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Daniel Mietchen
Why I’m Not In The Mood To Celebrate Open Access Week - http://acrlog.org/2010...
"These ideas are worth reading and thinking about, but any new ideas for fixing the broken publishing system must take into account the disciplinary prestige factor." - Daniel Mietchen from Bookmarklet
Mr. Gunn
Peer review provides £209,976,000 public subsidy to commercial publishers - Boing Boing - http://www.boingboing.net/2010...
"The Open University's Martin Weller looks at the Peer Review Survey 2009's numbers on free participation by UK academics in the peer review process for commercial science journals and concludes that 10.4m hours spent on this amounts to a £209,976,000 subsidy from publicly funded universities to private, for-profit journals, who then charge small fortunes to the same institutions for access to the journals." - Mr. Gunn from Bookmarklet
I would still love to see a model where my reviewing work would get me credit for 1) a free submission; 2) a free OA (gold) publication. - Egon Willighagen
While I chose not to respond, the very first comment is one that always bothers me: The society publisher justifying high library subscription prices because those subscriptions pay for the rest of the society's budget. In times when libraries lack adequate funds, that's simply not an acceptable argument, but it sure does keep popping up. - Walt Crawford
I'm with Walt. If the society will die without the journal, then hurry up and die already. - Bill Hooker
The only OA journals that charge bunches of money to publish, far as I can tell, are in fields where there's bunches of public funding sloshing around. Why does it have to cost so much when so much is done for free and distribution online costs close to zero? (Even scientists with complex formulas and images do their own layout fer crying out loud!) I'd love to get a group of libraries... more... - barbara fister
"Why does it have to cost so much?" -- that's the question, innit? Of all the publishers out there, I think PLoS is probably the best guide to what it actually costs to compete in the current system, since they have an incentive to charge not the most the market will bear (like a for-profit does) but the least that they can make do with. Since I think the "prestige journal" concept... more... - Bill Hooker
I'm thinking of humanities journals published by small societies formed around the interest of a handful of like-minded scholars - which publish three or four issues/year, five or six articles per issue, unpaid editor and board; why should it take more than 2 FTE to run that baby? The U of MN press, which has 50+ books in its fall catalog and publishes six journals appears from its... more... - barbara fister
What I've seen of BePress looks pretty simple - not cheap for an annual subscription, but cheap if it meant it actually worked without a lot of effort. Haven't looked too closely, though. 'Cause then I'd just cry that we can't afford it. - barbara fister
Who cares about typesetting in an online publication? or by typesetting do you mean tagging the content in SGML fashion? (the author should be doing that anyway) - awd
Oh, I'm sure they know the difference between SGML and their elbows. - DJF
The author should be doing proper SGML? Interesting. Boy, am I glad I don't write scholarly articles... and I think Dorothea's right in general: Presentation at a level appropriate for scholarly papers isn't a gimme. (OK, so I rarely argue with Dorothea where production etc. are involved. Big surprise there.) - Walt Crawford
Specially Gruesome Markup Language? Sure, I can write that. - Bill Hooker
Considering I'm barely literate in the HTML subset of SGML, I'm not saying I expect the author to produce valid SGML, I'm saying in a SGML fashion (using Word (shudder) as an example: the title is labeled Title, section Headings are Header [n], etc etc. - awd
Dude, HTML isn't a subset of SGML. The only thing they have in common is all the annoying angle-brackets. - DJF
@DJF see what I mean? :) - awd
Speaking as an author who has relied on conversion peasants without even, at the time, knowing such folk existed -- D0r0th34's right. You'll never get authors to stick to even a simple layout that could be readily auto-converted into markup. So my question is, how much does care and feeding of a conversion peasant cost? The question at the end of that rainbow is, of course, how much of what publishers charge is necessary and how much is profit? - Bill Hooker
I would like see a comparison of the production costs of Nature, a commercial venture that sells advertising (probably at a very high rate considering its impact and the cost of the items being advertised to a specialised market), to the production costs of The Economist, a commercial venture that sells advertising (ditto), but also has to pay for all of the original content that it produces every week. - DJF
Another society journal, running on less than the PLoS ONE charges: http://www.biogeosciences.net/submiss... . Apparently sustainable - they (European Geosciences Union) continue to expand their portfolio. Also interesting is that the typesetting issue is factored into the pricing - this provides for an incentive to use TeX or at least to care about layout standards. - Daniel Mietchen
+1 DJF - it would be interesting to compare Nature with a similar outfit that has to pay for all its content. - Mr. Gunn
As far as the cost to run a small publishing house, would it make sense to add some money to pay people for their peer-review time as well? - Mr. Gunn
Let me ask the question in a different way: If you took all subscription fees in every library on this planet, how much of that money would be needed to sufficiently staff and equip each library to publish all the papers from their own institutions themselves? My guess is that the subscription costs would easily cover everything and then some, because libraries don't need to make a... more... - Björn Brembs
Doing journalism and publishing what might be the most prestigious science journal (I'm not sure about the various flavors of Nature, because I'm not familiar with them, but the mothership itself) are different, but in some ways not so much. A large part of Nature is staff-written news, opinion, commentary, both online and in print, and with a much higher frequency than most scholarly... more... - barbara fister
Thanks, Dorothea, for the under-the-hood look. It seems as if there should be a standard word processor for academics that does what it takes to make papers look good. (TeX works for scientists, but then ... they passed organic chem.) When I say "how hard is it, really?" I'm thinking of the smaller society journals, published infrequently, that turn to commercial publishers to manage... more... - barbara fister
As someone with, er, intimate knowledge of one particular humanist's interaction with technology, I can say anecdotally that Dorothea speaks truth. - Catherine Pellegrino
Yeah, but twenty years ago our college had a typing pool because some of the older faculty needed someone to type up their handwritten book manuscripts; typing wasn't part of their job. (Yes, I am ancient.) The tools will get easier and the faculty less afraid of them, and someday typesetting will as expected as coal scuttles and the maids it took to haul them away. I should start the legal process of changing my name to Pollyanna soon.... - barbara fister
*stands up and applauds* Dorothea, I love you. It goes without saying, of course, but after your comment, I had to say it. - Ordinarybug Heather
I think I'm not entirely sure what we are arguing about here. I'm willing to take Dorothea's word that typesetting is necessary to have a book or journal look professional and easy to read and so on. at the same time, I know how relatively easy it is to publish things electronically. So is the problem that easily-published journals and ebooks will lack authority and not gain acceptance due to their shoddy typesetting? - Steve Beeblebrox
Because if that is the case, I'd like to see us work the problem from both ends: try to raise the standard of quick-and-dirty typesetting by degrees while flooding the market with poorly-typeset stuff, thus degrading everyone's sensibilities and making the ugly and hard-to-read stuff more acceptable in the short run. - Steve Beeblebrox
So many traditional journals also offer crap typesetting that there's gotta be a niche there just RIPE for taking over... - Marianne
Sorry, pure ignorance on my part. I'm trying to learn. (You and Walt can probably go halfsies on a hitman for me.) I guess given that the most interesting stuff I read these days is not typeset, I am wondering what I'm missing. Then again, I have ranted about how ugly most e-books are because they all look alike, have no page design, and are are mass converted to look all alike. Then... more... - barbara fister
Without wading into an argument about whether humanities authors could/should handle markup languages (for the record I think if you've got a PhD in anything, well... markup isn't brain science or rocket surgery) -- the fact remains that at every OA journal I've seen, people who submit BEAUTIFULLY PRE-TYPESET docs in LaTeX STILL get charged as much as people who send crapulous Word docs. </rant> ... which is about the one thing about OA that still really bugs me, we do their work, they get paid - Andrew Clegg
Yes. That's the point, they send you a template, you produce a PDF that's basically print ready (apart from it has crop marks etc.) - Andrew Clegg
I reckon :-) I get on better with LaTeX than I do with any word processor I've met, but it stil takes longer... - Andrew Clegg
PS belated +1 for Egon's idea waaaay up there about getting a free pub. in exchange for your review - Andrew Clegg
@ Andrew - such differential charges were mentioned in the link I posted above (here again: http://www.biogeosciences.net/submiss... ). This is just one of multiple journals published by http://www.egu.eu/ that are handled in the same way. - Daniel Mietchen
Didn't spot that -- thanks. - Andrew Clegg from twhirl
@ D0r0th34 - a good example for excellent typesetting (in my view) of an OA book is at http://www.motionmountain.net/downloa... . All TeXed, complete with embedded videos. And even in terms of content, it is one of the best physics textbooks that I know. - Daniel Mietchen
Graham Steel
via Fb, 1st published Manuscript by Dr Bertalan Meskó is "Peripheral blood gene expression patterns discriminate among chronic inflammatory diseases and healthy controls and identify novel targets" and can be found in BMC Medical Genomics. Go Berci, go... #openaccess http://www.biomedcentral.com/1755-87...
Berci.jpg
Nice one, Berci. - Mr. Gunn
Thank you very much! - Berci Mesko, MD
Congratulations, @Berci :D - Andrew Spong
Graham Steel
Just finished making 10 ports. of egg fried rice and 4 pints of curry sauce. Time for beer #1 before getting into hardcore cooking mode.
frying-rice.jpg
AJCann
Ash and Lightning Above an Icelandic Volcano - http://apod.nasa.gov/apod...
Ash and Lightning Above an Icelandic Volcano
"Why did the recent volcanic eruption in Iceland create so much ash? Although the large ash plume was not unparalleled in its abundance, its location was particularly noticeable because it drifted across such well populated areas. The Eyjafjallajökull volcano in southern Iceland began erupting on March 20, with a second eruption starting under the center of small glacier on April 14. Neither eruption was unusually powerful. The second eruption, however, melted a large amount of glacial ice which then cooled and fragmented lava into gritty glass particles that were carried up with the rising volcanic plume. Pictured above two days ago, lightning bolts illuminate ash pouring out of the Eyjafjallajökull volcano." - AJCann from Bookmarklet
My beef with Iceland: this thing has gone up before, and you knew it would do it again, so that all the world would have to talk about it. Why then did you have to give it such an unspellable jawcracker of a name?! - Bill Hooker
Agreed, Bill. Eyjafjallajokul is one hellova jawcracker. Full deck:- http://en.wikipedia.org/wiki... That aside, this one is the wordl's first to have it's own twitter account:- http://twitter.com/Eyjafja... - Graham Steel
I can't believe it has its own Twitter account, although "I'm a lava, not a fighter" had me rolling with laughter - Benjamin Tseng
Jonathan Eisen
PLoS ONE is too fast: new paper from my lab (on a in vitro metagenomic simulation) is out, 2 days after last one - http://www.plosone.org/article...
Now you're just bragging. :-) - Bill Hooker
Bingo - Jonathan Eisen from iPhone
show off! :-) - Björn Brembs
More like PLoS ONE cannot catch up with you. A whole two days later? :) - Kubke
AJCann
Research Trends: Social networking in academia - http://www.info.scopus.com/researc...
Research Trends: Social networking in academia
"Interest in social networking as a research topic has also risen in recent years (see Figure). Since 2004, the annual growth of academic publications on the subject has surpassed 21%, but how has this scholarly interest matched actual social-networking interest among academics?" - AJCann from Bookmarklet
Same old same old. "Facebook for scientists" and no mention of friendfeed. - AJCann
Agreed, poor coverage and little community insights. Still, at least, they link to Crotty's blog post "Science and Web 2.0: Talking About Science vs. Doing Science" http://ff.im/fBJ7z - joergkurtwegner
BTW, I simply hate sites without commenting options, even if we know better, we cannot comment there ! - joergkurtwegner
Every site has a commenting option. It's called friendfeed. If content publishers don't want to take advantage of social tools, that's up to them. - AJCann
@AJCann - Still, I wrote them an eMail linking to this thread and offering "trend" corrections for their "trend" analysis. The point is we know FF, how many people reading their article do? - joergkurtwegner
I'm curious about the "recent survey of more than 3,000 researchers by a leading publishing house" mentioned. They cite Crotty's post, but it's not mentioned there. - Jason Priem
Pedro Beltrao
Papers for iPad : mekentosj.com : Software for Research - http://mekentosj.com/papers...
Papers for iPad : mekentosj.com : Software for Research
looks nice :) the main reason I would buy a tablet would be to read papers ... this is so far the best device for what I need. I wonder if I need a mac to sync a collection of papers to this app. Hope not. - Pedro Beltrao from Bookmarklet
Congratulations @mekentosj! Papers for iPad is one more reason to buy an iPad. Seems to work similar to the iPod/iPhone version, i.e. direct import and/or syncing with Mac. - Martin Fenner
First interesting app I've seen for the iUnicorn, nice work :) - Andrew Spong from Android
So I guess from what Martin says - you still need to have a Mac to manage your account. That's too bad. - Christina Pikas
Peter Binfield
PLoS ONE gets great review - 4 3/4 stars out of 5 - in the Charleston Advisor! http://everyone.plos.org/2010...
Thanks! We're really pleased :) - Peter Binfield
Also thanks for putting it up - had tried to get there before, but without luck. - Daniel Mietchen
Nils Reinton
Bill Hooker
Comments from respondents: "I'd also want really good stability, equivalent search, and archives from a paid FF clone." ($10); "Maybe not FriendFeed itself, but a similar service that I actually trusted? Would definitely pay a small fee." ($10); " It would need to improve, though!" ($50); "Even a $0.01 fee will stop people signing up." ($0) - Bill Hooker
I'm one of the $100 datapoints. - Bill Hooker
I was a $10 datapoint, but so much depends on the details. I could go higher, but it would have to be pretty damn cool to justify me spending $100 on it. - Mr. Gunn
Just noticed, there are two datapoints missing. Those are the totals Surveymonkey gave me, but they add up to 26 and it claims n = 28. - Bill Hooker
Bill, I'm also another one of of the $100 datapoints (although maybe I'm not since 2 datapoints are missing). - Graham Steel
Just wanted to clarify my $10 vote was based on friendfeed exactly as it is now, with search that goes back further into the archives, and with assured stability. I'd pay more for something more tailored to research and with more professional analytics features. - Mr. Gunn
The missing two datapoints are both $200 -- either I simply missed them the first time I looked, or they have just caught up between the counter and the analysis page. - Bill Hooker
So, $1030/28 approx = $37 per person if we let everyone pay what they think is fair. TLS has about 1300 users, so 1300 x 37 is around $48K per year. This is, of course, nonsense for many reasons, not least of which is n=28, but still. I'm getting the impression that we couldn't raise enough to roll our own, but maybe we could get buyin to an existing service? I'm not sure how that would... more... - Bill Hooker
This is just a hunch, but I figure that a much larger percentage of the non-respondents would be in the $0 camp due to increased likelihood of apathy about which services they use. Also, don't forget the non-TLS scientists, e.g. 878 subscribers to Science2.0 who don't completely overlap. - Matt Leifer
I agree about the apathy -- if they can't be arsed to respond they're not likely to be willing to pay! It's probably just silly to do calculations like mine up there without at least gathering a much larger sample. I can't bump the survey because that seems to have stopped working, so I'll post updates with links back to the OP every so often this week, and see just how many respondents we can get. - Bill Hooker
I would not pay - I think any charge would kill the participation to a level below critical mass for proper networking. I think we could find free hosted alternatives if necessary - Jean-Claude Bradley
This is the problem in a nutshell. Unfortunately, it takes money to support the service. ($100 datapoint) - Walter Jessen
I was one of the lazy buggers who didn't get around to answering - I'd be prepared to pay for some form of service but my suspicion is that a more imaginative business model is required. Some form of freemium or pay for privacy system might work. Other suggestions include paying for archive access or paying to make your archive available...but I'm not sold on any of these I have to... more... - Cameron Neylon
@Cameron I didn't think of this before, but your comment made me think of the Evernote business model. I think that could work quite well. The basic service would be free; additional features such as analytics and archiving would require a monthly or yearly fee. Article here: Using ‘Free’ to Turn a Profit: http://www.nytimes.com/2009... - Walter Jessen
I think if we want (master/PhD) students and post-docs involved (which I think we do), we should also consider institutional fees... - Egon Willighagen
@Egon, or "lab" fees (such as 10 licenses for substantial discount). I sort of lean towards agreeing with everyone (ha ha). It's worth more than $100 to me right now. But as Jean-Claude says, FF wouldn't be anywhere near as good as it is now if it had had a fee originally. A big grant (such as the NSF one OpenWetWare obtained) would be appropriate. But even those aren't stable enough. So, probably commercial or private foundation would seem best ownership. - Steve Koch
It's also worth somehow making a very clear presentation to facebook as to how valuable friendfeed is for scientists around the world. It's not impossible that they couldn't keep it running, perhaps in collaboration with scientists. I'd tolerate instrumentation-related and other ads around this site. - Steve Koch
Considering that social networks for scientists are often labeled "Facebook for scientists", I think asking Facebook directly to let this one turn into one that fits this description may have chances of success. And, as Steve points out, manufacturers of scientific instrumentation might well be willing to advertise in this space, thus providing a way to cover the operational costs. - Daniel Mietchen
I think Steve and Daniel are onto something there. How about a letter to Facebook making exactly that case? -- i.e. you have got something here that scientists are using and don't want to lose, that could grow into a real "Fb for scientists", and that we'd be willing to let you stick some advertising on; if you make a commitment to it we'll help spread the word. - Bill Hooker
So another concept that has been kicking around is the idea of a non-profit foundation that is supported by and integrated at some level with a range of commercial suppliers who build on an open source(ish) base to provide paid for services but where users could choose to run up their own installation(s) or if that's not appropriate use a hosted service. So Wordpress.com/org Apache or... more... - Cameron Neylon
I'm liking the sound of Cameron's idea much more than the idea of making a plea to Facebook. I worry about Facebook being so in bed with marketers and not respecting privacy. - Mr. Gunn
I hear you on the privacy concerns, MrG, and I also like Cameron's idea a lot. A whole lot. That non-profit could do other things besides run our FriendFeed replacement... - Bill Hooker
I worry about Facebook being curators of a site that is widely used by the science community. In the past, they have shown themselves to be purely driven by the profit motive, with concessions to users only being made under duress. If we were talking about Google then that would be one thing, but I don't think we'll hear a peep out of Zukerberg if we write to Facebook. - Matt Leifer
I worry about the Facebook/google approach in two ways. One is that in such a big pond you'd only ever get a small voice. The other is the risk of disappearing under the need to make money as Matt mentions. Something that can leverage the high quality work done and vast resources committed to consumer services but that balances that against the need for researchers to have a strong (but not necessarily the only!) voice would be the aim or whatever we can put together. - Cameron Neylon
I agree with your comments, Matt and Cameron, but still think it may be good to contact them and point out that there is a sizable community of researchers who would like to run (and improve) their own installation of Friendfeed and whether they could (a) make it open source entirely (don't think they will, but asking is probably OK) or (b) give the code to a scientific institution -... more... - Daniel Mietchen
Agreed. Worst case is there's no response. - Walter Jessen
My experience with getting site sponsors is that biotech companies do not like to sponsor sites unless they have significant reach. I'm only now starting to get people interested in advertising on LabSpaces. I don't know what kind of support you're looking for from instrument companies, but my pleas for $100 a month to host on a dedicated server and support a minor ad budget were turned... more... - Brian Krueger - LabSpaces
Brian, that's very useful feedback, thanks. - Bill Hooker
I agree site sponsors or advertising isn't either going to pay enough nor be reliable enough to give people confidence. I would certainly agree if the question to Facebook/Friendfeed is "would you give us the/some source code and if so under what circumstances" - I'd be happy with the code as it was prior to the UI change even - I can think of a few ways it might be possible to get it hosted - few different organizations probably under different conditions. - Cameron Neylon
I also wonder how much money you'd need from the get-go. My site is hosted on a $10 a month virtual host box and although they say its unlimited bandwidth it can only handle 30 simultaneous connections. Bandwidth has only ever been a problem for me when the site gets hammered by Reddit, Fark, et al. So at the outset, you guys could definitely run this off of a small budget, assuming... more... - Brian Krueger - LabSpaces
Its the setup and maintenance costs (I'm kind of assuming this is a full time job for one person at minimum) that are the big issues. - Cameron Neylon
@Cameron, what kind of maintenance are you expecting? Once the site reaches critical mass, then maybe it will require constant attention, but if it stays on the sub 1000 users level I don't think it would be a huge effort. I maintain my site all by myself. It takes an hour every morning before work and an hour every night to set-up the news queue and clean up the spam. Most of the... more... - Brian Krueger - LabSpaces
Would US$50k do for a start? http://ff.im/gXoNX - Daniel Mietchen
That's a fantastic offer, Brian. I guess we should check into that. - Mr. Gunn
I thought I would just mention that AOL has a friendfeed like service at http://lifestream.aol.com I don't think it has been mentioned yet in our "what to do if friendfeed implodes discussions". It's pretty similar to Google Buzz in that it allows you to import from a limited number of services and doesn't support anything like groups/rooms yet. Still, playing with it for a while I found it to be a better user experience than Buzz, so it is another one worth watching. - Matt Leifer
It's hard to take anything.aol.com seriously - Mr. Gunn
I know, but post Time-Warner, AOL actually has one or two good sites, e.g. http://spinner.com. Most of their successes are not branded AOL for obvious reasons. - Matt Leifer
Bumping this as a reminder that two weeks are left to put in a proposal for US$50k on an Open Friendfeed, see http://ff.im/gXoNX . - Daniel Mietchen
@Brian -- how about that $50K? Would that buy six months of your time, plus trimmings, to set up and maintain an Open Friendfeed? If so, I think the proposal could be put together on that basis: we have someone willing to be Benevolent Dictator for the coding and do the maintenance, we have X users who want this NOW, we think it's worth doing to get FF out of the hands of the for-profits and into the hands of the user community... - Bill Hooker
That would be more than enough money to run the site for a couple of years. I can probably use a lot of the labspaces backend for authentication, so it shouldn't take more than a week or two of coding to get off of the ground. Let me know if you need help writing the proposal! - Brian Krueger - LabSpaces
Actually, it looks as though they require institutional backing. Also, I registered for the site but cannot find any mechanism for submitting an application -- the "apply" links all take you to the privacy statement. - Bill Hooker
Bill, I had reported that problem a while ago and it appears to have been fixed. I am stuck at a different step - getting a Grant ID - because the form would not accept any phone number I entered. The likelihood of small bugs like these seems to be one of the reasons why they start out small, and I consider it a Beta anyway, as long as the review process is not open. - Daniel Mietchen
Update on the fineprint: It's basically like the usual NIH grant application. Specifically, affiliation with a US institution is required (any volunteers?), and so is agreement with a "no indirect cost" stipulation once an award is being made. More via https://apply.fundscience.org/user_ap... . - Daniel Mietchen
That same FAQ page, however, also states a severe thematic restriction: "we encourage doctoral students to apply for FundScience support of projects pursuing hypotheses related to the pathogenesis or modeling of diseases including Crohns and Familial Mediterranean Fever, and diseases predominantly affecting the developing world." Bye-bye, FF clone? - Daniel Mietchen
Daniel - yes I ran into the same problem - Jean-Claude Bradley
We could probably work around the institutional affiliation part, but given the disease focus my feeling is that they would not be interested in funding a FF clone. - Bill Hooker
OK, so we will have to say good bye on this one. Another option for a grant is at http://ff.im/hGFHZ - Europe and Global Challenges - and I think we could give the transition to open science a try. Funds up to Euro 1M are possible, so the FF clone may fit in as part of a broader concept. - Daniel Mietchen
Mr. Gunn
Science in the Open » Blog Archive » “Friendfeeds for Science” pt II – Design ideas for a research focussed aggregator - http://cameronneylon.net/default...
"One thing that really annoys me is seeing an interesting title and a friendly avatar on Friendfeed and clicking through to find something written by someone else. Not because I don’t want to read something written by someone else, but because my decision to click through was based on assumptions about who the author was." - Mr. Gunn from Bookmarklet
When I click, whether or not the post was authored by the poster, I'm clicking based on the reputation of the poster, and also of the author, if it's apparent. What annoys me is clicking through to find a post on a site like Digg, that further references another site. I haven't tried it out yet, but apparently Cliqset can pull in comments on a blog as comments on the item in Cliqset, so maybe it could pull in post author as well? - Mr. Gunn
Presumably if things are marked up properly with reasonably standard RSS or Atom tags (or even better dublin core) it shouldn't be too hard to capture this information. I'd be less fussed about trying to disambiguate in the short term. But yes, you click through based on presumed context and I don't think any service is really getting that right yet - and I think right for researchers... more... - Cameron Neylon
Incidentally if the above link breaks (my fault for tagging it wrong) then this is the right one: http://cameronneylon.net/blog... - Cameron Neylon
agreed, the service icons issue was what really kicked off the whole train of thought for me. And distinguishing between Flickr posts and Flickr favourites seems to me like something that is important - and perhaps more so for researchers. - Cameron Neylon
Yeah, that was my issue with the service icons too. All a service would need to do is capture the post author when it aggregated an item, but if the intervening site in the case of a favorite didn't capture that, then it would be harder. - Mr. Gunn
Sounds like cliqset is starting to gain momentum as the front-runner alternative to FriendFeed. - Michael Barton
I think they're among the best, but there remain some issues, and none meet the ideal from Cameron's latest post. Buzz would have been my pick due to the built-in network, but since the developer of Cliqset has already joined the discussion it seems like they are probably going to be more responsive. I don't see the Buzz developers joining this thread anytime soon. The third best... more... - Mr. Gunn
Cliqset is absolutely out of the running as far as I can see, but as MrGunn notes, that conversation is in this thread: http://friendfeed.com/neilfws.... - Bill Hooker
Bill, I think nothing is available that works for us right now, so I'm just trying to think of the shortest route to getting there when the time comes. In my shortlist of "least crappy" services I have Buzz and Cliqset, but I realize that either or both of them might not realize their potential and become what we need by the time we need it. Writing our own might be the best, given we can find the resources as a group and also assuming it doesn't turn out to be way harder than we think. - Mr. Gunn
Have been trying to think whether there might be a funding scheme that could help to kickstart something but drawing a blank. Also just has the potential to leave us where we started...with np business model - Cameron Neylon from Android
It may be worth drawing up a business plan and presenting it to facebook via blogs from the most eloquent of us (that wouldn't include me, except as an endorsee). Related to other threads around here, many of us are willing to pay for what we have now, but many aren't. Perhaps we could patch together some "donations," which would prove that we're serious. Then we could present Facebook... more... - Steve Koch
Particularly since we're people in pursuit of making science better, it would be good PR for Facebook at a minimum. - Steve Koch
A proper business plan would be a really valuable thing...I need to look into that for something related anyway so I could try to make that available (might be difficult because it would be done by out tech transfer people and they might object to making to it freely available) - Cameron Neylon
I think there is a business model here. Have a 'open and free' platform for 90 days of postings/comments and thereafter the comments/post are archived. This is valuable information, so academic libraries could subscribe to this database? It's something I have been thinking about for a while. Imagine a freemium model of F1000 for instance... - Chris Leonard
@Chris: not sure I'm following. Do you mean a model where after 90 days everything gets locked up behind a paywall? - Bill Hooker
I think that's essentially the idea - although a micropayments approach would be an alternative or an author pays model for archiving and availability - but if its a diverse model then you can't rely on availability which doesn't really fit with the open aspects... - Cameron Neylon
@Bill: Yes. As a pragmatic approach to getting payment for a service, this is what I suggest (in clearer terms). 1 - All posts with no comments are archived behind a paywall after 90 days. 2 - All posts with comments are archived 90 days after last comment. 3 - Archived posts are only available to those with a subscription, probably through an academic institute. Now, I acknowledge this... more... - Chris Leonard
Speaking as a non-scientist and pseudo-librarian, I'm guessing that getting academic libraries to subscribe to/pay for a formalized version of gray literature, basically a forum, is going to be a very tough sell. - Walt Crawford
Just brainstorming here, but what about other organizations or non-profits such as Science Commons (http://sciencecommons.org/), the Open Knowledge Foundation (http://www.okfn.org/) or OpenWetWare (http://openwetware.org/)? - Walter Jessen
@Chris, I'm unlikely to participate in a "public" forum which then takes my comments, intended for the public domain in case they are ever useful to anyone, and locks them away behind a paywall. I suspect many here would feel similarly. - Bill Hooker
I agree that I'm uneasy with comments going behind a paywall - but arguably a pay for archiving "or take responsibility for it yourself" might work - in a sense subscription vs pay for storage is not so different. Walter - I could imagine folding a project like this into OpenWetWare, I don't think Science Commons or OKF have the interest or the resources to support something like this... more... - Cameron Neylon
Jonathan Eisen
European research funders support UK open access repository | Wellcome Trust - http://www.wellcome.ac.uk/News...
Chris Miller
Ask Metafilter: I would like to see examples of simple, well-designed websites run by individual scientists. http://ask.metafilter.com/146115...
"Remember those semi-personal, semi-professional scientitific pages which were once prolific on university servers? They're usually maintained by one person and filled with photos and descriptions of their experiments, equipment, idle tinkering and occasionally their personal hobbies. The scientist might be available for hire as a consultant, but the website's primary purpose is as a reference resource ("You'll find the specs for that on my website...") and as a general record of one person's adventures in science." Many of these sites have interesting content but are a visual and structural mess. I'd like to see some counter-examples, where simple, clean design supports the content and makes the site a joy to use. I'm not really looking for regularly updated blogs or sites which host science journalism." - Chris Miller
Feel free to leave responses here and I'll shuttle them back into that thread. - Chris Miller
Piotr Rotkiewicz' site http://www.pirx.com/ - Deepak Singh
The always wonderful Love Lab Page http://www.lovelab.id.ucsb.edu/ - Andrew Thaler
Egon Willighagen
Poll: are you educating students, and teaching and/or requiring them to use one of the Web2.0 media, like blogs, etc, to report about their work? If so, please respond, so that we can do some rough statistics...
Trying - find some strong resistance and the occasional enthusiastic adopter. I don't push it very strongly or "force" people to do it - Cameron Neylon
no students to educate :) But when I did have them,, I encouraged the use of blogs as info sources - Rajarshi Guha
At Cambridge Uni they require you to use a lab notebook, and that is and remains uni property... I think requiring students to keep a lab notebook is not a bad thing... now, since my field is already electronic anyway, an electronic notebook is easier to 'expect' ... - Egon Willighagen
Oh yes, I do enforce an electronic and open lab notebook - but I struggle to get people to use it effectively and there is real reticence to put actual data there (but happy with graphs for some reason - I really don't get that) - Cameron Neylon
Don't require it, but encourage tendencies in this direction, and try to counter the misinformation and scorn I hear on a regular basis in group meetings etc. re blogs, at least. No one has ever wanted to try to use the open lab notebook aside from me. - Heather
Yes, we use Blackboard (www.blackboard.com) for most if not all courses in the graduate school. - John Hogenesch
I suggested it quite often but was turned down because the sources could not be trusted in my teachers opinion... - Joost Plattel
For undergraduate physics majors, we're doing Open Notebook Science on OpenWetWare. http://openwetware.org/wiki... They're "required" to do this, I guess, but nobody's protested yet. For undergraduates and graduates in our research (not teaching) lab, we're also doing ONS on OWW. This isn't required (decision is up to the student), but so far all have opted for it. - Steve Koch
"so far all have opted for it" -- it makes my day every time you or one of your students leaves a comment like that, Steve. :-) - Bill Hooker
Glad to hear Bill -- their boldness and commitment to science makes me really happy too. Plus, all the positive feedback they get from you and others makes _their_ days! - Steve Koch
I am a student in a class that requires keeping a journal (reflections about teaching) and we are encouraged to use a blog - Kubke
Not much 2.0 here. I'm preparing some lectures on 2.0 tools, but these are for PhD students not for undergrads. Next academic year might bring a major reboot - if not to integrate, I hope to start separate "Science 2.0" course. - Pawel Szczesny
Björn Brembs
Martin White: Sample Cover Letter - http://astro.berkeley.edu/~mwhite...
"Enclosed is our latest version of Ms # 85-02-22-RRRRR, that is, the re-re-re-revised revision of our paper. Choke on it. We have again rewritten the entire manuscript from start to finish. We even changed the goddamn running head! Hopefully we have suffered enough by now to satisfy even you and your bloodthirsty reviewers." - Björn Brembs from Bookmarklet
That's coming in very handy. Just as I am about to submit my third revision... - Victor / Mendeley Team
Martin Fenner
Andrew Perry
Sweet .. syncing my Dropbox on the new laptop - it's found my desktop on the LAN and is downloading directly from there !
Mr. Gunn
Slashdot Science Story | Call For Scientific Research Code To Be Released - http://science.slashdot.org/story...
Slashdot Science Story | Call For Scientific Research Code To Be Released
""Professor Ince, writing in the Guardian, has issued a call for scientists to make the code they use in the course of their research publicly available. He focuses specifically on the topical controversies in climate science, and concludes with the view that researchers who are able but unwilling to release programs they use should not be regarded as scientists." - Mr. Gunn from Bookmarklet
That all sounds good, but can anyone parse the following? "For example, interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran, and one in every 37 interfaces in the language C. This is hugely worrying when you realise that just one error — just one — will usually invalidate a computer program. " - Mr. Gunn
are differences in module interfaces really prejudicial to results? Sounds kinda like BS on the face of it, to this non-expert. - Mr. Gunn
Haven't read the research by the Kent prof yet, but I think what is meant is that API inconsistencies result in incorrect use of the API, which in turn means that incorrect assumptions will be made. And that, in turn, means that data is incorrectly processed, resulting to incorrect conclusions... I can confirm that to be the case in (the use of) the CDK too... - Egon Willighagen
I think what might be meant is inconsistent typing. So if we one function returning double precision value, that is then sent to a function taking an integer*4 (this is for Fortran), you will loose precision and hence downstream your results may be quite incorrect. Similarly for C, when one might pass a long to a function taking a double. So yes, inconsistent interfaces/type definitions could lead to wrong results. (This may not apply to other languages that will automaticaly coerce data types) - Rajarshi Guha
The cited research is, however, 13 years old! And a chem- and bioinformatics software projects have very much improved since then... so, those statistics are outdated... - Egon Willighagen
Hey, 13 year old Fortran code is brand new :) - Rajarshi Guha
@Rajarshi: the paper discusses two issues... one actually focuses in the API use (but concludes that a requirement for .h files in C++ is not the answer), while the second experiment focuses on error propagation... here integer/double conversion certainly do not help, but it seems to also look at the number of computations, where randomness due for precision just adds up... causing single digit precision at the end of the calculation... - Egon Willighagen
Of course, I should have read the paper :) - Rajarshi Guha
Same here :) I think we both had half right :) - Egon Willighagen
OK, I get that part, but does it make any sense then to compare error rates *among languages* as if that's somehow relevant to the argument? "It's programmed in Fortran so therefore it's 37/7 times more likely to be an invalid program?" - Mr. Gunn
In one sense no - given that you can write bad code in any language. But at the same time, certain languages provide better support for correct programming in various ways. A simple example is C - where you can peacefully go beyond the end of an array and you may or may not get an crash and Java, where if you beyond of an array your program will stop with a specific error message. So I... more... - Rajarshi Guha
But it makes no sense whatsoever to discount any arbitrary piece of code, sight unseen, just because of the language it was written in, and it still seems nonsensical to try to compare "error rates" between languages. Surely the quality of the code far exceeds any predisposition the language might lend to making an error! - Mr. Gunn
Yeah, that is a bit of a stretch. Yes certain languages are more error prone, but I think scientific code is bad cause most (especially back in the day) scientists were terrible programmers. - Deepak Singh
@Mr Gunn, yes, that'd be pretty wrong to discount code based on language. Is that what the article said? (I really should read it!) - Rajarshi Guha
LOL @ Neil Yeah, I don't get it. Of course, the main message was the good part, but this is why scientists have a hard time making themselves heard and understood. This also might be why we can't have nice things, such as being understood. At any rate, the main idea, that open peer review, which depends on open access, is a "Good Thing" remains. - Mr. Gunn
Alexey
LOL god: Too stupid to understand science? Try religion. - http://lolgod.blogspot.com/2010...
LOL god: Too stupid to understand science? Try religion.
ehh, gotta say I'd not-like this if I could. I know plenty of smart people (scientists even) who happen to be religious, and plenty of stupid scientists. And I'd forgive the generalization if the rest of it were funny or insightful, but frankly it's not. my two cents... - Andrew Su
indeed about 50% scientists are religious, but I think they should take a joke. If they will draw funny cartoon about non-religious scientists I'd appreciate - Alexey
Love it! Hilarious :-) But may indeed not work both ways ... - Björn Brembs
http://ff.im/fIv4S It is not funny at all, Alexey. This picture insult us. Made this joke in Russia and you will be in the prison. - Denis Stankov
"If your brain is too small to hold two thoughts in it at the same time, try being a non-religious scientist." Alexey, you will appreciate this. (I can see the cartoon in my mind's eye, but would rather not spend time drawing it to insult all non-religious scientists just because one of them insulted me and claims he will find this funny.) - Ruchira S. Datta
I recall someone once said that the human mind is not limited in its capacity to hold mutually exclusive opinions. :-) - Björn Brembs
I'm with Andrew. I myself don't quite see how a religious worldview is compatible with being a scientist by trade, but then I don't really understand QED either. And I'm not the dumbest scientist I know. The argument I always get back is that "those religious types" are trying to shove their beliefs down our throats etc etc. I get why that's a bad thing; I don't get why doing it back is a good thing, or how this kind of sneering is supposed to solve the religious expansionism problem. - Bill Hooker
You're going to have to explain that "mutually exclusive" bit to me very slowly and clearly, Björn. After all, I'm stupid. Oh, and I'd appreciate it if your explanation applies to my specific religion. Since the cartoon generalizes across all religion, that should not be a problem for you. - Ruchira S. Datta
@Ruchira, I even didn't think that simple sharing picture about science-religion could insult someone. I think if author of this cartoon aimed to poke religious people, it could be insulting for some of them. When i was sharing this i didn't aim to poke and insult religious people. If it happened, probably I was wrong when was sharing it here. Well, you made me think. - Alexey
Okay thanks Alexey. - Ruchira S. Datta
I'm so happy that Alexey was changed today. - Denis Stankov
@ruchira: the quote means that the people you mentioned don't exist as we all can hold two thoughts at the same time - some even mutually exclusive ones. - Björn Brembs from iPhone
All right, Björn, I will spell out my cartoon for you. On the left there is a smiling person with a large brain. The brain is visible inside the large forehead of the person. Inside the brain are written the words "Religion" and "Science". They fit there. On the right there is a person with a small brain visible. Inside it is written the word "Science". The person is frowning and trying... more... - Ruchira S. Datta
this would be funny as wel :) it's just a cartoon - Rajarshi Guha
Now Ruchira's cartoon I would like. Yeah, potentially offensive, but to me it's a new and interesting take on some aspect of society. Thought provoking, biting social commentary... But I find the cartoon above neither funny nor new, and in the absence of either, then I think Bill's label of "sneering" is pretty spot on. - Andrew Su
@Ruchira: lol :-) No need to explain it to me, I'm not the one who's not getting it, dude - calm down, breathe and think a little before you write. You're getting the whole story the wrong way around. And please don't embarrass yourself more by asking me to explain it to you, I would do it. :-) No offense! - Björn Brembs
For the record, I don't like Ruchira's cartoon any better. I understand that R felt provoked, but I'm sure the author of the first cartoon was responding to some perceived trespass as well. "He started it" hasn't really worked for me since I was about four years old. - Bill Hooker
So, funny! - Mary Spiro
Wait I especially love the orbital versus the halo, nice touch! - Mary Spiro
Mary Canady
Would love to have feedback from the experts here! I did a quick survey of the traffic to social applications for scientists: Are Any Social Networks for Life Scientists Gaining Traction? | Biotechnology and Life Science Marketing Consulting: Comprendia - http://comprendia.com/2010...
Would love to have feedback from the experts here! I did a quick survey of the traffic to social applications for scientists: Are Any Social Networks for Life Scientists Gaining Traction? | Biotechnology and Life Science Marketing Consulting: Comprendia
One thing that wasn't clear to me was the rationale for excluding Mendeley - you say its a desktop app but it is also a social web service. I agree it would be difficult to separate the two out and do a fair comparison with other pure web sevices but the comparison would still be interesting - is there less web traffic as a result or does the desktop app drive more web traffic. The other really interesting thing to know would be stickiness and clickthroughs but I guess this isn't accessible info? - Cameron Neylon
Friendfeed didn't make it? - Björn Brembs
and what about Chemical blogspace, with about 1000 unique visitors per month over the past two years... bit targeted scope, but the counts are the more impressive... - Egon Willighagen
Nice overview, and are visits alone a good metric (aka click-stream)? - joergkurtwegner
Cross-posted in the other thread... My two cents: Based on our experience, compete.com (and the others, like alexa.com, quantcast.com) traffic data is wildly off the mark - simply because their sample demographic is not representative of our audience at all, and has a huge margin of error especially for smaller sites. I find that a good way of tracking relative buzz of services compared to each other is to check www.topsy.com for how many people twitter about it. - Victor / Mendeley Team
I like how you have discussed Biomedexperts and I am happy to see it on the top of the list regardless of the quality of visitor metrics. I hope Biomedexperts is gaining traction, it's the only social-web tool I have found useful apart from friendfeed (and twitter I guess). - Nils Reinton
THX, and funny that 3 of us are all working on something similar ;) Yes, compete.com is likely inaccurate, but before this I really had no idea about the hype vs. actual popularity. Also, @Cameron I think the only people who will know clickthroughs will be the owners of the sites (for now?). I didn't know Mendeley was a social app (sorry @mrgunn) but since this is not its primary focus, wouldn't the numbers be misleading? @Bjorn friendfeed was excluded b/c you can't get subdomain, etc. info from Compete. - Mary Canady
p.s. I think topsy's a good idea, and it would be cool if someone could mine Delicious and some sort of inlink analyzer (I use http://ericmiraglia.com/inlink... but it's buggy) and add those values to the uber spreadsheet started by Anne Pajon/referenced earlier: http://bit.ly/abwT8l Should we start a Goog site to collaborate? - Mary Canady
p.p.s sorry for the spam. a nice way to get the 'buzz' about a set of sites is to sign up for a free hubspot account, and add all the sites as competitors. You'll get the number of delicious links and other info, and some of it is downloadable, I believe--I'd do it, but I already used my 7 day trial--anyone want to take on? - Mary Canady
delicious bookmarks can be misleading too. For example, we (CiteULike) have added an automatic sync-to-delicious which might add a significant bias. I think one mustn't confuse "buzz" with "use". - Fergus Gallagher
Thanks for this post Mary. I'm pretty sure that biomedexperts is the biggest of these sites in traffic terms. Another good place to get traffic data on various sites is adplanner.google.com . It's reasonably accurate in my experience. (I'm with citeulike). - Kevin Emamy
No worries, Mary. I haven't been talking about the social features of the software much because they haven't been the strongest features. As you know, I'm a proponent of letting the social features grow around the existing uses of the content - sort letting the latent networks emerge, rather than trying to put that up-front, much as Flickr and Citeulike have also done. - Mr. Gunn
One thing I've noticed over the past year working with the Mendeley community is that traditional metrics derived from advertising (impressions, page views, etc) really fail when it comes to social media. Not only do they fail because of all the different ways of sharing links, but more fundamentally because all traffic is not created equal. As others here have said, a click on... more... - Mr. Gunn
Looking at usage numbers over time might be even more interesting than absolute numbers. Some of the sites you mention haven't seen much growth recently. - Martin Fenner
I agree with Victor that these stats have huge margins of error. For example, I just put your top 5 into alexa.com, and the order changed quite a bit: http://ff.im/fQorv . - Daniel Mietchen
Didn't anyone notice that I said 'quick and dirty'? ;) This analysis is meant only to get a rough idea and to stimulate discussion. I think that a more complete picture could be gleaned from all the ways we have to monitor, and @mrgunn great idea I may do a survey...stay tuned...I'm already paying for surveymonkey this month anyway... - Mary Canady
I don't think an online survey is meaningful to gauge the relative use of different apps - the (self-) selection bias will be massively skewed (by poll hacking, for example, or PR/marketing). Just think about how pointless a "Do you prefer Windows or Mac?" poll would be. Since I assume you can't afford a properly randomized study, I would think page-views and similar are your best metrics, even given their limitations. - Fergus Gallagher
measuring trends is a great way of describing current usage and make predictions about future directions - Mike Chelen
Open Knowledge Foundation
Interested in making an open data catalogue? Virtual meeting on 11th February 2010 - http://blog.okfn.org/2010...
Bill Hooker
Doctoral student and OAD (http://oad.simmons.edu/oadwiki...) asst editor Nancy Pontika is studying copyright negotiations between authors and journals; if you are an author who has been through this, she'd like to talk to you. (Edit: her email is in comment #2 below.)
(via the BOAI Forum) - Bill Hooker
You can read a little bit more information about this study in the OAD list "Research in Progress" http://oad.simmons.edu/oadwiki.... You can email me directly @ pontika.nancy@gmail.com - Nancy Pontika
Matthew Todd
Open-source science takes on neglected disease : Nature News - http://www.nature.com/news...
Our open chemistry project featured. - Matthew Todd from Bookmarklet
@Matt, great article. I'm curious - how do you think a free, peer-reviewed question and answer site like Chempedia Lab (http://lab.chempedia.com) could fit into your project? If you haven't thought about it, I encourage you and your student to try posing your toughest experimental question and see for yourself. - Rich Apodaca
Rich - I like what you've done, and this is a useful resource. I joined a while back but realised I had no 'credits' so couldn't do much. Any way of giving people more of a running start? The other thing is that for experimental wet lab sciences we need more multimedia capability. I'm thinking initially of attaching picture files to answers, or maybe .dx files for NMR spectra. Can we attach things to comments (not just initial posts)? - Matthew Todd
It certainly would be helpful to be able to view JCAMP-DX files - Jean-Claude Bradley
Graham Steel
2009 Science Commons Symposium Image - http://steelgraham.posterous.com/2009-sc...
2009 Science Commons Symposium Image
Posted via email from Graham's posterous - Graham Steel from Posterous
Christopher Harris
am in the middle of a long and occasionally expensive mission to obtain permission to use copyrighted figures from a number of neuroscience journals. am I right in assuming no permission requests are necessary for using PLoS figures? if so, lesson learned.
yup they both use Creative Commons Attribution licenses, which allow share & remix with the only requirement being attribution http://creativecommons.org/license... - Mike Chelen
Daniel Mietchen
Just got this reply to a reprint request: "If I provide you a copy of my article, I will be in breach of my contract with the publisher so I am afraid you will have to get it directly from the publisher or the journal's website."
Publisher #FAIL - Graham Steel
Amazing! How would the publisher know? Or the author gets paid for each download! - JJ
Ugh. Which publisher is this? Is the author sure the contract is that draconian? - Bill Hooker
The journal is at http://www.informaworld.com/smpp... . If I enter their ISSN (1753-8165) into http://www.sherpa.ac.uk/romeo... , the policies look more or less normal, though sending out eprints is not explicitly mentioned. - Daniel Mietchen
It looks like I have access... If you're still interested in that paper, I haven't signed anything with the publisher... - JJ
I'm thinking that this may be more a case of the researcher not knowing their rights. Have they handled reprint requests before? - Mr. Gunn
Thanks, Neil - I sent him that link ( http://bit.ly/drkdjJ ) and hope he will reconsider. Ad JJ: Thanks, will get back to you if he doesn't send the file. - Daniel Mietchen
Similar one I got "Thank you for your interest in our work but I am very sorry, I don't control the pdf. The pdf is owned by the publisher and must be acquired through them." This one is from Biophysical Journal. - Ignacio Sanchez
I think the authors are not informed properly and react with closing down. Honestly, even if authors have a limited number of "author version", do they not all have some? - joergkurtwegner
Case example. In 2007, I was in close correspondence with the author of this Manuscript http://www.cda.org/library... Prior to release, the California Dental Association (CDA) finally provided us both (at a large push) with access to the PDF, but we were only allowed to share this with ONE researcher in the field - WTF?? The author and I were sent about 30 reprints each instead and we challenged the CDA on the lack of open access issue. - Graham Steel
I then had this letter http://www.cda.org/page... published on the CDA website and in an unrelated development a few months later as I blogged about here http://mcblawg.blogspot.com/2007... (note the comment from the Editor-in-Chief of the CDA himself) the Journal decided to move to OA. Publisher #PASS Ordering dead tree reprints these days is simply a Publisher cash cow, and this experience was very much a real eye-opener. - Graham Steel
No further reaction from the author, but meanwhile I got the file (thanks to the sender!). - Daniel Mietchen
Bill Hooker
FEATURE: Interview With Stevan Harnad - http://www.infotoday.com/IT...
Nothing new for those who are already familiar with the Original Archivangelist, but a good primer for anyone wondering "who is this Harnad fellow I keep hearing about?" - Bill Hooker from Bookmarklet
Thanks for saving me the clicks, Bill ;-) - Mr. Gunn
Bora Zivkovic
If you have a picture of yourself wearing stuff from the #PLoS Store, let me know...
I assume you mean anyone except me - since that is pretty much the only pictures I have of me - Jonathan Eisen
Correct ;-) - Bora Zivkovic
We also sell mouse mats Jonathan... :) - Peter Binfield
Kate Porter
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