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Science 2.0: Lin posted a message
“I have some questions:Why should we stick with Blog and Wiki?Are they really good enough?Can they really work well?”
Sunday at 8:46 am - Link
Who says we should "stick" to blogs? Wiki and blogs are only parts of Web 2.0 - Ahmet Yükseltürk
experiment and use whatever works - Jean-Claude Bradley
That's the beauty of these kind of technologies. They're cheap & easy, and therefore concerns about sticking with them are lessened. With less investment upfront, if you are unhappy with results, you can try something else and not worry about lost time/effort/money. - andrew colgoni
"Failure for free", is how Clay Shirky describes it. - Neil Saunders
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The Life Scientists: Jere posted a link
yesterday at 7:08 am - via Reshare - Link
Possible, maybe - but limited by the willingness of hospitals to share. - Jere
These guys are all about using aggregating publicly available data sets to achieve better results (or new discoveries) than any one of them alone could. Pretty cool stuff. Disclaimer: they're in my department ;-) - Shirley Wu
nice initial sample size: "Quantitative clinical laboratory data, consisting of 1,104,316 measurements across 656 distinct lab tests. In total, this data represented 4,844 patients across all ages that were diagnosed with one or more of a set of 12 chronic diseases... - Attila Csordas
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Science 2.0: Bora Zivkovic posted a link
yesterday at 4:28 pm - via Reshare - Link
Oh man, people are still quoting those old 3QD essays. I have *got* to get that content onto a wiki so that it can be updated! - Bill Hooker
Because you put it best, for ever. - Bora Zivkovic
I find the effortless interchangeability of open-access and peer-review models in the text rather confusing if not misleading - without even going into the pros and cons of subscription-based / open-access publishing on the one side and peer-review/preprint models on the other. - Joerg
I agree. Open Access (OA) has nothing to do with changing/reforming existing peer review models or whatever. Just about the last thing OA needs is a reputation of "doing away with (journal) peer review". - Wobbler
Is the whole article that one page? (I could not see any more). Incredibly superficial, for example does not mention the fact that ArXiv has an indexing system. - Maxine
Good post at Back Reaction about this article and peer review in general.http://backreaction.blogspot.c... - Maxine
That reminds me, perhaps we do need a formal term for making manuscripts publicly available for peers to peer review and "traditional" journal peer reviews that reveal the identities of the peer reviewers. As of right now, "open peer review" refers to the latter and not the former. Might be confusing to use that term for both. - Wobbler
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Pawel Szczesny posted a message on Twitter
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Science 2.0: Eva posted a message
“This is more about teaching than science: I'm looking at some notes I took during a teaching course last year, and I wrote down this: "Lectures online: have been cases of student selling it to publishers as their own work." Is that a valid argument against putting things online? [more in comments]”
23 hours ago - Link
If you put lectures online, and someone then steals it to get it published somehow, isn't the fact that you already had it online *proof* that it was not theirs? Isn't it more dangerous to *not* make lectures available, because then you have no leg to stand on if someone takes your material. - Eva
I should note: the instructor for this particular course was not a scientist, but a history lecturer, so the teaching material was his original thoughts. In science this is different of course, but you could still consider someone selling something to an educational publisher. - Eva
I think you answered your own question Eva -- timestamped archive in, say, the Wayback Machine is a pretty good starting point if you have to go after someone. - Bill Hooker
It's a very poor argument against, without more details such as: how commonly does it occur? One or two isolated cases? A constant stream of plagiarism? Were any of the cases documented, or is it hear-say? It sounds like someone using an anecdote to support their own opinion. - Neil Saunders
I can't really remember the context of it, that's the annoying part. It's in a section about how to design a course. It comes right after the advice to not use your personal e-mail address for corresponding with students during a course, and right before the advice to ask a student to orally defend a dubious essay that might be plagiarized, but I wasn't taking continuous notes, so it's just a list of things I felt like writing down. - Eva
There was a court case addressing the question of who owns the notes taken from a course lecture: Williams v. Weisser (1969). The court found that "the lecturer retains a property right to his words spoken before a limited audience" and ruled in favor of the professor, who had sought permanent injunction and damages. In that case, the professor had a leg to stand on, although I'm sure he had to provide proof that the ideas were his own (e.g. by making his notes, musings, etc available to the court) - Hilary
I think the benefits would outweigh the risk, but perhaps it is a reason to be explicit about the license. - Matt Leifer
I agree about being explicit about the license. Any work that you make public should have a license that you and your institute feel is appropriate. - Allyson Lister
According to Brian Clegg at Nature Network where we've had similar discussions, content you write belongs to you, you do not need a licence or copyright statement. However, plagiarism is rife all over the internet as we know - eg the NYT and other US media recently tried to stop bloggers using just a few lines of their content in blog posts. They failed - for now - , but it is instructive that the limitations they wanted were draconian. I agree with some of the commenters above that it can be costly and time-consuming to prove you wrote it first, even if you are right. But any respectable publisher would use due-diligence before being "sold" something to publish- this would certainly include an internet plagiarism check (easy enough) and should include some kind of peer-review of the item being "sold" before a decision is reached to publish it. Publishers have entire legal departments for this kind of thing. - Maxine
prevent car theft by having no cars - Frank
Er, you mean like not teaching or not writing in the first place? - Maxine
Blog
14 hours ago - Link
These things are exquisitely sensitive to ionic concentration, which makes them a little difficult to work with, since all your buffers have to be adjusted to within nanomoles of one another in salts. - Mr. Gunn
I've never understood how you can make systems like this scale adequately. For high throughput you need to wire up thousands or millions of pores, which can be done, but not manufactured cheaply. But you need it to be cheap because the pores are likely to get blocked. Still there are some very smart people who I have a lot of respect for working for the Oxford company - I expect they've certainly got solutions in mind - Cameron Neylon
Kevin Kelly often writes that it's a wrong bet to say that something is technologically impossible, so I'm pretty sure they will find the way :). - Pawel Szczesny
Oh yeah - I'm just intrigued as to _how_ they're going to prove me wrong :-) These are not people I would choose to bet against on finding a technological solution - Cameron Neylon
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“Anyone planning to be at ASHG in Philly next week? Faces to handles drinks at some stage?”
November 4 at 2:57 pm - Link
Someone from Nature will be there and blogging the conference. Not sure who yet - most likely one of our science journalists - but watch this space so you can meet up if you like: http://blogs.nature.com/news/b.... - Maxine
@maxine - sure, would be great - Chris Cotsapas
You can keep an eye out for two colleagues of mine: Alain Hovnanian and Matthias Titeux, who will talk about gene therapy in the skin for Netherton's disease (I think). Matthias is a highly approachable postdoc and a friend, and it would tickle me if you accosted him on the strength of a name tag on my behalf. - Heather
I'm in Philly, if you want assistance in coordinating a spot for meeting up for drinks. - Jill O'Neill
@heather - will have to see if I can find him in this mess! @Jill - thanks, might take advantage of that offer. Any tips on where to find good cheesesteaks downtown? - Chris Cotsapas
Just found out that senior Nature editor Magdalena Skipper is there. - Maxine
And our science journalist has just got going http://blogs.nature.com/news/b... - my colleague Brendan Maher who is based in Philly so I should have guessed. Hope you can catch up with Brendan or Magdalena, Chris. - Maxine
Seem to have missed them. The meeting had a bit of a disjointed feel this year - or maybe it's just that it's the 6th week travelling for me. I think I'd met Magdalena a few years ago at CSHL/Genomes - she might even have still been with NRG? - Chris Cotsapas
Yes, she hasn't been with Nature for very long. She was briefly a publisher for NPG after leaving NRG, but now is back on the editing beat, I'm glad to say - she has replaced Chris Gunter at Nature. - Maxine
Twitter
Pawel Szczesny posted a message on Twitter
Blog
16 hours ago - Link
...and the last thing we can do is hopefully break down some of the old boys club that really dominates a lot of the access to the research materials in science, right now it's not who you are and how smart you are it's who you know and where you work... - Duncan Hull
isn't "who you know" a factor of "who you are"? - Rajarshi Guha
Rajarshi, no. - Pawel Szczesny
Ditto. - Paulo Nuin
Pawel, why? - Rajarshi Guha
John W's point, I think, is that the web has the potential to democratise the accessibility of ideas. You don't have to be an invited keynote speaker to voice your thoughts anymore. - Neil Saunders
I agree with that. It still seems that you need to be 'plugged' into the appropriate community to be considered trustworthy (?) - Rajarshi Guha
... and when you are plugged in such community, doesn't matter how bad you are, you are one of them. - Paulo Nuin
Comment deleted :) Neil and Paulo described it better. - Pawel Szczesny
I may be wrong, but I think there is bit of a mix-up of the ability to voice one's thoughts vs. democratising access to ideas. As I understand John, he is mainly talking about how to make sure that everyone has access to whatever text and data they need access to in order to do research. With open access you don't need to be part of any network to have access. (cont'd) - Lars Juhl Jensen
Neil is also right that web gives everyone the chance to voice their thoughts; however, in this case the big question is if anyone listens? As Rajarshi says, if you are not part of the appropriate community, no one may care what you say. - Lars Juhl Jensen
My friend Phil Lord http://homepages.cs.ncl.ac.uk/... always said "Science is more like an aristocracy than a democracy" (or words to that effect). I wonder if this means that "Scientific Royalty" will be doing everything they can to prevent a revolution by the underbelly of Science? - Duncan Hull
Oh, yes they will. I can tell many stories of the Royalty in Brazil, many stories. One worse than the other. I don't know about Canada, though. - Paulo Nuin
I agree with Paulo -- many of the existing aristocracy will push back hard on anything that threatens to move science towards a "meritocracy". Can't talk about it just yet but have been smacked around a little myself. Off with their 'eads I say! - Bill Hooker
Don't forget that the interwebs also has this kind of things. Some people can get away with anything they post/publish/write, some people comment/post/write better and never get heard/read. Like Lars said. - Paulo Nuin
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Egon Willighagen posted a message
“/me is working on visualizing the Solubility RDF data in Bioclipse...”
11 hours ago - Link
Still in progress, but a first screenshot is being uploaded to my blog... - Egon Willighagen
wow ! I don't think I might be of any help here Egon :-) . I will look carefully your sources to see how you've integrated this into CDK/eclipse. - Pierre
BTW, does someone know of a Java library to interact/read from Google Doc spreadsheets? - Egon Willighagen
very cool! - Jean-Claude Bradley
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Rajarshi Guha posted a message
“License suggestion - I need to make a dataset available, and I don't care who uses it or what they use it for as long as they don't blame me for anything. Can anybody suggest a suitable license for this?”
7 hours ago - Link
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The Life Scientists: Maureen posted a link
9 hours ago - via Bookmarklet - Link
"A new study shows that the cancer drugs imatinib (also known as Gleevac by Novartis) and sunitinib (Sutent, made by Pfizer) halt diabetes in mice." - Maureen via Bookmarklet
It seems more like prevention to be honest - a stay of execution for the remaining beta cells if the autoimmune problem can be held back, but I'm not sure what it can do once most of the beta cells are destroyed. Of course it might open the way for replenishment (transplantation or recovery of beta cells from precursors)... not sure. Interesting though! (Disclaimer: Just my ideas, not necessarily that of my employer's) :-) - Jo Brodie
Yes, the claim for "halting diabetes" will have to be examined. It'll be good to see the actual PNAS article...this was a press splash before publication. - Maureen
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The Life Scientists: Chris Lasher posted a message
“How do you filter your RSS feeds from journals? Or do you at all?”
yesterday at 5:02 pm - Link
I have too many entries and need to declare feed reader bankruptcy. I'd like a better way to get my journal subscriptions so I don't have to do this again. - Chris Lasher
I don't filter - but I don't worry too much about tracking items as they arrive. Ever since GReader got search, I've viewed it as an archive that I can always revisit. For specific terms, I'd probably set up a PubMed search and subscribe to the feed from that. Still, I think there's a market for a "friendlier yahoo pipes" app which filters feeds for keywords, displays articles with terms highlighted + a tag cloud and so on. Might be a nice web framework project. - Neil Saunders
I don't filter, but i do categorize via NetNewsReader. I'm eyeing Planet Venus: http://www.intertwingly.net/co... Plug-able filters FTW. I'm contemplating how to add feed back into the filters so that I can setup an RSS SpamAssasin filter based on what I read. - Paul Davis
I'm using more and more 'saced searches' instead of firehose journal feeds. I just end up deleting a crapton of them unread. - Timothy Driscoll via Alert Thingy
No filter, read them all. I am a journal junkie, have to have them all. - Paulo Nuin
I use this filter http://pipes.yahoo.com/pipes/p... and I have a few pubmed queries set up - Pedro Beltrao
Probably not quite what you're looking for, but I use postrank.com to filter a bunch of my RSS feeds. It does a pretty good job of taking some of the big feeds (BoingBoing, TechCrunch and similar) and extracting just the most interesting. I use the postrank Firefox plugin to integrate with Google Reader. - Michael Nielsen
Pretty cool Pipe Pedro. Is there any reason you have done it by pulling the feeds direct from journals rather than as a series of PubMed RSS searches + filters based on your keywords ? - Andrew Perry
Does anyone use Barf? http://barf.jcowboy.org/ - Paulo Nuin
Used to use Barf to generate feeds back in the day when many journals didn't have their own. It's pretty outdated now, since most (all?) now do. - Neil Saunders
Yep, but there are a couple that I use from there still. - Paulo Nuin
I have a combo of ToC and search feeds in GReader. On abstract review, "Interesting" items get starred (and possibly shared) and later, theoretically, read. Starring is fairly inclusive and is analogous to an "interesting" tag, more than anything. Often reduces search space. - Chris Cotsapas
I have a 'daily' tag in Google Reader that contains all the feeds I want to see every day, including standing PubMed searches by RSS and Scopus alerts. Various other journal tables of contents go under other tags ('structural biology', 'high impact', etc), but I only drink from the firehose in a solid session once a month, when follow up any 'must read' articles and manually filter the rest. - Andrew Perry
@Andrew - I guess I could have filtered down the pubmed queries by journals as well but the idea is that from some journals I want everything and from others I filtered them by keywords. Plus I think yahoo pipes had just came out at the time :). - Pedro Beltrao
I subscribe to publishers feeds from a limited number of journals, but mostly rely on targeted keyword search feeds from PubMed. for details of how to make these, see the video at: http://smallworldz.wetpaint.co... Using Google reader, I can scan a large amount of data very quickly, but of course the trick is choosing the right keywords (and Boolean terms). - AJCann
Currently, I filter none of my feeds, and then feel guilty when I wake up one morning to 100+ new articles that have just been published and I just scan the titles! However, there are some interesting ideas here, which I will investigate... thanks! - Allyson Lister
I don't filter feeds, I subscribe to the results of certain key HubMed searches. This tends to generate 20-30 articles a day, which is easily manageable. And I don't think anything important has escaped my attention, I always already have the articles people give me to read. - Simon Cockell
I have few RSS feeds based on PubMed search queries - this goes as "high-importance" stuff, read from GReader daily. Also get a weekly digest from F1000 (configured around my research interests). - Yaroslav Nikolaev
I think collecting a ton of feeds over at Google reader (can take them!), and then doing a keyword search to find what you looking for works best.... Also a tag to get the "daily" feeds that you always read among the mass is good.. - Ntino
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The Life Scientists: Ntino posted a link
8 hours ago - Link
Anybody interested in setting up an microblogging server ? identi.ca above is open source and free for anyone to download and install, plus other instances "talk" to the central server... just so we can avoid central authorities :-) - Ntino
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Deepak posted a message on Twitter
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Deepak posted 21 messages on Twitter
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Science 2.0: Lin posted a message
“I think maybe we can create a new system of scientific study to take place the existing one(journal).And maybe a new system can do a lot of good to scientists and researchers.Journal is the most advanced media 300 years ago,but today,the Internet is the best! I believe that with the help of new...”
12 hours ago - Link
what? oh,on...it seems that there is a limit of the number of words. - Lin
I think maybe we can create a new system of scientific study to take place the existing one(journal).And maybe a new system can do a lot of good to scientists and researchers.Journal is the most advanced media 300 years ago,but today,the Internet is the best! I believe that with the help of new ideas and good mechanism we can make better use of the Internet and finally change the way of doing scientific research.(to make it better)...I'm writing some ideas about this and I wanna do a survey here.Two questions:What is the most serious problem we have to face when building an open science community? What is the best way of doing scientific research in your mind? Thanks for your answers! - Lin
Lin, there are probably too many ideas to fit in the space, as you have already found ;-) But if you check through the links here on friendfeed and dig a bit you will find a lot of conversations about this. There was a recent one on what "the biggest challenges for science" are and many people with many (and often differing) views on how to make it better. - Cameron Neylon
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Noel O'Boyle posted a message
“I give up. I've been trying to access the Crossref Simple Text Query (http://www.crossref.org/Simple...) using http post but just can't get it to work. I'd love to be able to use this with Ubiquity...”
November 11 at 3:32 pm - Link
what is the action URL for the form? That page is horrifically obfuscated. Morons - Rajarshi Guha
If I convert POST to GET and use the example query, I have http://www.crossref.org/Simple... - Noel O'Boyle
Need to figure out how to handle JSESSIONID... - Noel O'Boyle
Wouldn't use the form for this. There's almost certainly a reason it's obfuscated! Will email Noel... - Euan
Stay tuned for good news... - Noel O'Boyle
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Deepak posted a link
MobyPicture.com
10 hours ago - via Bookmarklet - Link
Amazon CloudFront Shirt. Wordle FTW - Deepak via Bookmarklet
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Rajarshi Guha posted a message
“Does anybody know how to include a <script> tag on a Wordpress blog that is hosted at wordpress.com? I'd like to embed Gists, but Wordpress seems to remove the <script> tags from my post”
Friday at 7:06 am - Link
Not allowed at Wordpress.com. They permit only a few trusted javascript widgets. - Neil Saunders
Aah, thanks - Rajarshi Guha
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Deepak bookmarked a page on delicious
11 hours ago - Link
EC2 gem for ruby/rails - Deepak
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