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Jean-Claude Bradley's Likes - View full feed
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Cameron Neylon shared an item on Google Reader
13 hours ago - Link
focused on the information sharing aspect, appropriately so. - Mr. Gunn
I had a long talk with David today - there could be great synergy with our work on anti-malarials and certainly with the Open Science community - Cameron he's on your side of the pond - Jean-Claude Bradley
Ah - then I should defintely make contact with him. Left a comment on his blog this eveing about the open source drug discovery thing. - Cameron Neylon
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Heather Piwowar shared an item on Google Reader
yesterday at 7:55 am - Link
Some very good points in there: "Whilst there are clear benefits to be achieved from providing teachers and students with the opportunity to share ideas in the context of stimulus artefacts, many hold reservations about 'giving away' their intellectual property." [...] "Their main concern is to access reliable, relevant content and information, but the ability to form connections between these resources is one way of adding value to the collection." - Thomas Brox Røst
many people concerned about "giving away their IP" need to have a talk with a VC. Was it Kawasaki that said something like "Nothing is novel anymore, and if someone has never thought of your idea before, it's probably because it's a dumb idea."? - Mr. Gunn
I've also had some contact with people preparing a report on Web2 and science so I need to talk to them and then point them here :) - Cameron Neylon
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Michael Nielsen bookmarked a page on del.icio.us
yesterday at 10:41 am - Link
Insightful rant - it's better to define a job more by it's output than by what's actually done day-to-day. That's why "Movie Director" is better than "Project Manager". - Michael Nielsen
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Egon Willighagen bookmarked a page on del.icio.us
July 3 at 12:39 am - Link
More online (bio)chemical community building. Cheers Rich! - Egon Willighagen
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Jonathan Eisen posted an entry on The Tree of Life
July 2 at 8:45 am - Link
Congrats - Ricardo Vidal
I plan to have many more ... I am going to submit some old unpublished stuff to PLoS One as well as many new things - Jonathan Eisen
Congratulations! - Bill Hooker
Jonathan, you should title one of those upcoming PLoS papers "Tree of Life" and we'll all link to it and cite it feverishly! http://is.gd/Kxk - Duncan Hull
You may not worry about having the term "Tree of Life" lost to Hollywood, but when the next Angelina Jolie movie is titled Nodalpoint lets see what you do .. - Jonathan Eisen
yes, that wouldn't be good. Speaking of nodalpoint, I'm surprised Bosco Ho http://boscoh.com and Greg Tyrelle http://tyrelle.net aren't to be found wasting time on friendfeed... we should invite them to join the party... - Duncan Hull
"Wasting time"?? I resemble that remark! - Bill Hooker
We actually stole Nodalpoint from William Gibson. As for Greg, ironically for a web pioneer, he maintains almost no web presence whatsoever. Too busy in the Taiwanese corporate biotech sector. - Neil Saunders
Unfortunately http://www.nodalpoint.org seems to be either not responding or redirecting to Melbourne IT services http://www.flickr.com/photos/d... I've emailed greg... - Duncan Hull
Nodal fine for me just now. - Neil Saunders
Must be a weird hemisphere thing, are you down under in Oz where they have different InterWebs® or across the pond at ISMB? - Duncan Hull
Yeah, we get last weeks Nodal :) Proxy/cache thing maybe? - Neil Saunders
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Mr. Gunn posted a link
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July 1 at 1:35 pm - via Bookmarklet - Link
Anyone using this? - Mr. Gunn via Bookmarklet
Hadn't heard of it, but it looks interesting. - Bill Hooker
yes looks interesting - would be nice to see an example from our FF group here - Jean-Claude Bradley
If they'll ever approve my application, maybe we could get that worked out, JCB - Mr. Gunn
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Sally Church shared an item on Google Reader
July 1 at 7:08 pm - Link
People finding people via data rather summarises the success of FriendFeed. - Neil Saunders
Indeed it does, Neil - Sally Church
This is a great piece, but I have a minor quibble: data is not so central to day-to-day practice in some scientific communities. Certainly, it's less central in much of theoretical physics, economics and computer science than it is in (say) observational astronomy. - Michael Nielsen
Michael, I use "data" in a rather loose sense of the word. It could be publications of common interest, or some other lower level concept that people can coalesce around. - Deepak
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Matt Wood posted an item on Tumblr
July 1 at 5:54 am - Link
Hey, Matt, if you are talking on FF and Twitter on the conference you should set up a FF room for the conference to prove it! :))) - Attila Csordas
I can only prove my presence on the conference if I call it the Science (micro)Blogging 2008 conference. :) - Attila Csordas
Attila - excellent idea! http://friendfeed.com/rooms/sc... - Matt Wood
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Duncan Hull bookmarked a page on del.icio.us
July 1 at 9:21 am - Link
Nature Science Blogging conference 2008 - Duncan Hull
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Matt Wood posted a message on Twitter
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June 30 at 7:10 am - Link
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Michael Nielsen posted an entry on Michael Nielsen
June 30 at 8:40 am - Link
There was recently a Brazilian paper using the h-index to show the Brazilian scientific productivity. I will find the link but I don't know if it is in English. - PauloNuin via twhirl
@PauloNuin Thanks. :-) - Roger Chen
There's a paper out from the IMA that debunks the h-index even further: http://is.gd/J8p - S V via twhirl
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Attila Csordas posted a message on Twitter
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June 29 at 2:25 am - Link
"So you use Nature Networks, but what do you really think of the impact of Web2.0 on research?" - rather implies that Nature Network is a Web 2.0 application. It isn't and that's part of the problem. Perhaps "NN not working?" is a better tagline. - Neil Saunders
Ooh, Neil, that's a bit harsh! And wrong, I think. The group is set up by the "Talk Science" team at the British Library as part of their series of seminars. It has not been set up by the NN team and it is not at all "implying that NN is a web 2.0 application", it is about "web 2.0 as applied to science research". The BL talk related to this topic is happening next month, and the group is partly there for pre-meeting discussion of topics. If you would like to visit the group's NN page itself, rather than just commenting on the title I've posted here, you'll see the BL's agenda right there on the first page. - Maxine
Yeah, I was just being devil's advocate. Or overly harsh. Or something :) That and conference preparation stress. I have visited the group page (how else would I quote the opening sentence?) and I do see that it's web 2.0 + science, rather than NN specifically. The opening line does appear to equate NN and web 2.0, though. - Neil Saunders
I think the scientists who are using NN are probably interested in the social web and hence the questions the group is asking - at least that's how I read the opening sentence. Hope your conference preparation stress reduces soon! Good luck with your talk. - Maxine
I would love to go to this talk. Not everything Web 2.0 for Scientists is working. David Crotty (CSH Protocols) has written a lot about this. - Martin Fenner
Well I signed up and it asked me to join Nature.com first. Now I have access to free science and medicine article on Nature - big thank you! - Sally Church
I hope you can make the talk, Martin. It's in September, actually, not "next month", sorry for my mistake above. - Maxine
I think very little "web 2.0 for scientists" is working. In terms of not only uptake, but also the type of sites being developed. It's the data that need to be social, not the people. - Neil Saunders
I hope you can come over for the talk, too, Neil, to liven things up! - Maxine
Just joined up. I must quote Jon Udell ... "Data finds data, then people find people" (channeling Jeff Jonas) Link: http://blog.jonudell.net/2007/... ... We need to realize that web 2.0 has multiple aspects. I believe that we are not spending enough time trying to channel the programmable web aspect of web 2.0 (the data part) and too much time with the social (read people) aspects. - Deepak
Isn't there room for both, though, Deepak? The internet is a big place. - Maxine
Didn't you get the memo? Programmable web data is Web 3.0 :-) - Eric Jain
Hi, are you "the" Eric Jain whose name is on ClaimID? I use ClaimID for my open ID but every time I use it, from whichever computer, I have to log in. Any tips? - Maxine
Maxine, more than enough room, but communities build around common interests, not around interfaces, so the data has to come first. The latter are important too. Without good front ends, you can have all the data you want, but people are not going to come together - Deepak
Eric, I seem to be missing a lot of memos these days :) - Deepak
Never heard of ClaimID... - Eric Jain
Maxine, I use (sort of) ClaimID and have to log in each time, too. Sometimes I bother to press carriage return a few times, sometimes I don't. - Heather
Since there's always questions about what is Web2.0 good for in science, let me point out that people get funded to study string theory without people expecting practical applications to come immediately. Maybe we're a little too quick to judge science 2.0? - Mr. Gunn
Sorry, Eric, the name is "Jan" Rain, obviously no relation. I use a site called "claim id" as my open ID site as I was recommended it by one of the NN users (can't remember who). I wish I didn't have to log in so often -- most sites have a "remember me" or "keep me logged in" option that is good for a few days or a day at least. - Maxine
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Deepak commented on a blog post on Disqus
June 29 at 12:27 pm - Link
"I'll take the notoriety while it lasts :). It was worth a good chuckle" - Deepak
Cool! :) - Egon Willighagen
Funny. And not totally surprising :) - Neil Saunders
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Bill Hooker posted an entry on sennoma's Feed
June 27 at 6:24 pm - Link
Thanks for pointing this out Bill and commenting on there - it is interesting the level of animosity the concept generates for people who speak before they read. - Jean-Claude Bradley
At least it is an opportunity to clarify some misconceptions - Jean-Claude Bradley
I just don't get people. It's not like anyone is saying that ONS is the only way of doing science. It's "a" way, and a perfectly fine one if someone so choose, but then if anyone equates science to just wet lab work is hopelessly lost - Deepak
Yeah, I don't get the animosity either. I do know it's very common in science though, and I don't understand why that should be. Shouldn't researchers be both *curious* and *positive* about new things? - Bill Hooker
I am not sure it is even worth responding anymore. The whole strategy of that blog seams to be to irritate people enough to comment and come back to the "discussions". - Pedro Beltrao
I take back this last comment. Whoever writes the blog does have interesting and useful blog posts in there. I don't get it why once in a while he/she has those posts full of insults that clearly look like flame bait. Just for the fun of it here is a link to a rinsed version of the RSS feed of DrugMonkey (http://www.feedrinse.com/servi...) - Pedro Beltrao
There's an art to using a combative, abrasive style in this way. Personally, I think RPM at ScienceBlogs has it and this guy doesn't. I just find it very tedious and go elsewhere. - Neil Saunders
@Neil: absolutely agree there's an art to it, but I like PP and think RPM should dial it back a few notches, because he has lots of good stuff to say but just doesn't have the gonzo style down. - Bill Hooker
On a related note --- what do people recommend for electronic lab notebooks in general - either the closed kind or the open kind? I am trying to move my lab to all electronic notebooks with the long term goal of posting a lot of stuff openly but I need to start with a good electronic notebook ... - Jonathan Eisen
@Jonathan - can of worms, mate! There is no good, free/open-source, one-size-fits-all ELN solution. Most people here are using wikis, blogs or a combination (blikis). - Neil Saunders
One to keep an eye on though, as an online solution is SmartNote: http://smartnote.miraibio.com/.... Good if you do mostly DNA sequence stuff. - Neil Saunders
@Bill - question of personal taste, I guess. I'm not a fan of science bloggers who feel the need to project a contrived writing style. It just obscures the message for me. - Neil Saunders
Thanks Neil. The problem with the wiki/blog option is getting non techno people to use it. We have a lab wiki. Still hard to get everyone to use it for lab notebook stuff. Will check out smartnote - Jonathan Eisen
Jonathan - as you know I'm still a big fan of the general purpose wiki as lab notebook. One of the advantages of Wikispaces is that it has a decent visual editor and a highly simplified WikiText. But not matter what you use it will take more than technology to get your group members to enthusiastically use it. - Jean-Claude Bradley
Agree, Jean-Claude and Jonathan. My attempts, even with a visual editor and a training course, have failed to encourage lab members to edit our internal lab wiki. It was set up initially to only share our small sequence datasets, with the idea that this could be a pathway toward lab members using the wiki for protocols, and maybe even migrate to an open space like OWW eventually. It seems to be a real difficulty for the non-techno crowd, and it seems that they won't even try. - Andrew Perry
We get some use from our lab wiki and a LIMS that I hacked together, but only under great duress - basically the boss demands participation. Unwillingness to try is a source of continual frustration and incomprehension to me. The benefits are clear (I hope), the users are not stupid (I hope), nor computer-illiterate (if they can set up and manage Facebook, they can manage a wiki). It's either not a priority for them or else they're just lazy. - Neil Saunders
The problem we are having is integrating multiple formats - handwriting (e.g., lab notes), pictures (e.g., non digital images), digital images, analysis, etc. It is not that people are technically fearful, it is that getting people confortable with the idea of doing everything on the computer and changing practices (e.g, taking notes on the computer not by hand) will take some time. - Jonathan Eisen
I sometimes wonder if the free-form nature of wikis confuses some people. It means that they have to define their own structure for storing data. This is why I think the world needs a good, free, open-source ELN (and a LIMS) with flexible, but defined form fields: date/time, title, aim, upload (image/spreadsheet/text/whatever), notes and so on. - Neil Saunders
I think that's a big part of it, Neil: it took me a long time to grok wikis, and (by labrat standards) I'm a geek. Add to that the baffling tendency of scientists to sneer at anything they don't understand (I swear, outside their research, this is true -- and I have no idea why it should be so), and you have a recipe for Luddism. - Bill Hooker
A lot of reluctance is not related to technology - it is just human nature. Most students that I have had would not even keep a decent paper notebook without constant vigilance on my part. Some get it - and those who do of course will end up on top after they graduate and carry their skills to the workplace. - Jean-Claude Bradley
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Deepak posted a message on Twitter
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June 26 at 9:42 am - Link
Now got as far as commenting on the post even. Been busy for a few days... - Cameron Neylon
Delayed Open Notebooks? - Egon Willighagen
Slowly opened notebooks - Deepak
I usually just say it is a type of Partial Open Notebook Science - Jean-Claude Bradley
I still don't believe in scooping :) - Neil Saunders
I think delayed notebooks wouldn't prevent scooping, considering that scooping in notebooks is even an issue. - Ricardo Vidal
I am with Neil .. and after this weeks workshop even more frustrated - Deepak
I put in my more than two cents on this thread. I think the jury is out on which model works for which scientific field until more people from more fields try it out. So far there are a couple physicists, chemists, one molecular embryologist :-) and perhaps some biostatisticians? but we need larger sample sizes and more representativity. Where are the astronomers, the mathematicians (presuming they even keep lab notebooks), the geneticists, the cell biologists...? - Heather
How long does it take comments to come up at Scienceblogs? I made two some five hours ago... maybe the moderators are still in bed or something. Grumble. - Heather
Can anyone point to an example of scooping? I don't think it happens nearly as much as people think, and as you all know, proper ONS uses timestamps anyways, right? - Mr. Gunn
@Mr Gunn: I can give you one example of an attempt, when a certain Prof Scumbag found out from my PhD supervisor what I was working on, he put a postdoc on the same question. Happily I knew the postdoc, and he just kept "oh, I haven't got to that" until I'd published! Note that I have no proof, you'd have to take my word for this. Similarly, stories abound: I don't think I've met a PI who didn't have a story of someone throwing together a sloppy paper to scoop their conference presentation. - Bill Hooker
...cont'd: Very seldom does anyone take actual action. All I did, after all, was sabotage the attempt: I didn't make a formal complaint. We all know why I didn't, but that doesn't make it right. I have only one example where action was taken: this paper (http://www.pubmedcentral.nih.g...) contains this addendum (http://www.pubmedcentral.nih.g...) only because a senior scientist complained to journal editors and so on. - Bill Hooker
...cont'd: For instance, I could point to a paper which contains a bunch of crap (I can vouch for this) because it was slapped together after A saw B's presentation at a conference (I can't verify this -- which is why I won't point to it). My point, and at long last I do have one, is that timestamps are only half the answer. The other half is a willingness to follow up, assuming good faith error but willing to lay on the hurt if there really is a bad actor involved. - Bill Hooker
I've heard about people slapping together papers after seeing a conference presentation, and conceivably one could do the same after seeing an online presentation about research too. Now the question is whether such slapped together papers end up in better journals and cited more than the more complete research reports. If the slapping together is done by a more well-known lab, I can certainly see this being a problem, but I can also see well known successful labs being less likely to be bad actors. - Mr. Gunn
"whether such slapped together papers end up in better journals and cited more" I think they usually do, because the culture places such a premium on being first. - Bill Hooker
Short-term, maybe, but long term, like over 10 years, would the sloppy paper be expected to have the most cites? Want to find some crap papers from 1998 and do a quick experiment to see? - Mr. Gunn
I'm always in favor of finding out by experiment, but I don't have time for that one right now... Thinking more about it, I would expect the sloppy papers to have a shorter half-life just as you indicate. Problem is, science is self-correcting on a long timescale, but grant/hire/tenure decisions aren't. I do like your proposed expt; maybe put it on a BioGang backburner and let it simmer a while? - Bill Hooker
I would add it to the wiki, but it seems that my registration has yet to be approved... - Mr. Gunn
Mr. Gunn when did you apply for an account at OWW? - Ricardo Vidal
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June 26 at 6:13 pm - via Bookmarklet - Link
Very preliminary, no details - but another small step to finding those microbes? - Neil Saunders via Bookmarklet
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