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Yaroslav Nikolaev › Comments

Yaroslav Nikolaev
Open science at web-scale: Optimising participation and predictive potential : JISC - http://www.jisc.ac.uk/publica...
The report written by UKOLN at the University of Bath and the Digital CurationCentre, identifies openness, predictive science based on massive data volumes and citizen involvement as being important features of tomorrow's research practice. - Yaroslav Nikolaev from Bookmarklet
"Consultation Challenge 4: Credentials, Incentives and Rewards - The potential impact of these changing practices on established business models for science and scholarly communications is raised: new notions of reputation and trust are developing which challenge established norms." - Daniel Mietchen
Deepak Singh
When “good enough” just doesn’t cut it - http://mndoci.com/2009...
Is this a symptom of writing software for publication and then moving on? - Michael Barton
It's a symptom surely of what the measured endpoint is - getting the data out for the paper - not producing something that has real utility. It's the good enough _for what_ bit that is the problem here surely? - Cameron Neylon
It's all of those things. Worth remembering that in many cases, academic researchers who write software are not professional software developers. I think in the past and to some extent now, many people would answer "yes, good enough is just fine". I'm encouraged to see a new generation of computational biologists who clearly have been trained in software development and care about things like re-usability, reproducibility, testing, version control, distribution and so on. It is getting better. - Neil Saunders
That's fair - constant suprise to me that I seem to know more about software development best practice than the academic researchers I talk to. I blame Greg Wilson of course...need to get Software Carpentry or similar course made compulsory for all science undergraduates :-) - Cameron Neylon
And to those who don't get why this is important: we should spell out the cost (both financial and in time) to a research project, every time a new person starts on a project and has to clean up the mess of files and code left by their predecessors. I've seen this time and time again. - Neil Saunders
Or write it into the grant conditions. That spells out it out pretty clearly... - Cameron Neylon
Neil, I agree with you. I think that's going to change, as more and more software developers enter the life sciences, folks who care about maintenance, quality, etc. But the PIs are still a problem. Of course, this is not just academic research though. I've seen it in companies and perhaps that's the difference between between someone who stays middle of the road and someone (someone could be an entity) who excels - Deepak Singh
couple of off topic things: I think your RSS is not working, or you might have changed it. It doesn't show up on my GReader. Also your Fork Me link to GitHub is not pointing to your account. - Paulo Nuin
Paulo, the feed seems to be OK at this end. and yep, do need to fix that Fork Me link. Thanks - Deepak Singh
Survival of the fittest will show how good things are. In the (free) open source world quality/time_to_invest will show, and for commercial world the quality/price will do the same. - joergkurtwegner
Joerg, I think that's beginning to happen, especially with open source alternatives pushing purchasing behavior. Plus expectations have changed. No one is going to use an internal search engine with a several millisecond response time, when you are used to Google - Deepak Singh
Perhaps I'm the pessimist, but if all scientific software were merely 'good enough' I'd be in heaven. Good enough would at least imply that it compiles/runs/etc. - Paul J. Davis
I think "good enough" in software is favored when an individual needs to get something done and faces limitations in terms of time or financial resources in accomplishing the task. Within those constraints, "good enough" is the best way of making progress rather than waiting 'til someone writes the best possible code. It shouldn't remain that way, but if its cutting edge research, a clear market demand may not have been established as an incentive for some one to create a particular piece of software. - Jill O'Neill
Jill, I've seen enough evidence where that's not the case. PI's tend to lose interest when they have papers published, or if a grad student or postdoc leaves. In the case of commercial entities, it's a cultural thing. Constraints can lead to phenomenal code. - Deepak Singh
Isn't it similar to the evolutionary selection, with academics having a set of "pressures" different from those needed to develop #1-type software? Once the paper gets published, there is no pressure for researcher to improve the code, and things remain "good enough". While in a commercial setting there is always strong pressure from the side of the customer/competition, which drives the development further. I.e. to solve the problem one needs to bring some kind of pressure element to the academic setting. - Yaroslav Nikolaev
Victor / Mendeley Team
Interviewed by the BBC for the 1st time today, wearing these socks. On close inspection seems an odd juxtaposition. http://yfrog.com/0l2gxj.
Victor Interviewed by the BBC for the 1st time today, wearing these socks. On close inspection seems an odd juxtaposition. http://yfrog.com/0l2gxj.
next step – barefoot in parliament?! ;-) - Yaroslav Nikolaev
Pedro Beltrao
Seventh graders describe scientists before and after a visit to Fermilab. - http://ed.fnal.gov/project...
Seventh graders describe scientists before and after a visit to Fermilab.
Seventh graders describe scientists before and after a visit to Fermilab.
This one is lovely: "Their jobs sound very interesting because they can do whatever they want and they still get paid for it." ;-)) - Yaroslav Nikolaev
Arikia
I get to Beta test Google Wave!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! The world is so exciting today.
congratz! ;-) - Yaroslav Nikolaev
Thx! I'm pretty excited :) - Arikia from email
Cameron Neylon
To all those people asking about Wave invites a) I don't know if/how many we get b) please form an orderly queue :-)
Since I have seen lots of people asking, but nobody offering, I conclude that the new invites haven't gone out yet. Has anybody actually received a new account today yet? - Matt Leifer
i've seen someone tweeting that he has 8 invites. don't know if it was fake or not. now i start forming the queue :) - Endre Sebestyen
Is this the queue :) - Kubke
Are we forming the queue here then? If so, here I am :) Thanks! (allyson.lurena at that gmail email account) - Allyson Lister
The BBC suggest that each account gets 5 invites (http://news.bbc.co.uk/1...), but I read on Techcrunch yesterday that each account got 8 nominations (not invites, merely suggestions...). There's obviously no definitive info out there. Anyway, if there's invites going, and this is the queue, count me in :) (sjcockell at googlemail) - Simon Cockell
I saw some comment about release at 4pm BST but no idea where that came from or if it is accurate - Cameron Neylon
Queuing... - Yann Abraham
This totally reminds me about how I got my googlemail account. Consider me enqueued :) - Dan Hagon
I hereby formally join THE Wave queue :) - Graham Steel
queuing: bjhaugen@gmail.com - Brian Haugen
Hi. rich.bradshaw at that gmail thing. - Rich
Me? barton.michael@gmail.com - Michael Barton
And me (but you already knew that...). - Jan Aerts
I will queue belatedly, but hope for an account of my own :D dan.swan at the googleplexes mail servers - Daniel Swan
Queuing up in orderly fashion. - Jill O'Neill
queuing. this is like Wimbledon. - Sarah Kendrew
guess I'll also get in line. google acct: michael.kuhn - Michael Kuhn
Tapping foot in line: rvidal - Ricardo Vidal
News is popping up everywhere that the invites are rolling out, but I do not believe it... - Egon Willighagen
Invites for sale on ebay already... - Ricardo Vidal
Lines right up: tseng.ben - Benjamin Tseng
Waits patiently in line. wordsforliving@gmail.com - Jannifer @wordsforliving
Crossing my fingers...brian.j.krueger@gmail.com - Brian Krueger - LabSpaces
Those Ebay buyers are going to be sorely disappointed when they find that it's not an invite but rather a nomination, which I read a Google's way of saying "we'll know if you try to let in a SEO or spam account". - Mr. Gunn
Ok - it looks like I have eight - can other people on the sandbox confirm numbers and we can see about dividing these things up. Also can anyone who got their own invite delete the comment above? - Cameron Neylon
I can confirm 8 invites... which are really nominations, it seems... - Egon Willighagen
Line gets crowded ;-) pls count me in: yar.nikolaev [] gmail.com - Yaroslav Nikolaev
I make it 17 names above - and I've seen at least three other requests (Richard Akerman, Mike Ellis, David Bradley). So not sure how to do this. My inclination is to prioritise based on people who will be able to put some direct effort into building (but not necessarily coding) things. - Cameron Neylon
Can I just check whether Bjorn, Andy, and others with sandbox accounts have any free invites? - Cameron Neylon
Would it be worth getting those interested in obtaining accounts to write a short abstract (say 100-200 words) about the sorts of projects they'd use their account for? - Dan Hagon
According to http://twitter.com/larsras... no more invitations are being processed until tomorrow (Sydney time) - Nick Lothian
To all those wondering what is going on here - we are trying to coordinate the invitations we have with the people who want them. Its a bit of a slow process. - Cameron Neylon
Shouldn't Wave make that process faster? :) - Jan Aerts from Android
Yes, Jan. There's a wave weve set up for tracking who's got them and who still needs them. Everyone from this thread (that I know - please don't spam this thread ;-)) has been added. - Mr. Gunn
Since I haven't heard from Google, yet, I'll place myself in this queue for Wave invites. First name, last name, gmail. Thanks for organizing the process. - Chris Lasher
Cameron - Thanks for your efforts to match requests to invitations. Hopefully there'll be enough to go around for everyone on this thread who asked for one. Btw, because I didn't mention it above, my gmail account name is axiomsofchoice. - Dan Hagon
Jan, Wave makes the communication faster and more efficient in some ways but it doesn't help that much for human processes - like making difficult decisions. Also as far as I am aware the invitations I haven't sent haven't actually flowed through the system yet so you're not missing anything as yet... - Cameron Neylon
Oh, I'll add myself late to the list. rni.boh at gmail (you know the rest...). - Bob O'Hara
Would like to add myself to the queue as well ;-) - bala chandar
I would like to add my name to the list too - mhanwell at gmail if there are any invites still out there. - Marcus D. Hanwell
I have now been nominated for an invite (it's "in the mail"), so I've removed my comment above. Thanks @robsyme ! - Andrew Perry
I got mine too. Thanks - Deepak Singh
Got an invite as well today, and removed my comment above. Thanks anyway. - François Dongier
I have some Wave invites now. If anyone here still hasn't got one, post your email here (or direct message me if you prefer). - Andrew Perry
Maxine
A single author identification system - http://blogs.nature.com/nautilu...
The advantages are so obvious. What are the real-world problems for getting this established? Thanks for posting this. - Björn Brembs
would be nice to have it as an OpenID as well ;) and have it really open, not owned/authored by a for-profit organization.. - Yaroslav Nikolaev
OpenID+. Having a site that (a) function as OpenID provider, (b) contains information about you (e.g. department, contact details) that _you_ are in control of (i.e. edit/hide), (c) can autogenerate your publication list, and (d) allows you to manually add other contributions to the advancement of science (e.g. open source projects). We'd need the backing of one or more major publishers, but stranger things have happened. Can't we set something up like that? - Jan Aerts
Sounds like a good idea. One ID to rule them all.... - Allyson Lister
+1 Jan. Between OpenID and the auto-publication-list generators at places like Nature Network and BioMedExperts, it seems like most of the necessary functionality exists, just not in one place. - Bill Hooker
There are initial investigations being made (certainly within the field of publishing and the library community) towards institutional identifiers which may well be easier to handle than trying to do the individual author identifiers. - Jill O'Neill
But institutional identifiers alone will not work. I've moved quite a few times and saw that people still try to contact me on the email address from two jobs back, because that was the email of the "corresponding author". - Jan Aerts
Would it help if journals suggested to authors that they include their OpenID with their address details, if they have one? That should be pretty easy to do. - Maxine
Maxine: Yes ! That would be great ! It would be nice to see that OpenID just like we can see the DOI of the paper ! This would motivate the other publishers to do this ! - Pierre Lindenbaum
Maxine: Yes, yes, yes! That would be absolutely brilliant! Are Rafael, Simon, and Peter (or Bora) about? This might actually work! - Cameron Neylon
I'm not a guru about OpenID. Can it be then used later to find the publications/geoloc/social networks ? - Pierre Lindenbaum
In the medium term I agree with Maxine: let journals suggest to authors to include their OpenID. But I'm also with Deepak's comment in the "related entry": we should separate our author ID from our general online identity. I'm still brooding on how this all could be incorporated into a system where you as a researcher can update your scientific contributions yourself in a central place... - Jan Aerts
Pierre: I suppose you still need a central website/database, like researcherID.com for example (I know: not open and stuff...). Ideally you'd log in using an OpenID which would also be your researcherID. Even better: the system could function as an OpenID provider itself (that would keep your scientific identity separate from your general online identity). But the website would then have all functionality to find publications/geoloc/social networks. Am I (a) kicking in open doors or (b) making no sense? - Jan Aerts
Jan: That makes sense. Of course it would be great if the NCBI could be this OpenId provider (well, at least for the biologists... ) - Pierre Lindenbaum
Pierre: NCBI could indeed be an OpenID provider, but it should be limited to that. We need a separate entity doing the publication/geo... functionality. This is important enough that it should be the core function of the entity providing it. Also: would be nice if we could add contributions like "have helped in discussion about blabla on FriendFeed" :-). (Or is that "distracted discussion from blabla") - Jan Aerts
All you really need is a unique identifier - it could be an openid or it could be a random string. The advantage of openid is that it acts as a pointer to a service which treats you as a resource. Services can then connect that to any other information that is available. The other advantage of openid is that the provider is completely irrelevant - it can be anybody from the journal to NCBI to an institution to a third party. You're never tied into one provider. - Cameron Neylon
I'll say there was an interesting meeting early this year sponsored by CNI to bring publishers, A&I vendors (like Thompson Scientific), library reps (including OCLC and LIbrary of Congress), and others with interest in this to talk about it. OpenID was mentioned but many publishers and vendors already have their own (internal and not eager to share) identification systems. I'm not sure if anything definite came out of that meeting unfortunately (and I was there). - Sarah
Maxine, if you get this proposal rolling, your name will be legion :) - Neil Saunders
Sarah - quite a few of these points were made in the EMBO piece at the link. In fact, probably the article is a report arising from that meeting - though there is not much information of that sort, or about the author, there (ironically!). I will ask about the "display openID" and get back to you - will not be instant because one person is away until new year, but I won't forget. - Maxine
BTW there has been a lot of discussion on this in Nature over the years too - since 2006 when I started the author blog I have attempted to capture the discussion there, see: http://blogs.nature.com/nautilu... (includes Raf's correspondence in fact). - Maxine
Finally got round to blogging about this. Let me know what you think....http://blogs.openaccesscentral.com/blogs... - Chris Leonard
@Chris : in my view, this central repository (CrossRef/NCBI?) would associate this ID with a FOAF file containing all the information you want to publicity release :, your interests, your web accounts, your contacts, your publications.... - Pierre Lindenbaum
Yes, sounds good Pierre. According to the EMBO article at the link and various others, one issue is all the world's registration systems recognising the ID. Other issues, also. As we mentioned in another thread very recently, I am following up on this and it is on the agenda of a wider discussion about authorship and related issues that is going on between various journals - I will keep people posted with what I hear. - Maxine
One major problem with setting up UAIDs seems to be the identification of a single provider of these IDs, and the monopoly that would result from it. So I feel like asking a provocative question: does one really need to have only one UAID provider ? When nucleotide databases were started, new sequences were communicated either to EMBL or Genbank, or even to other, more specialised,... more... - Etienne Joly
Attila Csordas
PLoS ONE: Mobile Phone Radiation Induces Reactive Oxygen Species Production and DNA Damage in Human Spermatozoa In Vitro - http://www.plosone.org/article...
"Purified human spermatozoa were exposed to radio-frequency electromagnetic radiation (RF-EMR) tuned to 1.8 GHz and covering a range of specific absorption rates (SAR) from 0.4 W/kg to 27.5 W/kg. In step with increasing SAR, motility and vitality were significantly reduced after RF-EMR exposure, while the mitochondrial generation of reactive oxygen species and DNA fragmentation were significantly elevated (P<0.001). Furthermore, we also observed highly significant relationships between SAR, the oxidative DNA damage bio-marker, 8-OH-dG, and DNA fragmentation after RF-EMR exposure." - Attila Csordas from Bookmarklet
tough choice ;-) - Yaroslav Nikolaev
Bill Hooker
Branislav Kropilak: long exposures of airplane landings, factories, windmills, etc - http://www.kropilak.com/...
Branislav Kropilak: long exposures of airplane landings, factories, windmills, etc
I thought Pawel in particular might enjoy these. - Bill Hooker from Bookmarklet
geometry play in garages & billboards is really amazing! thanks Bill! ;-) - Yaroslav Nikolaev
I had the idea to do something like the garages series, but I never had the time and frankly, I don't have the technical chops to do it at that level. I bet those images are stunning at, say, 100cm high. - Bill Hooker
Nice find Bill! Thanks a lot. I haven't seen Kropilak's photography before. - Pawel Szczesny
Deepak Singh
Canon EF-S 55-250mm f/4.0-5.6 IS Telephoto Zoom Lens for Canon Digital SLR Cameras - http://www.amazon.com/dp...
Canon EF-S 55-250mm f/4.0-5.6 IS Telephoto Zoom Lens for Canon Digital SLR Cameras
Most of my bird pics on Flickr are taken using this. I think it's a great lens for the price; not high-end by any means but very acceptable and you can get great results with use and practice. - Neil Saunders
it would be a starter lens. One thing this trip taught me was how much we should have bought an SLR esp since the wife is a really good photographer (I suck at composition) - Deepak Singh from IM
Join us on the dark side... Buy a Nikon ;). - Pawel Szczesny
That's what my dad would say (he's a die hard Nikon guy) :) - Deepak Singh
Pawel +1 ;-) - Yaroslav Nikolaev
Attila Csordas
what makes Zurich such a cool place for having high-tech Research Centers there like Google, IBM geography, culture, money, laws, politics?
Tax breaks, and political neutrality? - Sung W. Lim
ETH (swiss version of MIT), advanced startup culture + a lot of foundations eager to invest in high-tech - Yaroslav Nikolaev
Yaroslav Nikolaev
Socio-technological evolution and the emergence of multiconsciousness - http://yarikson.wordpress.com/2009...
A rather more compelling reason to be interested in Open systems than competitive advantage for individual scientists... - Bill Hooker
would be interesting to run a simulation of an extensive (i.e. bigger than flat & round worms) multicellular system bearing neurocrine, but lacking circulatory-endocrine communication...do you have any experts in mind? ;-) - Yaroslav Nikolaev
Unfortunately, no -- but if there are any to be found, I suspect they are on FF. :-) - Bill Hooker
well I am not sure how to answer this, but Adrenal cells in all three zone (zona fasciculata, zona reticularis and zona glomerulosa) secrete the steroid hormone in response to circulatory-endocrine communication via ACTH hormone released by pituitary gland (which is 2nd in HPA series). Removal of the pituitary gland leads to little or no hormone synthesis in the zona fasciculata or... more... - Abhishek Tiwari
And how sharp is the transition between the cortex layers which become incapable of hormone synthesis upon pituitary gland removal? Assuming that fasciculata>glomerulosa migration takes place, differential behavior might simply mean that different signaling cascades are activated in the glomerulosa layer due to local environment conditions....although I'm not sure how this relates to the value of open/networked communication for stability of a multicellular organism?! - Yaroslav Nikolaev
I was just commenting about "multicellular system bearing neurocrine, but lacking circulatory-endocrine communication", otherwise transition must be very slow although theory itself is not well established. - Abhishek Tiwari
Yaroslav Nikolaev
Сomputational evolutionary biologist wanted! ;-) Would someone in this group be able to model the stability of a large multicellular (animal) organism depending on the presence/absence of the circulatory+endocrine communication system? Or at least evaluate the complexity of a task..
The idea is that an open and transparent communication system is necessary and sufficient to maintain a large multicellular organism. The "sufficiency" seems to be proven by the prosperity of vascular plants...Would be great if someone could prove the "necessity" component as well! more detailed concept is here http://yarikson.wordpress.com/2009... - Yaroslav Nikolaev
Yaroslav Nikolaev
Could we Garden on Mars? [Starts With A Bang] - http://scienceblogs.com/startsw...
Would you garden on Mars? :) - Andrei
i'd love to open a bar there ;-) - Yaroslav Nikolaev
Yaroslav Nikolaev
Rethinking Leucine Zipper – a ubiquitous signal transduction motif : Nature Precedings - http://precedings.nature.com/documen...
In this essay we attempt to reconsider the concept of the “Leucine Zipper” (LZ) protein oligomerization motif. Reasoning on the wealth of existing data, we suggest that despite of the structural similarity with highly stable extended “Coiled Coil” motifs, on the functional level short and moderately stable “Leucine Zippers” might stand out as a distinct group. Namely, this family of oligomerization motifs facilitates combinatorial protein-protein recognition in the course of signal transduction events, thus going beyond the structural role of the extended “Coiled Coils”. Summarizing the existing knowledge on stability, specificity and folding of Leucine Zippers we demonstrate how a simple set of rules, applied in the context of the universal coiled coil scaffold, creates a robust LZ interaction vocabulary. Owing to the high abundance of Leucine Zippers, this motif might account for coupling of distinct protein signalling pathways into a unified intracellular signalling network. In the... more... - Yaroslav Nikolaev
Uh ty, Nature Precedings! Ne znal o takom. Chem -to napominaet PLOS. - Andrei
Abhishek Tiwari
What If Scientists Didn’t Compete? - TierneyLab Blog - NYTimes.com - http://tierneylab.blogs.nytimes.com/2009...
"What if scientists, instead of rushing to publish or perish, chose to cooperate? Sean Cutler decided to do “a little experiment,” as he calls it, and you can see the results in the forthcoming issue of Science. " - Abhishek Tiwari from Bookmarklet
Wish I could 'Like' twice - Andrew Clegg
If you divide the impact factor of the publication by the number of authors, then you might find out that the outcome of the sum of efforts is less than the sum of independent publications would be. After all, the amount of data obtained by these people does not depend on whether it is published in a single article in Science or several articles in more specialized journals. In fact,... more... - genereg
This is part of how the Gates foundation is trying to accelerate research, by tweaking the incentives so scientists cooperate. I find one of the Tierney article statements misleading: scientists are ultimately competing for funding, not ego. - Wladimir Labeikovsky
"scientists are ultimately competing for funding, not ego" -- I completely agree with this. in many cases, scientists also "cooperate" just to get better funding, not to make better science. - genereg
natural curiosity could provide sufficient energy to drive science without necessity of competition. but for that kind of thing to function academia might need "unlimited" resources...or a more even resource distribution.. - Yaroslav Nikolaev
"...or a more even resource distribution..." - like it was in the Soviet Union or China. Means the end of the current US grant system. - genereg
sharing data with competitors, an interesting concept - science article http://dx.doi.org/10... and summary http://tinyurl.com/cl688w - joergkurtwegner
I don't think cooperation and competition are exclusive. And both can lead to waste if taken too far... - Eric Jain
+1 Eric. Balance is key (and right now I think the balance is tilted way too far towards competition). - Bill Hooker
cooperation and competition go hand in hand. although opposing teams in a soccer match may be competing, they have a mutual pact the goal of which is to have each team play their best. - Mike Chelen
Mike, football teams aren't trying to build a reliable body of knowledge. I don't think the analogy holds up. :-) - Bill Hooker
Bill, they are trying do the best in their field (hehe), isn't the same true for scientists? - Mike Chelen
By determining goals, method of achievement, and providing feedback competition can be designed to encourage cooperation. - Mike Chelen
Bill Hooker
TED fellowships: all expenses paid to a TED conference, give a TED talk, author spot on the TED blog. - http://www.ted.com/index...
Might be a great way to advance your research or Open Science agenda... - Bill Hooker
've had a discussion yesterday – why haven't anyone presented open science ideas at TED? Bill, Michael, Cameron, JC aren't you up for this? ;-) - Yaroslav Nikolaev
Open Science TED talk? That would be just so awesome..... - Graham Steel
Yaroslav - it would be great but it is pretty hard to follow Bill Gates :) - Jean-Claude Bradley
Yaroslav -- I was indeed thinking of Jean-Claude, Cameron and a growing number of others who are actually *doing* Open Science. The TED people seem pretty forward-looking so I don't think it's necessary to have already changed the world, just made a good start on that project. A TED talk would certainly put ONS on a LOT of peoples' radar, which is where collaborations come from, which is the secret to ONS success... - Bill Hooker
Yes, I like to see this at TED too. - Meryn Stol
*squints eye, looks askance, scratches cheek* - Karen James
Care to elaborate, Karen? - Bill Hooker
My feeling, at least as far as I am concerned is that I've still got a bit more "doing rather than talking" to get on with here. JC has actually got out and done a lot more - Cameron Neylon
Bill - Sylvia Earle, who I believe is involved in a partnership with the Beagle Project, won one of the TED Prizes this year. I'm guessing that's what Karen is referring to. - Michael Nielsen
Yaroslav - Sure, it'd be great fun, and would, I hope, do some substantial good for open science. - Michael Nielsen
great, seems we might expect one of you on TED 2010?! ;-) Or what about this one – http://www.ted.com/pages... I believe we could make some open biocrowd-sourcing to help financially! ;-) - Yaroslav Nikolaev
I brought this to the attention of Peter Suber yesterday who has given this his full approval. - Graham Steel
actually was the Open Access concept ever presented at TED? there are many scientists who are not aware of these ideas...Graham, do you think Peter might consider presenting OA as well? - Yaroslav Nikolaev
Damn, Yaroslav, I like the way you think. Peter Suber would be an *excellent* candidate for a TED Fellowship, and community financing to send someone to a TED conference regardless of fellowship awards is also a great idea. (Before anyone nominates Peter, note that he has had health issues and may not be up for the travel. Still a great idea.) - Bill Hooker
I just flipped through the "tech" category and found no OA-specific talks but a number of related ones that I think set the stage for an OA talk: Jamais Cascio (http://www.ted.com/index...), Kevin Kelly (http://www.ted.com/index...), Yochai Benkler... more... - Bill Hooker
Nice work, Yaroslav and Bill. I wasn't aware of Peter's health issues. As such, can I throw another hat into ring - what about John Wilbanks? - Graham Steel
John would be a brilliant choice as a first step... - Cameron Neylon
JohnWilbanks++ - D0r0th34
+10 on John!!! Ideally it would be John + Michael/JC/Bill, since OA and OS perspectives are slightly different...although it is not clear of what are the chances of securing two fellowships?! - Yaroslav Nikolaev
John Wilbanks is another great idea, and more complementary to than competitive with Peter Suber: Peter for OA, John for Open Data. I'm flattered to be mentioned above but won't accept a nomination: I'm not *doing* anything but cheering from the sidelines and imo that's not the face the Open (Notebook) Science community/movement/whatever wants to show the world. - Bill Hooker
Interesting development. TED have been in touch !! Following comment was posted on my above blogpost overnight "Hi, we'd very much be interested in seeing an application from one of you working Open Science projects! Cheers, Tom Rielly TED Conferences". - Graham Steel
great news Graham!! ;-) this year only TED@Oxford (July 21-24) is left for the Fellowship..Can you ask Peter whether he might consider that one a possibility? - Yaroslav Nikolaev
w00t! awesome news, Graham! - D0r0th34
Cool, Graham. - Meryn Stol
John will reply in more detail later, but says he would be honored to take part in this!! - Yaroslav Nikolaev
Yes, it was xlnt to hear from TED via the blogosphere. I established contact with Tom Rielly last January as I mentioned in this post, BTW, you must watch Tom's Ted Talk, it's a hoot.:- http://mcblawg.blogspot.com/2008... Looking forward to hearing from John :) - Graham Steel
yay John! - D0r0th34
Whilst we're here, can I also flag up POP!TECH:- http://www.poptech.org/ . I am now able to confirm that Hope Leman has submitted a nomination for Jean-Claude and is in the process of doing the same for Cameron and Michael. With this in mind, i.e., wheels are already in motion, it's most certainly worth giving this a shot. POP!TECH Fellows page:- http://www.poptech.org/sifello... - Graham Steel
TED is a slightly different entity and imo, taking all of the above into consideration, John would be the most, but not only, practicable person to self-apply for a TED Fellowship before the 3rd April deadline for this year:- http://www.ted.com/pages... - Graham Steel
John has applied for the fellowship, and Graham made sure Tom Rielly (TED) is updated on this! hoping its a safe bet & we will see Open Science at TED soon! ;-) - Yaroslav Nikolaev
Whilst this thread is currently off the FF radar, a quick resume. Thanks to all involved in this discussion (on and off web) John Wilbanks has put himself forward as a TED Fellow (TED have been advised by myself), and POP!TECH nominations for Cameron Neylon, Jean-Claude Bradley, and Michael Nielsen should now be complete. A big thanks to y'all !!!! - Graham Steel
awesomesauce! - D0r0th34
sweet! - Björn Brembs
For the public record, here's what I said to Tom Rielly - Partnership Director TED Conferences on 4th April:- "Dear Tom, I've just been informed that John Wilbanks http://revminds.seedmagazine.com/revmind... has applied for a TED Fellowship. As Vice President of Science, John Wilbanks runs the Science Commons project at Creative Commons. On behalf of the Open Science Community, we wish him lthe best of luck in applying for a TED Fellowship. Warm regards, Graham" - Graham Steel
Graham and Hope, many thanks for all the legwork you have both put into this. Is there anything to be gained by sending Tom Reilly individual or a joint email further supporting John's application? - Bill Hooker
I think if we are to do something, it probably would be better to send Tom a joint email. - Graham Steel
This thread is pretty much fossilized by now, but for completeness: http://beta.friendfeed.com/the-lif... - Bill Hooker
Matthew Todd
Draft letter to publishers asking for position on open data/research - http://canwepublishopenproject...
To allow for easier editing, this is now on wikispaces. Can people please suggest/adapt/improve this letter so that we can send to publishers? Also needs to be clear who this letter is actually coming from, so I'm suggesting you sign if interested. - Matthew Todd
Made a couple small edits, one suggestion, and signed. Has there been any movement on the question of whether to make this a project of the OKF working group on open data? - Bill Hooker
Commented and signed. Journal's will have a hard time responding to this if it doesn't fit within their already established guidelines. - Andrew Lang
Working on the working group - it's not quite as fast moving as around here... - Cameron Neylon
Question: Are you sending this to journal editors (editorial function but not necessarily paid staff) or are you sending this to publishers (paid staff of publishing entity)? To me, it's not entirely clear and you would get different responses depending upon the role. (IMHO only) - Jill O'Neill
I'm still a bit worried about the emphasis on the word open - I would argue for focussing on the specific issues. There is a real risk of bouncing publishers into less helpful policies by making them think we are trying to violate copyright by stealth. There is the principle and then there is the outcome - which is it that you want to achieve in this round? - Cameron Neylon
JIll - the hard part is finding the right person to write to. I think we'll start with the cooperative "Open" or "open-like" publishers/journals/people. Large publishers may say it's up to individual J editors - but the reverse will also be true. - peter murray-rust
+1 Jill -- we need to get responses from all the way along the food chain. That's definitely something to keep an eye on. - Bill Hooker
OK, re-edited. @Cameron, I think you're right. I reduced the level of the word 'open' and am re-emphasising the prior-disclosure-of-data angle. Could people please take a second and read this draft? http://canwepublishopenproject... - Matthew Todd
I'm still not sure I get the levels, maybe because I'm not an experimentalist. I'm getting confused with 'results' and 'data'; and are we talking about papers: reporting the data or interpreting the data or both? That would make a difference to me. - Andrew Lang
Ah, the difference between results and data is indeed a difficult one to define. let me give this a shot: data is what you produce all day, results are what you publish(unless they're negative, in which case you just wish you could publish them, or you write them up for JNR or something). - Mr. Gunn
Even in the computational sense there can be differences. Using Mr. Gunn's descriptions a molecular dynamics trajectory is data, the interpretation of those trajectories are the result. - Deepak Singh
Yes, my intention was to use data as raw, and results as interpreted, but I realise this is subjective. Also, the 'levels' I've used may not be incremental, i.e. given that a publisher is level 2 may not mean they agree to level 1. Maybe need other descriptors. John, Paul, George and Ringo? - Matthew Todd
I think incremental levels would be a good idea. Then journals could be scored 0,1,2,3,4. - Andrew Lang
It isn't immediately clear to me that these are levels that are sequential though. A journal may have a liberal view on published data but not e.g. on conference presentations, or vice versa. - Cameron Neylon
Perhaps we could use colours a la SHERPA/RoMEO. - Bill Hooker
Excellent idea! + Bill will get a third dimension for fooling around with numbers ;-) - Yaroslav Nikolaev
I just read the most recent version and think you will elicit answers successfully. In your planning, you may want to remember that these types of policy questions frequently must go up the management structure before a policy position can be stated. You aren't necessarily being ignored by anyone if it takes a while to get an answer. - Jill O'Neill
Sorry, have been distracted and not looking at this properly. The text looks quite good now. I would be inclined to put in a couple of examples (will try and do this now). I will chase on the question of ROMEO, either by email or at OKCon this weekend with Rufus and Jonathon. My suggestion would be to go to NPG first with this. They have essentially said that all of this is ok in recent editorials. Then try and get NPG, PLoS, ROMEO in room together - Cameron Neylon
Occurs to me that colours might be a bad idea, if we are going to try to get RoMEO to host the data. They already have too many damn colour codes. We don't want to end up classifying journals as "green with a yellow tip and a white stripe" or some crap. - Bill Hooker
You don't think we'll have publishers falling over themselves to earn the puce and aqua paisley? - Cameron Neylon
People are requesting membership of the wiki at http://canwepublishopenproject.... Is that necessary? Can't people edit anyway? What's the advantage of membership of a wiki? - Matthew Todd
If they're signed in it will autorecord who makes which edit. That doesn't really matter though since if Anon makes a good edit, it will stick -- plus they can sign in via the "notes". So, no advantage, but if people want to be part of the team that sounds good. - Bill Hooker
Sorry about the request - it was just an automatic response - been signing on to so many of these things now that I just press the request membership button first without thinking to try the edit button :-) - Cameron Neylon
Mat - people often forget to login so their editing will be anonymous. But I would recommend that you leave it like this - it is a hassle to get people to set up and account and approve them. But if they make a request might as well approve them. - Jean-Claude Bradley
Karen James
British Council grant proposal successful; going to Brazil!!! Details soon on The Beagle Project Blog http://thebeagleproject.blogspot.com/
Rock and Roll :) - Graham Steel
w00t! - Bob O'Hara
Congrats - dead jealous! - Stephen Curry
great news! luck+3! ;-) - Yaroslav Nikolaev
congrats! Brazil is such a great place!! - Björn Brembs
Hey thanks everyone! Blog post here http://thebeagleproject.blogspot.com/2009... - Karen James
Yes, Brazil is w.o.n.d.e.r.f.u.l! - Paulo Nuin
Jean-Claude Bradley
Fooling around with numbers, part 2 - http://www.sennoma.net/main...
the Nature folks are going to love you for this Bill :) - Jean-Claude Bradley
I don't like the first plot, as it is not clear of the Nature block covers *all* Nature publications... it now suggest that all Nature is good... - Egon Willighagen
Ah, so Elsevier are evil. :-) - Bob O'Hara
I'd be happy to run a few more analyses if someone else can extract more data. - Bob O'Hara
@Bob: I think I extracted all there is to be had into the text file available at the blog post. What more were you looking for? - Bill Hooker
@Egon: a quick count of the dots makes clear that the Nature block does not contain enough points to cover all of NPG, though -- just as the Elsevier block does not contain enough points to represent all of their journals. I've updated the text a little to try to address your point -- fixed enough, or still a problem? - Bill Hooker
@Jean-Claude: I thought about that, but I do enough Nature-bashing to even things out. Credit where it's due after all. :-) - Bill Hooker
I was thinking of things like splitting it by subject area. Number of subscriptions would be nice too, but I doubt you could get the data. - Bob O'Hara
I thought you might be thinking of that. I may split up the smaller Elsevier dataset by hand, and even have a go at extracting the subject area information from ISI or somewhere for the larger UC set. If I get anything useful I'll blog it and share the data there. - Bill Hooker
cool stuff! can't wait to see "part 3" ;-) - Yaroslav Nikolaev
Deepak Singh
Samuel Barber - Adagio for Strings, op.11. Uncut - http://www.youtube.com/watch...
Samuel Barber - Adagio for Strings, op.11. Uncut
Play
shame about the sound quality really - I've sung the transcription a few times but not for many years - Cameron Neylon
This performance was four days after 9-11. - Karen James from twhirl
pity there is no "love" button on FF ;-) - Yaroslav Nikolaev
Shirley Wu
Attila Csordas
Creationism Slips Into a Peer-Reviewed Journal | NCSE: the Warda and Han article was the #2 "most accessed" article for all of 2008 in the journal Proteomics - even though it was retracted. - http://ncseweb.org/rncse...
"A strange thing happened in the scientific literature recently. A pair of creationists, who have seemingly legitimate scientific credentials, attempted to publish some creationist assertions in a peer-reviewed journal. Their effort was nearly successful, mostly because they hid their pseudoscience in the middle of the article, surrounded by legitimate scientific discussion of unrelated topics. Luckily, they were caught just in time, and it turned out that they were pretty clumsy. In fact, if they had been just a bit more clever, they might have gotten away with it." - Attila Csordas from Bookmarklet
That would have been an embarrassment for Proteomics. Well, I suppose it's still fairly embarrassing. - Chris Lasher
What a bunch of muppets -- the journal AND the reviewers AND the incompetent godists - Andrew Clegg
+1 Andrew. I'd hardly say their claims were hidden in the middle - the title sets the tone. A big fail from editors and reviewers. - Neil Saunders
As a long time fan, I protest the use of the term "muppets" as any kind of perjorative! - Bill Hooker
Sighs very deeply... and the creationists will claim suppression no doubt - Sally Church
quite shocking..hopefully transparent peer-review suggested by EMBO will improve the quality of reviewers work... - Yaroslav Nikolaev
ever played 'Toblerone'? - General Kafka
What's Toblerone? Apart from the obvious. - Andrew Clegg
I think that people are way too hard on the reviewers in this case. I actually think that they likely should not be blamed at all. Imagine the following scenario: I submit a manuscript without nonsense; you review it and recommend "minor revision"; I revise manuscript addressing your few points and silently add some nonsense elsewhere in the manuscript. Would you go through the entire manuscript again just to ensure that I did not silently change the parts that you have already approved? - Lars Juhl Jensen
I do acknowledge that the title is odd - but usually the title of a review paper is decided between the authors and the editor, and journals like titles that grab the readers attention. So the reviewers do not have much to say on that front. The worst "crime" committed by the reviewers is in my view to overlook one strange sentence that was likely added to the abstract during revision. - Lars Juhl Jensen
Lars, is there any evidence that the dodgy bits were added during revision and weren't there all along? Anyway, the title alone should have been enough to sound alarm bells, and I'm sure they would have noticed if that changed after the first submission - Andrew Clegg
Andrew, at a party in Heidelberg someone from Wiley told me that this was in fact what happened. Also, the editor-in-chief wanted to be open about what had happened, but he was silenced by the PR department of Wiley. I agree with you that the title should cause alarm bells to ring. But imagine that you are a reviewer, your alarm bells ring, you read the manuscript carefully, but you find that there is no nonsense in it. You then receive what should be a minor revision. Would you search for nonsense again? - Lars Juhl Jensen
Fair point. Before this incident, probably not. Now... Definitely :) - Andrew Clegg
Reading a boring review paper of 23 pages for a second time just to make sure that things have not changed ... I still would not do that now. I am not a masochist ;) - Lars Juhl Jensen
Journals should insist on Track Changes for Word submissions. Or just ask for everything in .tex format so you can just run diff :-) - Andrew Clegg
Yaroslav Nikolaev
review on P2P social aspects & technology – beyond file sharing. - Yaroslav Nikolaev
Richard P Grant
Post-publication peer review
What does that phrase mean to you? - Richard P Grant
Either people trying to replicate your results, or discussing(gossiping about) your work at a conference. - Mr. Gunn
journal club - laura
PLoS One - Björn Brembs
blogs - Paulo Nuin
critical comments from peers after publication that are easily retrievable by anyone - Pedro Beltrao
pre-publication peer review made open, encouraging post-publication review to keep up - Yaroslav Nikolaev
needless to say one needs infrastructure for maintaining both =) - Yaroslav Nikolaev
Does your work get cited, and is the citer ripping it to shreds? - Donnie Berkholz
ideally, mechanisms like the comments at PLoS (except, you know, actually with people contributing reviews) - Chris Miller
+1 PLoS ONE. - Bill Hooker
What a fascinating question and answers. Is that a formal term? I would say letters to the editor in the journal in which the article appeared. And then inclusion in a formal meta-analysis down the road. - Hope Leman
I don't know if it's a formal term. That's part of why I asked! - Richard P Grant
Ha, well I am glad you asked the question Richard as this is an interesting discussion. My question for Paulo would be, “But how much authority and gravitas do blogs have?” How does ResearchBlogging.org come into play, here? And Twitter retweeting of the paper? I would be interested in what Michael Nielsen would have to say here. - Hope Leman
When I said blog, I was thinking of Research Blogging. You can build a reputation to your blog based on the kind of post-reviews you make and the discussions you generate. It's quite easy to separate the wheat from the chaff, and find out who are the best "authorities" in each field and whho are the nutjobs. Of course is not a perfect model, but anywhere you find "star-bloggers" that are bad and survive on some kind of "streetcred" they accumulated before. - Paulo Nuin
Michael Nielsen seems to have that sort of reputation. - Hope Leman
For physics yes, what about life sciences? - Paulo Nuin
I am new to the subject of Science 2.0, but he seems like a thought leader in Science 2.0 to me, speaking as a medical library person. He is erudite and well versed on many subjects beyond physics seems to me. - Hope Leman
Science 2.0 and Web 2.0 are fad, a hype. - Paulo Nuin
But Paulo--aren't Friendfeed and this room and the above conversation Science 2.0 in action? - Hope Leman
Yaroslav Nikolaev
brain backup - the best method of self-preservation...hopefully coming soon ;) - Yaroslav Nikolaev from Bookmarklet
Meryn Stol
The Wired Presidency: Can Obama Really Reboot the White House? - http://www.wired.com/politic...
The Wired Presidency: Can Obama Really Reboot the White House?
"turning his innovative campaign and transition into Government 2.0 won't be easy. The nimble Obama startup is about to be absorbed into a stodgy, technologically backward behemoth: the federal government. Ahead are bureaucratic obstacles the campaign never imagined, along with the political land mines that transparency brings. Obama will have to preserve the enthusiasm of his supporters while engaging the larger group of people who either didn't vote for him or didn't vote at all. His task is to rebuild the personal connection that supporters felt they had with Obama the candidate, assuring them that he is listening to them—without being deafened by the cacophony. If he can do that, Obama can alter how the government engages its citizenry and accomplish what he really cares about: his own policy goals." - Meryn Stol from Bookmarklet
Ctrl+Alt+Del ;-) - Yaroslav Nikolaev
Yaroslav Nikolaev
Can you think of examples of commercial science/research companies using social web technologies (web 2.0) or SaaS for delivering their products and services? Seems one of the prerequisites for stimulation of "Science 2.0"?!
Reference management tools - CiteULike, 2collab, Connotea, Mendeley are the first step. But is there anything of more products/services type? - Yaroslav Nikolaev
Not exactly commercial, but have you looked at HubZero? - D0r0th34
Yes, Nature Publishing Group, eg Nature Protocols (web 2.0 Protocols Network), Nature Precedings (preprint server), Nature Network (social website for blogs, events and forums), various databases eg Signaling Gateway, Connotea (mentioned above) for bookmark sharing/organising, etc. All free to users. For a full list see the nature.com "A - Z" page. - Maxine
D0r0th34, thanks for the pointer! not exactly what I meant, but looks very interesting from the knowledge management perspective! Do you have any hands-on experience with the platform? - Yaroslav Nikolaev
@ Maxine, thanks! Nature with no doubt is a pioneer in this respect. But I was rather thinking about products/services closer to the research process itself, not knowledge management/dissemination. - Yaroslav Nikolaev
I don't; I've only seen it demoed. - D0r0th34
Service-based offerings in the sciences are still rare. I know of a few in the modeling/informatics space, NextBio and Entelos are perhapsthe most obvious examples from the top of my head - Deepak Singh
Aside from Deepak's examples, I can't think of a single service, commercial or otherwise, that uses what I think of as web2.0 (as exemplified by Wikipedia and Flickr) to deliver research tools. I think there is a real opportunity here for developers. - Neil Saunders
Deepak, Neil, thanks! Shame on me, forgot about science wikis - those definitely start to emerge! Beyond that it really seems quite a desert there..Entelos is rather Medicine2.0 (flourishing more than Sci2.0)...NextBio is a good example, but still of knowledge management & mining type, poorly adopted outside of [Bio]informatics...Can't think of straightforward SaaS application for science, but a nice "2.0" transition could be to get amazon-type interactivity into things like biocompare.com.. - Yaroslav Nikolaev
The mention of wikis reminds me to point to http://www.wikiprofessional.org/portal... - Richard Akerman
Yaroslav, you'll probably see a lot more this year. Actually I forgot a very good one, Assay Depot - Deepak Singh
@Richard, thanks! Science wikis definitely deserve a separate listing, sort of this one http://tinyurl.com/5bbnsg - Yaroslav Nikolaev
Deepak, that is a very nice one! keep'em coming! ;) I am surely looking forward - at least Health Commons shall show up this year! - Yaroslav Nikolaev
Well, it depends how you define Web 2.0. If RSS feeds and email alerts are Web 2.0 then the site I work on, ScanGrants is Web 2.0 and so is the search engine Mednar. - Hope Leman
Mainly the _social_ web component was meant - i.e. content being created/managed by users...// Pity cannot make font _bold_ in here ;-) - Yaroslav Nikolaev
Yesterday I had a meeting with the German company Cryptodesk https://www.cryptodesk.de/prod... which is offering SaaS to startup companies. Services are BSCW, travel management, accounting and tax management, CRM, logistics, ... The services are free for the startups. The revenue is coming from the service providers. Cryptodesk acts as an aggregator. Especially BSCW is a well known scientific collaboration platform. I use it for teaching, management of small and large international science projects. - Ralf Klamma
Thanks for the clarification, Yaroslav. Google's Knol appears to be dead in the water. And about six months ago Encyclopedia Britannica announced a move towards a wiki version--that seems to have vaporized. This is worth a look: http://tinyurl.com/9saj5h - Hope Leman
I don't visit Google's Knol, but what do you mean that they appear to be dead in the water? They seem to be growing in articles. Just 2 days ago or so I read something about Google Knol reaching 100,000 articles/knols in my reader. - Wobbler
Hi, Wobbler. Well, as far as I can tell it just is not gaining any traction or generating any buzz. See this interesting take: http://tinyurl.com/6uhv6u Google Knol six months later: Wikipedia need not worry - Hope Leman
After 6 months, Wikipedia had just a few thousand articles. I don't think the fact that it hasn't yet surpassed or rivalled Wikipedia is either surprising, or cause for the people behind Knol to be concerned. - Michael Nielsen
This doesn't quite qualify - not really user-generated content - but 23andMe provides a large social web component as part of its service. Get your genome sequenced, share it and discuss with others. They also try to use the community to gather data for research through surveys. All kind of one-way though - content mostly goes from company to users, with some user-user interaction. - Shirley Wu
Hi, Michael. The key difference is that Wikipedia didn’t have a Wikipedia to compete with. Knol has a Wikipedia to compete with. Wikipedia is pretty well entrenched and Google doesn’t seem to know how to market Knol. Anyway, won't it be fun to see what happens? As to Shirley’s point, if a large social Web counts and user-generated content is what we talking about then does the buzz and... more... - Hope Leman
NextBio is primarily at SaaS company at this point but we are working on building our community/social web component. The SaaS component was the first step in our development because it pays the bills. Now that we are financially stable we are taking on developing an online community which will help scientists find and share information using the online communication tools that are common in social networks. Lisa - NextBio
Hi, Lisa--this sounds intriguing, "...we are taking on developing an online community which will help scientists find and share information using the online communication tools that are common in social networks..." We blog about such matters at Next Generation Science. - Hope Leman
Deepak Singh
Best after hours discussion at #scio00 ... Does @neilfws really exist?
the skepticism is understandable; I exist in the future for most people :) - Neil Saunders
although Michael Nielsen will confirm that someone at least claiming to be me has physical form... - Neil Saunders
Neil, I haven't seen Michael Nielsen in person (how can I trust a random video posted on the internets?). That isn't a sufficient proof. - Pawel Szczesny
I can also confirm to have met a person at ISMB in Toronto who claimed to be Neil - Lars Juhl Jensen
Still there's no proof of Neil's existence, but I see some hints accumulating. One should probably do a meta-analysis? - Pawel Szczesny
I had dinner with him, and my wife met him too. He might be real. - Paulo Nuin
Please, help us to decide if he really exists http://tinyurl.com/7fla7c ;-) - Pierre Lindenbaum
So if we all say he doesn't exist - Mr. Gunn
... you could end up questioning existence of Australia ;) - Yaroslav Nikolaev
Thomas Lemberger
[REPORTS] Self-Sustained Replication of an RNA Enzyme - http://www.sciencemag.org/cgi...
its aallliiive :) - Pedro Beltrao
Pedro, +5! +)) - Yaroslav Nikolaev
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