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Jean-Claude Bradley › Likes
The US gov is inviting comment on the Public Access to Science and Technology. http://friendfeed.com/mrgunn... I know we have some comments, can we draft a quick letter?
Bora Zivkovic, Alejandro Montenegro, Cameron Neylon and 6 other people liked this
I assume international input is welcome.
- Mr. Gunn
Don't have much time to help draft but will try -- and will certainly sign.
- Bill Hooker
ditto Bill
- Jean-Claude Bradley
ditto Bill, too
- Graham Steel
Will be happy to contribute and carry work load. Would it be worthwhile to write an 'international' letter that could be forwarded to individual govts (a letter that would be put forward globally, and simultaneously, with signatures from around the world).
- Kubke
Can look over drafts and do tinkering if it is useful...or just sign if it isn't
- Cameron Neylon
Cool, I'll start something on Etherpad.
- Mr. Gunn
What should social software for science look like? - http://blog.openwetware.org/science...
Björn Brembs, Bora Zivkovic, Mary Canady and 15 other people liked this
FF doesn't meet all your requirements but it does seem to work well compared to the specialized services - at least in some fields
- Jean-Claude Bradley
Well I guess that's not surprising given my biases - at some level I'm more interested in what people think I've missed than my own predjudices though. FWIW I think a clever combination of DropBox, FriendFeed and some of the elements from StackOverflow, with perhaps a bit of the coordination ability of posterous would go very close to the mark. Still need better network and filter management tools though - somehow they need more configurability but less configuration...
- Cameron Neylon
OpenWetWare is looking to make a major overhaul in the next couple months, and has a bit over 1 year of funding left. I feel like this is an opportunity to at least try to do some of the things that most people think are necessary for SS4S. Not perfect, but better so that we'd have a better idea of what is really needed. I think the time frame (now; already funded) makes "not perfect" a...
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- Steve Koch
I really like what you said in point 10. It's something that I've seen far too many scientists being cavalier about. Federation, open protocols and specifications, along with open source, are very important to science.
- Christopher Granade
Might be worth seeing how far sourceforge meets your criteria. Certainly it's totally based around objects, i.e. software projects, and there are lots of high quality open source science projects whose code is hosted there. Although it has community/social networking tools I've personally never really used these and most visits I've had to sf have either been fleeting (to download...
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- Dan Hagon
Most Ugly & Useless Infographic Competition: The Winners - http://infosthetics.com/archive...
Rajarshi Guha and Jean-Claude Bradley liked this
To me, this shows a need for quantitative literacy across the disciplines.
- Andrew Lang
I have some ugly chem data to highlight after my class is over...
- Jean-Claude Bradley
#ahm09 interesting, scientists are afraid to share data because others might mis-interpret the data, though this hardly ever happens.
suelibrarian, Mike Chelen, Richard Akerman and 6 other people liked this
Has there been much research into this (i.e. quantified "hardly ever")?
- Sarah Kendrew
I think a bigger reason is they don't want people seeing errors - every experiment has some kind of "error" - especially an unmeasured quantity that turns out to be important in the end
- Jean-Claude Bradley
As I said on twitter, really think this is just an instance of the control imperative. Scientists are for the most part very uncomfortable with relinquishing direct control over anything that affects them - they want to make every decision as far as possible and the idea that for a framework to scale you have to give up control over thing seems very alien. But I too would like to see some data and analysis on the issue - a fair bit of high profile data misinterpretation going on at the moment.
- Cameron Neylon
scientists concerns can help be addressed by advancing methods and best practices, and by describing case studies to provide confidence. accuracy is an inherent purpose of knowledge sharing, it is a testament to the high level of skill that it is usually accomplished
- Mike Chelen
Well, the imperative to 'show your work' can make people very uncomfortable. I see this all the time in the Open Source world, where developers sit on their code polishing it instead of releasing.
- Michael R. Bernstein
I wish there was a universal format for submitting peer-reviewed papers; authors could post papers (once!) & then the journals bid on them.
Mickey Schafer, Cesar Sanchez, Nir London and 32 other people liked this
Oh, now that's an interesting idea, Karen.
- Graham Steel
Cyndy Parr tweets ( http://twitter.com/cydparr... ) "This is kind of what PLOS One envisions -- it goes up there, and then it could get chosen to be part of a hub". Iz true?
- Karen James
Thanks, Graham. Having just had a paper rejected by two journals in a row, I'm fed up to here *points to own eyebrows* with spending hours if not days re-formatting to meet the ridiculously precise but in no way substantive guidelines of different journals. It's not even rewriting, it's just pointless fiddling and a silly waste of time. If the taxpayers only knew...
- Karen James
There are two issues at hand here. One, a universal format for submission, Two, a bidding process on papers. The Neuroscience Peer Review Consortium points to how the second part of this kind of deal is working right now in some disciplines (http://nprc.incf.org/), the really really sad part about the first issue here is that the big publishers don't care what format you submit in (let...
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- Ian Mulvany
+1 for more standards for paper submissions, starting with reference styles. And for allowing submissions in the NLM DTD format.
- Martin Fenner
Ian, you may say they don't care, but when one is submitting a manuscript, one is trying to do everything one can not to give the publisher any possible little excuse to reject your paper without review.
- Karen James
Second time in a week that someone stated "publishers don't care about format of submissions". Again I ask: if that's the case, why do all journals make a huge deal about it in their instructions to authors?
- Neil Saunders
As for universal format: easily solved by writing our papers on the web. Imagine a simple forms-based interface with fields for title, authors, abstract, introduction... Imagine a button in Google Docs that says "submit this document to <insert journal here>" !! But currently, we all like to use our own word-processing software on our own machines, then upload a document in a multitude of formats. It's going to take a big shift in thinking and work practices.
- Neil Saunders
What Neil said: if journals don't care, why do they make such a damn song and dance about it? Why not explicitly say you can *submit* in any basic AIMRAD format? Worry about format after acceptance: either the journal can send it to India per Ian above, or if they make the authors do it at least they only have to do it once. My next paper (quit laughing) is going out in basic AIMRAD...
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- Bill Hooker
Note: this is easier for me to do than many, because I've basically given up on an academic career as currently constructed.
- Bill Hooker
"it's just pointless fiddling and a silly waste of time. If the taxpayers only knew" I think they should / deserve to know!
- Björn Brembs
+1 Neil "why do all journals make a huge deal about it in their instructions to authors?" and +1 Björn "I think [the taxpayers] should / deserve to know!"
- Karen James
Neil & Bill: maybe "don't care" is to strong a phrase. A manuscript does need to be structured correctly to fit into the journal's content management system (an application note looks different to a letter looks different to a research paper), have images properly resized and references in the right format so that they can be processed by systems that convert to them links etc.
- Euan
Also: what happened to that Wolfram word processor for papers that was supposed to do what Neil mentioned above with Google Docs?
- Euan
Ah, http://www.wolfram.com/product... but doesn't look like there's a great deal of support for life sci journals (BMC aside)
- Euan
the publishers i know would be delighted to standardise to NLM DTD for submissions -- would save lots of editorial time and production costs -- the publisher i know best sends accepted papers to be manually turned into xml which can then be used for PMC deposition and the semi-automatic generation of the HTML and PDF versions. But things like the Publicon app have taught publishers that implementing the technology to do something doesn't mean that it will happen in significant quantities! :)
- Joe Dunckley
I used Publicon when it was released a few years ago. Essentially a dead product now. Lemon8-XML does what Neil describes as "Imagine a simple forms-based interface with fields for title, authors, abstract, introduction... ": http://network.nature.com/people....
- Martin Fenner
These interviews (about eXtyles and Editorial Manager) might be interesting to those that care about submitting papers in the NLM DTD format, as I specifically asked that question: http://network.nature.com/people... and http://network.nature.com/people...
- Martin Fenner
There is a nascent version of that working in neuroscience http://nprc.incf.org/. Journals have formed a consortium where if an author submits to one journal and it gets rejected, the author can specify that the reviews follow the paper to another journal so that it doesn't need to be re-reviewed. This was viewed as a way for papers that have nothing wrong with them but which don't fit the scope of the journal can be published more quickly and easily.
- Maryann Martone
What about replacing "papers" and "journals" in the subject line with "proposals" and funders?
- Daniel Mietchen
What if journals said here's our LaTeX template. Put the right text in the indicated field, lotion in the basket, and anything else won't be accepted.
- Mr. Gunn
@Daniel Mietchen: Yes, that too! @Mr. Gunn: What I'm advocating is that there's a single LaTeX (or whatever) template - not that you'd re-paste for each journal.
- Karen James
karen, yes. The idea being you give them the text and they do whatever they like with the formatting.
- Mr. Gunn
Aside from making life easier for authors, it would allow sane computational use of papers. With PDF, you don't even know which image a figure legend refers to, except by guess work. The difficulty is that the journals don't see it as their problem. The solution is for the authors to make it the journals problem
- Phil Lord
I like the idea, Karen. Publishing an exciting paper should not a be a torture (for us!)
- Betül
Getting access to research papers is already too expensive. Wouldn't it just be more so if we invited a bidding war on each paper? Write good papers, and submit them to PLoS.
- Ted Slater
I'd like something similar for the review process. Instead of having to register for each journal/publisher managing logins and passwords for each, have a clearing house that manages reviewer information that the journals subscribe to.
- John Hogenesch
UT educator pushed technology as teaching tool - http://www.statesman.com/news...
Jean-Claude Bradley and Peter Miller liked this
Sad news on the passing of Leslie Jarmon - UT educator and SL pioneer. She was the editor for my journal of virtual worlds paper and she did a fantastic job.
- Andrew Lang
The google web toolkit (GWT) 2.0 is now officially available.
Jean-Claude Bradley, Dan Hagon, Cameron Neylon and Allyson Lister liked this
Rumours that first dark matter particle found - http://www.newscientist.com/blogs...
Jean-Claude Bradley, Marcos de Carvalho and Steve Koch liked this
"Update: in an email to the blog Resonaances, Nature's senior physical science editor Leslie Sage has squashed the rumours that a paper is about to appear in the journal "
- Björn Brembs
Amazing gel shows Ubiquitin is transferred one-at-a-time and on a millisecond timescale! - http://www.iayork.com/Mystery...
Andrew Perry, arek, Jean-Claude Bradley and 16 other people liked this
That's awesome.
- Bill Hooker
Ian York rocks, as do the scientists who did this.
- Mr. Gunn
Gels still speak, even without lasers...
- Mark A Jensen
My initial reaction was "how can anyone pipette that quickly !" ... but it seems they have some fancy quench-flow equipment to get around that problem. Very cool.
- Andrew Perry
Lord, grant me the strength to massage the data I can, the serenity to accept the data I can't, and the wisdom to know the difference.
Jean-Claude Bradley, Michael Kuhn, Duncan Hull and 4 other people liked this
Proposal for Science 2.0 lectures - http://freelancingscience.com/2009...
Piotr Byzia, Berci Mesko, MD, Steve Koch and 7 other people liked this
I think the compatibility of IP and ONS is a very interesting topic - Steve Koch has an agreement with his research office that might make it partially compatible
- Jean-Claude Bradley
Jean-Claude, thanks for the pointer. I need to look into that. Also, Paulo Nuin commented on the blog that I could (and I will) mention data attribution.
- Pawel Szczesny
That's a great list. And data attribution and citation, maybe data management in general would be good additions. Paulo on the ball as always...
- Cameron Neylon
Agree with Jean-Claude that IP / ONS is interesting. Happy to provide any info on our very narrow and limited experience with the issue here at U. New Mexico.
- Steve Koch
Steve - hopefully we'll discuss that a bit at the ONS session in NC
- Jean-Claude Bradley
Mendeley at LeWeb ‘09 - http://www.mendeley.com/blog...
Jean-Claude Bradley, Ricardo Vidal and Daniel Mietchen liked this
EtherPad Blog: Google Acquires AppJet - http://etherpad.com/ep...
Dan Hagon, Richard Akerman, Nicola Greco and 2 other people liked this
"We are happy to announce that AppJet Inc. has been acquired by Google. The EtherPad team will continue its work on realtime collaboration by joining the Google Wave team."
- Daniel Mietchen
from Bookmarklet
"If you are a user of the Free Edition or Professional Edition, you can continue to use and edit your existing pads until March 31, 2010. No new free public pads may be created. Your pads will no longer be accessible after March 31, 2010, at which time your pads and any associated personally identifiable information will be deleted."
- Daniel Mietchen
OK, now I have to start using Wave?
- Peter Miller
Etherpad was immensely more functional for realtime collaboration than google docs . This development was predictable..considering that wave is still so hard to grock
- Hari
I think the key for casual users of wave is that robot that email you when there is an update - Cameron gave me that trick. It was broken for a few days last week but seems fine now. Otherwise it is hard to keep checking wave for updates as part of your workflow. BTW - is there a way to get email alerts when wikipedia pages change?
- Jean-Claude Bradley
What is the address of that robot? Strange, though, that the supposed replacement of email doesn't work without it - let's hope this is just transitional.
- Daniel Mietchen
Daniel the robot can be added to any wave as wave-email-notifications@appspot.com
- Jean-Claude Bradley
There's also an XMPP jabber bot that sends you an IM when a wave is updated, that's what I use.
- Mr. Gunn
Thanks, Jean-Claude; put it on some waves and will see what this gives.
- Daniel Mietchen
Noticed that the bot was already on most of the waves I have been on for weeks, but not a single notification reached me so far. Back on topic: Etherpad will remain operative until at least when they release their source code. http://etherpad.com/ep... .
- Daniel Mietchen
Daniel - if the bot is working it shows up at the very top of the Wave - it might be set to OFF and it will give you a link to activate it. If you see a broken image it is not working at all
- Jean-Claude Bradley
Thanks - got the activation links in some waves, though not in others. No broken image.
- Daniel Mietchen
Got my first notification. Thanks, Jean-Claude.
- Daniel Mietchen
Submitted CAREER proposal & posted to Scribd: http://www.scribd.com/doc... Open proposal for an open science project!
mkz, Michael R. Bernstein, Graham Steel and 20 other people liked this
Thank you to everyone who helped and encouraged on this and offered future support! Among many things, one thing I'm a bit embarrassed about is the lack of details in the "broader impacts" and open science parts of the proposal. Definitely it needs more planning and better writing, and the panelists are going to point that out. Hopefully you all understand that it's a product of spending all my time trying to make the research parts as good as I could.
- Steve Koch
good luck Steve!
- Jean-Claude Bradley
A small step for a team, but a giant leap for #science .
- Daniel Mietchen
Good luck!
- Brian Krueger - LabSpaces
Thanks everyone! I sort of dropped off the map after submitting the proposal. One of my most successful attempts at actually vacating during a vacation.
- Steve Koch
Bummer! Just found out tonight that the proposal was not funded. I have done one read-through of the reviews. First of all, I am once again amazed at the time and effort the reviewers put into reviewing my proposal. There were 6 reviewers in total and they all had a page or more of feedback. And they all pretty much agreed on the main points: (a) interesting proposal that is worth...
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- Steve Koch
Thank you Jean-Claude, Andy, Cameron, and Drew for the Open Science support letters! I am sure that was key to the very positive reviews for Open Science. Thank you to everyone else on friendfeeed who supports me and our other lab members. We now have 7 months to obtain the preliminary data and get a couple publications, and indeed we are now poised to do so. I am confident the lab members can do this, and by eliminating (b) and (c) above, all signs point towards this being a very strong proposal next time.
- Steve Koch
well done all 'round! next time you'll knock 'em dead.
- D0r0th34
for the CAREER third time is often the charm - good luck for next round
- Jean-Claude Bradley
Thanks, Jean-Claude and Dorothea. The CAREER "3rd time's a charm" effect is part of the reason I submitted without strong preliminary data. (But I also thought we'd be able to generate the data in time for the 2nd submission. Now, though, I'm SURE we can before July :) )
- Steve Koch
After thinking about it for a couple days now, I am still very happy that they viewed the open science so positively. I think that's a big deal.
- Steve Koch
absolutely Steve - very good feedback about OS being a positive to the funders
- Jean-Claude Bradley
Steve, this looks really really promising. If you can come up with interesting data for the next resubmit, I think you have a great chance to get funded. Congratulations!
- Bill Hooker
Thanks, Bill!
- Steve Koch
PhD Dissertation analysing PLoS ONE Comments and Notes (vs Science) from the perspective of rhetoric: "Mutable Mobiles: Online Journals and the Evolving Genre Ecosystem of Science" http://www.lib.ncsu.edu/theses...
Jean-Claude Bradley, Bora Zivkovic, Daniel Mietchen and 2 other people liked this
Abstract: This dissertation addresses the related questions of how online communication technologies may be affecting communication in science and, more broadly, how new ways of interaction in online spaces may affect how texts enact genres. Genres have been usefully thought of as typified discursive responses to recurrent social exigences, and much recent work has shown that genres often work together in assemblages with other genres to address these exigences. The work reported here examines four online tools for post-publication feedback on and review of articles published in two scientific journals: the online-only, open-access journal PLoS ONE, published by the non-profit publisher Public Library of Science, and the prestigious journal Science, published by the American Association for the Advancement of Science. The communication in these tools is examined using both quantitative methods and qualitative rhetorical criticism as well as the perspective of actor-network theory. A...
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- Peter Binfield
'One of the bioscientists asked the data storage firm used by one of the labs recently about the costs associated with accessing data from studies conducted a few years ago. The company replied, "you wouldn’t want to pay us to do that. It would be less expensive to re-run your experiments."' Holy WTF, Batman.
Paul Bacchus, Steve Koch, suelibrarian and 6 other people liked this
Oh my!
- Katy S
See also "don't keep the raw data because if you do and we get into a patent dispute it will all be discoverable. Much cheaper to re-do experiments than pay lawyers to look at them..."
- Cameron Neylon
RT @VFielding:Toured Drexel U this morning, very impressive, had no idea this school is so cool. Great entrepreneurship program too.
Jean-Claude Bradley liked this
I am super excited about Chem4Word - an open source add-on for rendering chemical structures in Word!.http://research.microsoft.com/en-us...
Dan Hagon, Peter Miller, Cameron Neylon and 2 other people liked this
Molecular Representation, Similarity and Search - http://www.slideshare.net/rguha...
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Noel O'Boyle, Deepak Singh and Jean-Claude Bradley liked this
Slides from a Guest Lecture at Drexel University - http://blog.rguha.net/?p=460
Jean-Claude Bradley liked this
IBM: Computing rivaling human brain may be ready by 2019 http://news.cnet.com/geek-ge...
Piotr Byzia, Naz, Jean-Claude Bradley and 2 other people liked this
According to IBM, 'BlueMatter, a new algorithm created by IBM researchers in collaboration with Stanford University, exploits the Blue Gene supercomputing architecture in order to noninvasively measure and map the connections between all cortical and sub-cortical locations within the human brain using magnetic resonance diffusion weighted imaging. Mapping the wiring diagram of the brain is crucial to untangling its vast communication network and understanding how it represents and processes information.'
- Ami Iida
"some of the world's most prestigious universities have already managed to simulate the computing complexity of the feline cortex" - gotta be hype
- Jean-Claude Bradley
as a cat owner, I know that's a very low bar to clear.
- Mark A Jensen
They've known the connectome of C. elegans for 20 years and still can't make a model work like the real animal. We will still learn a lot from failure, though, as usual in science.
- Björn Brembs
Bjorn - that really is the point - the connectome is not enough. Even is simple species like elegans is there not hormonal and other modes of communication besides synapses? Is it understood why the models don't work well?
- Jean-Claude Bradley
A Presentation to Students at Drexel University Via Webex and Skype - http://www.chemspider.com/blog...
Alexey, Peter Miller, Graham Steel and 3 other people liked this
It was an inspiring talk Tony - thanks for taking the time. In all the talks we had at U of Ottawa 20 years ago I don't think we could have guessed that this what would be happening to chemical information today.
- Jean-Claude Bradley
I like the way you can click on different parts of the InChIKey and have it do searches automatically - I didn't know that before - very cool.
- Andrew Lang
JC...if you'd asked me almost 20 years ago whether I'd be working on a project like ChemSpider the answer would be a big no. I certainly wouldn't have envisaged the progress that we have seen in computer-based chemistry....the internet wasn't even a term we had heard back there in Ottawa!
- Antony Williams
yes we actually physically went to the library back then :)
- Jean-Claude Bradley
Finished a proposal for three lectures on practical aspects Science 2.0 targeted towards PhD students.
Steve Koch, Jean-Claude Bradley and arek liked this
The overview of the proposal is already on my blog: http://freelancingscience.com/2009...
- Pawel Szczesny
Fwd: FriendFeed not dead yet, so it appears, so we can discuss #scio10 in the room there: http://friendfeed.com/science... (via http://friendfeed.com/coturni...)
Kubke, Jean-Claude Bradley, Michael Nielsen and 2 other people liked this
FriendFeed not dead yet, so it appears, so we can discuss #scio10 in the room there: http://friendfeed.com/science...
Steve Koch, Mr. Gunn, Jean-Claude Bradley and 3 other people liked this
Why Doesn’t Size Matter…for The Brain? - http://www.scientificblogging.com/mark_ch...
Jean-Claude Bradley, Björn Brembs and Steve Koch liked this
"So, here’s a plan. I would like to hear your hypotheses for why brains increase so quickly with body mass (namely as the 3/4 power). I will let you know if the idea is new, and I will see if I can give your idea a good thrashing. What’s at stake here is our very framework for conceptualizing what the brain is. Perhaps you can say why it is a computer, and that greater body size brings in certain subtle computational demands that explain why brain volume should increase as it does with body mass. Or, more exciting, perhaps you can propose an altogether novel framework for thinking about the brain, one that makes the enigmatic “size matters” issue totally obvious."
- Daniel Mietchen
from Bookmarklet
Have yet to go through the comments but will probably join the discussion, as I am collecting interesting tidbits to put into http://en.citizendium.org/wiki... .
- Daniel Mietchen
First thought is that this might be the fractal dimension of the nervous system and that brain growth is just a response to nervous system growth.
- Andrew Lang
I'm going to do a round of looking at some of the Science Social Networking sites again. Is anyone active on ResearchGate, Epernicus etc. and interested in testing functionality?
Jack H. Pincus, Dan Hagon, Elizabeth Brown and 23 other people liked this
I'm interested in joining the testing. Need to agree on criteria for comparison before starting, though.
- Daniel Mietchen
I'm willing to keep an open mind but so far FF surpasses these in terms of networking and ease of use. But if you want to experiment I have accounts in many of these and I would be willing to try.
- Jean-Claude Bradley
I'm really just looking to make sure that things haven't moved on and improved significantly, particularly in the light of the NIH projects.
- Cameron Neylon
I tend to migrate to social networking sites based on "pull" - virtually the only time I go on LinkedIn or Facebook is when I get an email alert to something relevant to my interests. I would assume that if there was anything really cool going on in these new sites I would get these alerts generated by actions by you and my other friends.
- Jean-Claude Bradley
BTW Cameron - that is one of the issues I'm finding with Wave - I tend not to check it because I don't get alerts that there are updates - is there a way to get an email alert for Wave updates?
- Jean-Claude Bradley
Yes, there is an email alerter. I'll add you and it to Wave...
- Cameron Neylon
Agreed to the general point though - if there isn't a pull, I'm not going there really. And I think that is a big issue with Wave - people just aren't checking in.
- Cameron Neylon
@Jean-Claude I don't think there's currently a way of doing this with the current interface without adding a robot but I saw there's a robot on the Haskell public wave which has similar support http://wave-xmpp.appspot.com/public...
- Dan Hagon
I'd be interested in testing (I recently started looking over Epernicus for an article on NGS). Where is the email alerter for Google Wave? Currently, I'm using Waveboard (Mac), which alerts you when there's activity. However, it needs to be running in order to do so.
- Walter Jessen
Just added you to a Wave with the email notifier Walter...
- Cameron Neylon
New SNS from American Institute of Physics, got email invite today: http://www.aipuniphy.org/
- Andrew Lang
I have accounts on Epernicus, SciLink, Laboratree, and maybe could consider BenchFly a social networking site too, but like JC, I don't go to any sites besides FF and Twitter (and those are typically through 3rd-party apps), not even Facebook or LinkedIn, unless I get some alert. But I would be happy to see if anything's changed in those science-oriented sites I mentioned
- Shirley Wu
from twhirl
I do get alerts that new people have joined the organic chemistry group in Research Gate but there is no discussion and my questions have not been answered there by anyone so not much motivation to check in.
- Jean-Claude Bradley
I have accounts at NN, Epernicus, BioCrowd and SciLink. I have begged for account deletion at the latter for months, to no avail and have not visited most of the others for as long as I can recall. So: active - no, interested - no. It's all FF/Twitter for me.
- Neil Saunders
It's alright - this is a benefit of the doubt exercise - making sure that things haven't changed or that we've missed something. My brief look around yesterday suggested that nothing much has but I wanted to make sure I'm not missing something.
- Cameron Neylon
What about the criteria for comparison other than some "pull" functionality (which they all seem to have, to different extents)? Does usability boil down to feed import/ export and (hierarchically) threaded conversations ordered by novelty and importance, as at FF?
- Daniel Mietchen
When considering the usefulness of the individual platforms, perhaps discipline-specific ones should also be on the list? Besides http://polymathprojects.org/ (maths), these would include, for instance, http://openanthcoop.ning.com/ (anthropology), http://www.apecs.is/ (polar research), or this very life science group at http://friendfeed.com/the-lif....
- Daniel Mietchen
It would be worth doing a compare and contrast - also things like Math Overflow and even some of the chemistry blogs act more like community sites. Seems particularly apposite with respect to Pawel's blog post yesterday about the idea to set up a next generation sequencing community site.
- Cameron Neylon
I have a ResearchGate account but don't actively use it. I currently do some FriendFeed, Nature Network (where my blog is hosted) and Google Wave, but mostly Twitter.
- Martin Fenner
The last issue (November 23) of the German computer magazine c't has an article on social networking for scientists. They like ResearchGate and Mendeley, but also include ResearcherID, Scholarz (a German network), Nature Network, SciLink and Scientist Solutions: http://www.heise.de/ct...
- Martin Fenner
That c't article (which shall come out in some OA fashion soon) may serve as guidance but I found the choice of networks therein rather arbitrary, and the comparison between sites was done on a more general level rather than on the basis of specific criteria.
- Daniel Mietchen
The article makes two obvious omissions: a) no mention of CiteULike (or Connotea), b) no mention of the recent $12 Mio social networking NIH grant to U of Florida/Cornell University. There are some more things in it I don't like, so I wrote a letter to c't magazine.
- Martin Fenner
Cameron, what criteria were you thinking of using?
- Mr. Gunn
Key questions: a) What is the immediate impression on signing up? Is there a pull for people to come back? b) What functionality is being offered? Is it immediately available? How dependent is it on having a network in place? c) Funding model and stability d) User numbers, ideally active users and accounts, but whether we can get those is another question. Those aren't very objective criteria and they are built on my biases but nonetheless
- Cameron Neylon
Sorry if this is slightly tangential to the discussion, but I was imagining a new kind of social network for publication of research results here: http://virtualchrisleonard.co.uk/blog...
- Chris Leonard
Chris - when you talk about "credit" are you expecting tenure and promotion committees to count it or do you have some other system in mind? If you set something up I have content that might be suitable to play with. As for citability - in our last few papers we have used blog posts and wiki pages as references and have not had any problems with that - so I think the system is quite flexible and can accommodate the types of activities you are proposing.
- Jean-Claude Bradley
I think Chris means system credit or karma. The idea as I understand it is somewhere between Friendfeed and Stack Overflow
- Cameron Neylon
Thanks Cameron, yes, that's what I meant by 'credit' - however, by quantifying and metricising that credit, there is a possibility that one day tenure and promotion committees may want to use it as another measure of a scientists influence in a field. Apologies to Cameron for hijacking his thread. There is another discussion on this blog post here: http://friendfeed.com/chrisle...
- Chris Leonard
That's fine, it's not my thread, it the communities thread :-) Pointers are good, they link up the information.
- Cameron Neylon
Blog postings to replace (journal) papers and (in-depth) peer review a luxury that can only be acquired if paid for and to be replaced by blog comments instead? Weakening both readability and certification? That does not sound like a healthy idea.
- Wobbler
Wobbler: why should blogs lack any aspect of peer review? the standard of any publication depends on how editorial powers are used
- Mike Chelen
...and we already pay for peer review. It just isn't a cost transferred as actual cash.
- Cameron Neylon
But blogs do not have any editorial powers? What advantage do blog postings have over (journal) papers? They lack format = lack of consistency = lack of efficiency = lack of scalability. Are you seriously suggesting that blogging/blog posts have the potential to replace journal publishing/ (journal) papers as the primary scholarly communication model/channel? Upgrading the traditional...
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- Wobbler
@Cameron: that's true, but now peer review is at least mandatory for the primary scholarly communication model i.e. scholarly publishing. Replacing that with something else and having peer review only on request/payment is a very different story.
- Wobbler
Wobbler - there is a difference between requiring the peer review to be performed before making some information public and allowing it to take place after that. I do not see why the latter option would generally fare worse than the former. In fact, we already practice it here at FF, with numbers of likes and comments roughly indicating the popularity of a topic, while the quality has to be sought in the individual comments (and of course the source item that started the thread).
- Daniel Mietchen
... it isn't a cost transferred BY YOU as actual cash. Yet. It should be, in my not-terribly-humble opinion, however, because the market disconnect in the current system has proven ridiculously unsustainable. Wobbler, some of my blog posts have had more measurable impact than anything I've ever written. Sure, it's a lightning-strike sort of thing, and most of my blog posts languish in...
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- D0r0th34
@Daniel: I'm not talking about post-"publication" peer review. That's still different from random blog commentary on blog posts. There's no evidence that what we're doing here isn't just a "niche" thing that works well because we're a niche. There's certainly no consistency in quality in our blog postings (well, at least not in mine :p ). Not to mention a lack of consistency in...
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- Wobbler
@D0r0th34: No, we should absolutely not ignore lighting strikes. But we should see them as lightning strikes and consider them to be an exception more than a rule and focus our attention on something that provides that level of quality more as a rule than an exception. Blogs as a complement to (journal) papers is great. But once you start to see it as a primary source, a replacement for...
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- Wobbler
We don't know about our OA bets. As for slow-and-steady, a well-run blog isn't? Lightning strikes aside, building a reputation and a readership is hardly an immediate thing.
- D0r0th34
@D0r0th34: That's one more reason why blogging as the primary scholarly communication model is a broken idea. "Popularity" and "building a readership" will be important for blogs (and other post publication peer review models) to be visible/significant. But aren't we going after journals for using their JIF to attract peeps to read their stuff? How is "blog (poster) popularity" to get a...
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- Wobbler
I think the most important property of non peer-reviewed scientific communication is that the content be easily indexed and searchable. Relying on comments and rankings can be very misleading indicators for utility in long tail systems. For example we get over 100 searches a day for our solubility data via Google and Wikipedia but we have never had a comment or any type of feedback from the people who searched for and found information.
- Jean-Claude Bradley
Shrug. System-gaming goes on everywhere; there are a number of studies of citation-impact gaming, if you look. Also, why is connectivity a bad thing? We are talking about scholarly *communication* after all, right? Restricting "what counts" only to what goes through the baroque serials-publishing process is IMO an extraordinarily blinkered and limiting view of how knowledge really advances. Sure, it's not easy to come up with more inclusive views -- but that doesn't mean it's not worthwhile.
- D0r0th34
The problem is that I'm not sure we can talk about "gaming the system" rather than "an intrinsic part of the system that everybody will be forced to play or greatly risk invisibility" when it comes to blogs and other models relying on postpublication "peer review". PLoS ONE is, intentionally or not, already trying to stake their claim on an as large a readership/community as possible....
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- Wobbler
@D0r0th34: And connectivity can be unfair if your serious/scientific works are getting more attention than others simply because you've managed to draw a bigger crowd through non serious/scientific stuff. On a slightly more personal note: for someone who occasionally complains about the (lack of) readability of (journal) articles, I had expected that you, of all people, would appreciate...
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- Wobbler
I have to say reading down this I am unsure of whether the complaints apply to blogs or journal articles. Consistent structure and copy editing would be nice but it is rare for both blogs and journal articles. Quality is an issue across the board. Going back to peer review - it's only mandatory for the author, refusal rates for reviewers are going through the roof and unless we acknowledge that cost the system will collapse sometime soon.
- Cameron Neylon
@Cameron: Consistent structure and copy editing are rare for journal articles? They are? Not entirely sure about copyediting, but surely most, if not all, journal papers have a recognizable structure? And I don't think they're as rare or rarer than for blog postings. I also think the issue is with peer review, and not with the (journal) paper (format). As such, we should find ways to...
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- Wobbler
Of my recent papers, only one received close copy editing by anyone but me. And that was the Nature piece for which to be honest I would have been happier if the editor had got a co-credit. And formats are all over the place - maybe consistent for a single journal but that's not use to me. The costs of both peer review and publication are so high we need to find a way to lower them -...
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- Cameron Neylon
@Cameron: I'm not sure that's a convincing enough argument for me. Maybe your other papers were written clearly enough already? You're a prolific blogger/writer, Cameron. It's not weird to assume that your ability to communicate concepts clearly is higher than the average scholar. Maybe high enough to not warrant copyediting (in a lot of journals)? My impression of journals is that...
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- Wobbler
Well others can pitch in but perhaps a different anecdote. Until I started getting into arguments with Maxine Clarke I didn't even realise that journals might do copy editing. Nature and similar are very different beasts to the average of course.
- Cameron Neylon
So, generally speaking, only the high profile/impact journals provide copyediting services? Hmm, that is definitely not what I expected. If you had to estimate the % of journals that provide copyediting services, what % would that be? The (top) 10% of all journals?
- Wobbler
I have the same experience as Cameron - the only time my manuscript was copyedited was when I published in Nature
- Jean-Claude Bradley
So far as I'm aware, no-one here wants to replace peer-reviewed journals entirely by blogs. Yet that seems to be what you're arguing against, Wobbler. For some functions, journals are a lot better than blogs. But for other functions, blogs are a lot better than journals. At the least, I really can't imagine how, say, DHJ Polymath or Galaxy Zoo or the Open Dinosaur Project or [fill in...
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- Michael Nielsen
Most of this is as a response to an FF comment by Chris Leonard on the 23th of November in this thread, who is arguing for exactly that.
- Wobbler
Cameron, any progress on the roundup? Is there any information I can provide from Mendeley?
- Mr. Gunn
Right - getting there slowly! Have set up a wiki page (ignore the state of the rest of the site I am working on it!) at http://wiki.cameronneylon.net/index... You should be able to login with openids, any problem give me a yell. I would suggest a week by week schedule to dive into and try and use a specific site, give it a good shot and then report as we go. I...
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- Cameron Neylon
Cameron, what do you mean by "stability" - things like a service being bought/shut down vs. server outages? What about one week to agree on parameters and sites to check? I added data portability.
- Daniel Mietchen
I was thinking more of medium to long term financial stability - but technical stability is a good criterion in terms of functionality. Data portability is a good point!
- Cameron Neylon
Cameron, I spoke with Drew Endy, Bill Flanagan, and a couple other PIs that use OpenWetWare (Maureen, Pam) last week about the future of OWW. There are two major issues (a) funding and (b) overhauling the platform. I think funding will work out, if we can figure out what is the best way to do (b). Bill and Drew have some good ideas at this point, but in my gut I think we're still not...
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- Steve Koch
I guess my easy question for everyone who's familiar with OWW: Do you think with the resources we have (one full-time excellent lead developer) we can transform OWW into a killer openscience resource for many more people going forward? One thought that keeps coming to me is that something could be (needs to be) done to tap into the energy of the user base. I.e., obsessed students who...
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- Steve Koch
Another thing that keeps coming into my head since the conference call last week: FriendFeed is quite possibly very similar to what many people need for OpenScience. As far as science goes, we generate information from all kinds of different sources (Machine-specific data; gel photos; microsoft word; evernote; scratch paper; blogging; etc.). This needs to be aggregated and shared in a...
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- Steve Koch
Oh, and to clarify a bit: I don't want to replace FriendFeed with OWW. I want to use the FriendFeed model as a starting point for the new OWW. As an OpenScienceAggregator / Networking tool. As others have pointed out, much of the value of friendfeed is that it's not limited to scientists generating data.
- Steve Koch
Steve, that's a great way of asking the question. I'd go one step further and say how can we make it the framework in which we can integrate all the other things we do on other services. It's never going to be a no-brainer to move from what you use to something else - there is always the simple problem of the activation barrier to change - its a question of the balance. But my guess is...
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- Cameron Neylon
Cameron, I agree with you exactly: I don't want people to switch, and indeed I want to think "one level above." Do you think there's a real possibility for doing that?
- Steve Koch
If we could coordinate a series of activities and get proper funding then yes. Quite a lot of interest in the pieces of this (including the grant I'm currently rushing to finish), Chris's ideas further up this thread, OWW obviously, Mendeley/Citeulike/Zotero. But coordination is the hard bit - and getting agreement that its what enough of us want. Do I think we have a clear idea of what...
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- Cameron Neylon
Animation of influenza replication - http://www.microbiologybytes.com/blog...
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Eureqa | Cornell Computational Synthesis Laboratory - http://ccsl.mae.cornell.edu/eureqa
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"Eureqa is a software tool for detecting equations and hidden mathematical relationships in your data. Its primary goal is to identify the simplest mathematical formulas which could describe the underlying mechanisms that produced the data. Eureqa is free to download and use. Below you will find the program download, video tutorial, user forum, and other and reference materials."
- Fulaan, inna Hebel
from Bookmarklet
cool
- winckel
patient HM's brain microtomy live http://thebrainobservatory.ucsd.edu/hm_live...
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that is pretty cool
- Jean-Claude Bradley
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