamic and collaborative nature, scientists continue to produce grant proposals, lab notebooks, data files, conclusions etc. that stay in static formats or are not published online and therefore not always easily accessible to the interested public. Because of limited adoption of tools that seamlessly integrate all aspects of a research project (conception, data generation, data evaluation, peer-reviewing and publishing of conclusions), much effort is later spent on reproducing or reformatting individual entities before they can be repurposed independently or as parts of articles.We propose that workflows – performed both individually and collaboratively – could potentially become more efficient if all steps of the research cycle were coherently represented online and the underlying data were formatted, annotated and licensed for reuse. Such a system would accelerate the process of taking projects from conception to publication stages and allow for continuous...
- Daniel Mietchen
Lawrence Souder presented on this at the SLA this week (analyzing Redfield's blog posts and related communication) - links to his screencast and slides through here http://ff.im/FUaus
- Jean-Claude Bradley
I'm aggregating a list of resources (not rants!) about evaluating research and research impact at: http://beyond-impact.ietherpad.com/11... Additions v welcome!
I remain of the view that there are also very large opportunities for publishers getting into this arena to mismanage the process catastrophically...but will be very interesting to see...
- Cameron Neylon
Just watched/listened to this. @Cameron, I would be interested if you could expand a bit on your comment. Some observations that are new from Pete's previous talks/slides. 1) In the advent of PLoS ONE receiving an IF in July 2010, in Q3 2010, 1500 publications and in Q2 2011, about 3400. That is a massive increase. 2) This (in turn) leads to a projected figure of > 22,000 publications for 2011
- Graham Steel
3) Projection (albeit based on some basic modelling) that by 2016, about 50% of STM Manuscripts will be published in OA Mega Journals. It will be interesting to see how this plays out over that projected time-frame. Good talk, Pete.
- Graham Steel
I wonder how much staff is needed to manage 22K submissions at a reasonable speed (obviously more than it is hired right now ;) ). PLoS is turning into Mega Publisher.
- Pawel Szczesny
Congratulations to the PLoS team but... would it not be prudent to shift the conversation from the large volume to the post-processing metrics ? I think at this point it is not worth keep pointing out that PLoS ONE is growing so much. I keep hearing from colleagues this idea of PLoS ONE as a "dumping ground" and people confusing the PLoS brand in general with PLoS ONE. Since PLoS is not...
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- Pedro Beltrao
Well, as you can imagine - it is on the list and we are working on these things as fast as possible! Unfortunately development takes time. In the meantime, part of the beauty of OA is that we dont have to build it all ourselves. We have our Search API and (very) soon an API for our ALM program. The combination of these 2 could be used by anyone to build the tools you are suggesting.
- Peter Binfield
I would've had two questions after the talk: 1. Now that PLoS as a whole has been sustainable since 2010, when will the subsidizing of the community journals by PLoS One authors stop? I don't have cash burning holes in my university pockets and I'd rather only pay for my next PLoS One paper and not for the paper of a PLoS Biology author. If I'm paying for PLoS Biology, I'd like to publish there as well, please.
- Björn Brembs
2. If the Mega-Journals become the new hype and (because?) people start to realize that container means nothing, why would people chose one journal over another (both for publishing and for reading)? Surely, the 'neuroscience' tag in PLoS One doesn't mean anything different than a 'Open Mega-Journal of Neuroscience'?
- Björn Brembs
@Graham, will add that to the list of blog posts that I need to write..Bjoern two reasons presumably. Price and services offered, which would be a step forward in my view beyond current obsession with journal brand.
- Cameron Neylon
lol @Cameron: that's what I'm currently writing a blog post on. From the description, services are identical (minus IF) as are prices. One more reason for PLoS to have 'realistic' pricing for PLoS One, IMHO!
- Björn Brembs
I'd rephrase Bjoern's q1 as: now that PLoS has proven that OA journals can play the Glamor Mag game, PLoS Bio/Med etc have served their pupose -- so when will they be rolled into PLoS ONE?
- Bill Hooker
Waiting to see some familiar names on the contest registrant list.
- Mr. Gunn
from Android
In terms of the OA Mega Journal, what about BMC? Current portfolio of 216 Journals. Would it make any sense or not to move some or all of these over to a "BMC ONE" type Mega Journal? @Egon see this rather cool Mendeley/PLoS mashup http://www.youtube.com/watch...
- Graham Steel