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Mickey Kosloff › Likes

Cameron Neylon
Faculty of 1000 strikes a blow against the Ingelfinger Rule - http://embargowatch.wordpress.com/2011...
Maybe we need a run of "Give the finger to Ingelfinger" t-shirts? - Cameron Neylon from Android
With a list of journals to name and shame on the back? - Cameron Neylon
agreed, awesome :) - Heather Piwowar
It has always bugged me that JAMIA follows the Ingelfinger rule. You have Informatics in title! Be about maximizing use of information! - Heather Piwowar
@Graham: I get 403 errors... - Björn Brembs
hahahahaha, these are great - Meg VMeg
Love it, looking forward to seeing these on Camden Market. Actually, it's not just an issue with posters/abstracts, as some of the journals seem to have very similar policies regarding pre-publication release of data and pdb structures. Policies regarding data doi's are not clear yet, but Cell (Elsevier) recently told us if data released in this way represents a significant contribution to the importance of a related article, then access to it should be embargoed until the article is published. - Scott Edmunds
re: zazzle, I won't use a commercial site that *requires* me to sign in just to see their products. - Bill Hooker
And the flickr picture is Ingelfinger giving the viewer the finger. The hand should be the other way around, surely? - Bill Hooker
Jan Wessnitzer
Michael Nielsen
Georgia Tech, Duke University, and University of North Carolina - http://michaelnielsen.org/blog...
Björn Brembs
Peer reviews: make them public - http://www.nature.com/nature...
I've thought about including reviewers' comments in "behind the scenes" blog posts about my papers, as a step towards transparency. I'd certainly be interested in reading peer reviews of papers I've liked (or not liked). But on a broader scale, I wonder if institutionalizing this process would be a more feasible step towards reforming peer review as compared to, say, completely open/signed reviews (as Daniel alludes in his first sentence). - Jason Snyder
There are a couple of journals now that publish the referee reports along with paper (ex. EMBO J and Mol Sys Bio). I think it is interesting to be able to go read them for those cases where you want a lot of detail. - Pedro Beltrao
Starting to publish reviews along with the accepted papers is a good initial step, yet qualitative change is more likely to happen when reviews of rejected papers (or grants, for that matter) are likewise being made available. - Daniel Mietchen
Yes, BMC is ahead of the crowd in this regard, but they lose interactivity by publishing the review process only after (and only if) the paper has been accepted. The two-step process in use at EGU journals (where the submitted manuscript is public, as are the reviews and comments) is more inviting to community participation (about 25% of their articles receive comments from beyond the... more... - Daniel Mietchen
Submission fees do indeed not feature prominently in the discourse, and I agree that they merit more attention. - Daniel Mietchen
I like how Friendfeed's email updates for this discussion are delayed by 3.5 weeks... - Jason Snyder
Do any journals have policies about whether it's ok for authors to publish reviewers' comments (on a blog, for example)? Could get in trouble for doing it? - Jason Snyder
Good question. I"ve published reviews on my blog, but mainly grant application reviews. - Björn Brembs
Jason++ (interesting question!) - Egon Willighagen
Jason, I don't think it would be big trouble, I think they'd just ask you to take them down as a first step, if they care. Seems a worthwhile place to ask for forgiveness rather than permission. I'm planning on posting some conference reviews I've received this way, shortly... in addition to all the other good reasons, very helpful for newbie submitters and reviewers to see more examples, I think. - Heather Piwowar
Thanks for the feedback. We just had a paper accepted to Nature and, Heather, as you suggest I would like to provide an example. After hearing so many discouraging, through-the-grapevine stories I feel like sharing my experience could be helpful and encouraging for others. Whether or not my PI is game is another question... - Jason Snyder
I am planning an ESOF session on peer review for newbies - anyone game to get involved? http://en.wikiversity.org/wiki... - Daniel Mietchen
sofarsoShawn
"Technically the glass is always full." So Everybody HAPPY!
glasshalffull.jpg
love this - Tamara J. B.
The glass is twice as big as it needs to be. - Tinfoil 2.0
Perhaps it needs to be this large because something else is going to be added. :) - Heather
I need this on a t-shirt. - DB, Lil LB's Dad
Amira
Google Launches academic Citation Stats | The Scientist - http://the-scientist.com/2011...
Google Launches academic Citation Stats | The Scientist
"Google Scholar, a free, centralized portal for searching for academic literature from a wide variety of publishers, added a new feature last month—Google Scholar Citations (GSC). GSC will allow researchers to track who cites their papers and how often they are cited over time. By creating a public profile, an author’s citation data will also appear in Google Scholar search results when a user searches for his or her name. In addition, the service promises to provide “h-index” values that reflect a researcher’s productivity and impact in their field." - Amira from Bookmarklet
sign-up for launch http://scholar.google.com/citatio... \\ wondering how http://www.mendeley.com is reacting... \\ and for those in the mathematical sciences, check out the beta of INSPIRE http://inspirebeta.net \\ Never used this: http://academic.research.microsoft.com \\ In a few years, Google's three metrics (h-index, i10-index and Total Citations) will probably be part of the tenure process for a professor's "page rank," see http://ff.im/J5oIr - Adriano
I thought about Mendeley right away too... Thanks for the link to Inspire! GSC sounds cool... - Amira
Cameron Neylon
In which my heart goes out to Postdoc B - http://occamstypewriter.org/mindthe...
Nicely reflect the inability of funding and hiring agencies to fairly judge the quality of post-docs... - Egon Willighagen
as a complete outsider, I'm still horrified that someone is expected to have *3* postdocs that last as much as 12 years before they get to settle down into a long term job in a stable location (if they are lucky). I'm also horrified that you could go through all of these post docs and then not be able to find a faculty position. - Christina Pikas
Dunno where you heard those stories, but, ummm... my first post-doc was 1 year (center closed down), then 1.2 years (due to personal needs, I needed to leave NL to change scene), then 2 years (grants unsuccessful), then 3 months (to fill a gap), and now on a 1 year contract... - Egon Willighagen
Mine were 4 years, 2.5 years, 4 years. - Bill Hooker
Mine were 1y (would have been extended but left early), 1.2y (pump-prime funding, 'follow-up' grant unsuccessful), 3y (happy to keep me on, but as employee), 3y (fellowship). - Noel O'Boyle
Michael Nielsen
Many of these are excellent. - Michael Nielsen
great tips, but not a beginner's list! - Mickey Schafer
Björn Brembs
Why would you pay to get published? - http://onlinelibrary.wiley.com/resolve...
Hahahaha... funny story! - Egon Willighagen
Don't feed the trolls. - Noel O'Boyle
I was going to make a sarky comment given I can't access it but I did wonder whether there was more to article than just a disingenous claim that publishing with them was "free" or whether there was a joke buried in there somewhere? - Cameron Neylon
Good quote: "It seems doubtful that lack of access to their articles represents a sufficiently widespread concern to motivate authors publishing in OA journals" - Jason Snyder
What happens when everyone has gone open access but there's still all that good, old research published in subscription journals? Can libraries download entire digital archives prior to ending their subscriptions and make them available once they no longer pay the bill? Or might for-profit publishers continue to attract subscriptions long after they've become unpopular, just because people want/need access to the classic papers? - Jason Snyder
Email the author and ask for a reprint? - Egon Willighagen
wow... - Kubke
I'd love to see libraries get together and collaboratively write an application that downloads every single article each library has access to and build a large database of the scientific literature. - Björn Brembs
Jason - it depends on the subscription. Some licenses allow us to keep locally owned copies of content. Also anything that's in the public domain can be digitized and hosted. Bjorn - I doubt we (libraries) could write an application like you decribe for collecting journal article content. LOCKSS is a network that allows people to share (sort of) and Hathitrust has collected digital... more... - Elizabeth Brown
@Elizabeth: I think starting with the content where local copies are allowed by the license would be a good start. That should include all print subscriptions, be definition. One may successively widen the scope of such a database using fair-use and trying to create precedent as well as by support from science funders and eventually legislation. Creating awareness of the problem and initiating action would already go a long way, as far as I'm concerned. - Björn Brembs
Bjorn, thanks for responding. The problem is that the print content is part of the electronic license, so it can't be treated separately. Most, if not all of those articles are owned by the publishers. We can lend a print copy by ILL (using the first sale doctrine) but we don't have the same first-sale rights for electronic materials. I'm refering to US copyright law which is different... more... - Elizabeth Brown
Am halfway through with your post but need to run. Real quick: I was trying to say that libraries which have a print copy, already have a local copy. It will be hard to argue against local digital copies. - Björn Brembs
Ontario has done more-or-less what Bjorn is suggesting with our Scholars Portal Journals database. It has 20+ million article and is very easy to use. We've essentially negotiated our licenses with publishers to allow us to own and locally host the database. The good news is that it's an amazing resource, particularly for ugrads looking for "good enough." The bad news is that it leaves... more... - John Dupuis
Thanks for mentioning initiatives in Canada. In the US most licenses are negotiated at the campus (sometimes system level), and it seems to be harder to negotiate the access you describe. Another major licensing issue that comes up is ILL use - some of the ebook and e-journal licenses don't allow for ILL lending. Once this use is prohibited it's hard to negotiate back into a contract. - Elizabeth Brown
That's excellent, John! Now other libraries would have to do similar things and (as much as legally possible) get the databases interoperable. The proof of concept would already be enough to push for next steps, IMHO. - Björn Brembs
I agree with you Bjorn that the database interoperabilty should come soon. The biggest roadblock is getting standards in place and persuading publishers it's OK to do this. I still see the silo mentality in full force. - Elizabeth Brown
Bjoern Have quoted you in my blog http://blogs.ch.cam.ac.uk/pmr... . Do you have a formal reference about publishers negotiating impact factors? - peter murray-rust
@brembs Fantastic dissection, give us more of the same plz. - 'Mummi' Thorisson
@peter: the PLoS Medicine reference in the talk is as formal as it gets. The Current Biology example is just pulled from the ISI website. - Björn Brembs
speaking of downloading every single article a library has a subscription to, check out what can go wrong: http://kottke.org/11... - Jason Snyder
Rajarshi Guha
I will never be able to blend fruits again :( - Imgur - http://imgur.com/I1lXn
I will never be able to blend fruits again :( - Imgur
Indeed! - Markus Sitzmann
AJCann
Finally, finally, finally submitted our friendfeed manuscript :-)
Looking forward to it! :) - Berci Mesko, MD
Where did you submit it? - Björn Brembs
Iddo Friedberg
Michael Nielsen
Public talk about open science in San Francisco - http://michaelnielsen.org/blog...
I was thinking about two days ago that you should be doing a Science Friday gig on NPR! Maybe I should tweet the request:-). - Mickey Schafer
I was so hoping I could make this. Are you doing it again sometime soon? - Mr. Gunn
Mr. Gunn: I've no immediate plans to give similar public talks in San Francisco, unfortunately. - Michael Nielsen
On another note, just gave a talk about open science at Twitter, and they are a seriously cool company. Lots of very thoughtful support for open culture generally. - Michael Nielsen
Deepak Singh
Not Looking So Good At Eli Lilly (or AstraZeneca) - http://pipeline.corante.com/archive...
The image says it all - Deepak Singh
Egon Willighagen
Pawel Szczesny
Finding the truth is a waste of time, scientists say - http://nsaunders.wordpress.com/2011...
Who is this "Neil" character? - Bill Hooker
“I wouldn’t waste my time because I don’t believe it” - this is what science has always been. Scientists have more inertia than a galaxy. - Todd Hoff
@David_Dobbs @keithkloor how does this fit with http://twitter.com/David_D... ? - Daniel Mietchen
Heather Piwowar
My postdoc with @tjvision, @nescent, @dataone_org, and @datadryad has been extended. Whoo hoo! Very glad, it is a great fit. #ilovemyjob
What opportunities exist for you to move from postdoc to PI and keep doing the same kind of work? Clearly less of an issue when you like the postdoc you're doing, but still something to keep in view. - Bill Hooker
Yup, right on, that's the medium term goal. For now, for me, the benefits of this postdoc far outweigh alternatives so I'm going to keep running with my good thing :) - Heather Piwowar
Deepak Singh
Purity in the atomic force-fields of molecular dynamics simulations - http://boscoh.com/protein...
Bosco Ho
Spent the day filling out the us visa online application form. The whole day.
Bosco Ho
Purity in the atomic force-fields of molecular dynamics simulations - http://boscoh.com/protein...
Loved it. Well written Bosco! - Mickey Kosloff
Egon Willighagen
Egon Willighagen
SwissParam: A fast force field generation tool for small organic molecules - http://www.citeulike.org/user...
J. Comput. Chem. (2011), pp. n/a-n/a. Abstract The drug discovery process has been deeply transformed recently by the use of computational ligand-based or structure-based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure-based computational methods for drug discovery mainly involve ligand-protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to... - Egon Willighagen
Michael Kuhn
PLoS Computational Biology: Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs - http://www.ploscompbiol.org/article...
Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs #greader - Michael Kuhn
Mr. Gunn
Nominations for scientist rock stars wanted. I'm building a readership leaderboard w/ Mendeley and need rising stars & established greats.
I can make a decent list of Nobel candidates myself, so but I'd need help for discipline specific names, like Jaenisch or Schultz. Rising stars are particularly appreciated. Might be nice to take a little extra effort to try to think of someone who's not an old white dude, as well. - Mr. Gunn
So far I have: systems biology: Joanna Wysocka, Michael Elowitz, Alexander van Oudenaarden, Uri Alon, Uwe Sauer via @basjhj) - Mr. Gunn
Chemical Biology: Carolyn Bertozzi, Laura Kiessling, Kevan Shokat, Ben Cravatt, Don Hilvert, Tom Muir, and (much as it pains me) Peter Schultz (via @biochembelle) - Mr. Gunn
Metabolism: Craig Thompson, Tak Mak. Reuben Shaw (via @flutesUD) - Mr. Gunn
Autophagy+cancer peeps: Eileen White, Beth Levine, Guido Kroemer (via @flutesUD) - Mr. Gunn
Cancer biology: Carlos Arteaga, Pier Paolo Pandolfi, Michael Kastan, Wafik El Deiry, William Pao, Varmus (via @maverickNY) - Mr. Gunn
Cancer Biology: Frank McCormick, Tyler Jacks, Jeffrey Engelman, Bert Vogelstein, Charles Sawyers, Brian Druker (via @maverickNY) - Mr. Gunn
Mouse Models + cancer: Tyler Jacks (via@flutesUD) - Mr. Gunn
miRNA + cancer: Carlo Croce (via @flutesUD) - Mr. Gunn
PI3K/mTOR/metabolism: Gordon Mills, Lewis (Lou) Cantley, Jose Baselga, David Sabatini (via @flutesUD) - Mr. Gunn
lol - Mr. Gunn
Egon Willighagen
The Roots of Bioinformatics in Theoretical Biology - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 7, No. 3. (31 March 2011), e1002021. From the late 1980s onward, the term “bioinformatics” mostly has been used to refer to computational methods for comparative analysis of genome data. However, the term was originally more widely defined as the study of informatic processes in biotic systems. In this essay, I will trace this early history (from a personal point of view) and I will argue that the original meaning of the term is re-emerging. Paulien Hogeweg - Egon Willighagen
Simon Cockell
The Roots of Bioinformatics in Theoretical Biology - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 7, No. 3. (31 March 2011), e1002021. From the late 1980s onward, the term “bioinformatics” mostly has been used to refer to computational methods for comparative analysis of genome data. However, the term was originally more widely defined as the study of informatic processes in biotic systems. In this essay, I will trace this early history (from a personal point of view) and I will argue that the original meaning of the term is re-emerging. Paulien Hogeweg - Simon Cockell
Paulien++ - Egon Willighagen
Mark H
The unpalatable truth is that the anti-nuclear lobby has misled us all - http://www.guardian.co.uk/comment...
The unpalatable truth is that the anti-nuclear lobby has misled us all
"Over the last fortnight I've made a deeply troubling discovery. The anti-nuclear movement to which I once belonged has misled the world about the impacts of radiation on human health. The claims we have made are ungrounded in science, unsupportable when challenged, and wildly wrong. We have done other people, and ourselves, a terrible disservice." - Mark H from Bookmarklet
"I began to see the extent of the problem after a debate last week with Helen Caldicott. [...] In the debate she made some striking statements about the dangers of radiation. So I did what anyone faced with questionable scientific claims should do: I asked for the sources. Caldicott's response has profoundly shaken me. First she sent me nine documents: newspaper articles, press releases... more... - Mark H
"We have a duty to base our judgments on the best available information. This is not only because we owe it to other people to represent the issues fairly, but also because we owe it to ourselves not to squander our lives on fairytales. A great wrong has been done by this movement. We must put it right." - Mark H
This is a problem for a lot of things, not just nuclear power. Too many people take something that they heard somewhere or something they read on the internet and then run with it like it's a proven fact. People need to be called out on this more often just in general. - Kamilah Reed (K. Gill)
Search Google Scholar and you'll find a lot of articles hidden behind a pay wall, combine that with a general lack of data and it's difficult to find results for yourself. Here's The Chernobyl accident 20 years on: an assessment of the health consequences and the international response - http://www.scielo.br/scielo.... Kids are at obvious higher risk because... more... - Todd Hoff
So why should the "anti-nuclear lobby" want to mislead us all? - Maitani
Those evil anti-nuclear misleaders who are .. um .. profiting .. from .. burning coal ? - Terris of California
It's not about coal vs nuclear :) I can imagine multiple rationales - one is fear, straight out of the cold war - they *know* nuclear is deadly in some forms for sure, and nothing can ever, to some, make is safe. Also, nuclear is seen as war-related and unnatural to some and they will never accept it as it means (to them) buying into an industrial system. There's often a strong nature... more... - Iphigenie
Monbiot wrote (in "Heat", before his change of heart on nukes) that the projected cost of nuclear power seems to vary directly with how much one is in favour of it... - Andrew C (✔)
My only problems with nuclear are 1) the waste - we dont know what to do with it, nobody wants it. And we often dont know enough about our mid term geology to be sure where is safe. The good news is that it is highly probably that in a hundred years or less we will know how to mine that waste for more value and to neutralise it, but until then it still has to be somewhere. And for... more... - Iphigenie
Egon Willighagen
Rajarshi Guha
What Is Really Killing Pharma | OpenEye Scientific Software - http://www.eyesopen.com/en...
"I would suggest that pharma CEOs look to Hollywood for inspiration." hahahaha... yeah, that's what we need for new medicine: big explosions, hot looking products, and little story :) I also point out the irony of a cheminformatics company mentioned one pharma department charging another for services :) Otherwise, really good read, and really good points! - Egon Willighagen
Björn Brembs
On 'adequate' peer-review - http://bjoern.brembs.net/news...
Yes, this, exactly so: "To my knowledge, so far, no factual relationship between rejection rate in scholarly publishing and whatever one could construe as 'quality' has been offered that would stand any scrutiny." - Bill Hooker
Yet it seems like everybody claims there was a relationship like a mantra. - Björn Brembs
Well said (written). I only have a small comment regarding "journals which retract more papers than others have a worse selection process". Reiterating what many have said elsewhere, the high rejection rates at the GlamMagz also reflects their high visibility. A retraction has a high activation energy that is often not reached, even if a paper should be retracted based on its science. - Mickey Kosloff
Good candidate to look at for selection process: http://www.atmospheric-chemist... . On the order of 70% of submitted papers are accepted, yet the journal is leader in its field in terms of citations and even IF. The secret behind that: The initial submission is not hidden, as in most journals, but published as a "discussion paper", which keeps (most) authors away from... more... - Daniel Mietchen
@Mickey: indeed, visibility is a factor often ignored by the people who equate citations with quality - so I chose to also ignore it in my counter-argument. Once we both agree you can't do that, we're on a way to actually agree on something :-) - Björn Brembs
@Daniel: One more excellent example against the ludicrous connection between rejection and quality! - Björn Brembs
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