Attila Csordas › Likes

Jonathan Eisen
Calling for Nature Publishing Group to return all money charged for articles that were supposed to be free #OpenAccess -
I think you should ask for the OA publishing fee to be refunded too. - Steve Koch from Android
Bill Hooker
Goodbye academia, I get a life. – blog.devicerandom -
"Until not so long, I thought that it was worth it. It was something that I had never questioned so far. I wanted to be a scientist since when I was five. I had done everything to become a scientist. I was a scientist in one of the top universities of the world, in one of the top five research groups on the subject. I had won a personal fellowship to fund myself. Most of my self-esteem, of my very concept of self-realization, relied on myself being a scientist. The very idea of quitting academia was a synonim of personal failure." That right there is the engine of the pyramid scheme. - Bill Hooker from Bookmarklet
I've heard more senior scientists dismiss this attitude as a 'typical cynical postdoc, not skilled/smart/hard working enough to make it to tenure'. These same senior scientists were junior scientists in a very different time, usually before the huge expansion of the number of available PhD candidates, where the ratio of supply to demand of graduates wasn't nearly as imbalanced. This... more... - Andrew Perry
Re: the pyramid scheme that BH and AP bring up -- I completely agree and want to add one additional point: its not just that an untenable economic situation has emerged which grad schools sweep under the rung -- its that the community itself seems to look down on those who leave academia to join industry/business or publishing or something else entirely. High rates of failure at achieving tenure at impressive school X would be ok if young students/scientists felt they had viable alternatives - Benjamin Tseng
I agree Benjamin - I've noticed that in many academic institutions career options outside that system are rarely discussed openly, and leaving academia is considered failure (even if someone leaves to do something arguable more useful). Granting bodies usually want to encourage collaboration between industry and academia through special funding opportunities (eg, the ARC Linkage grants... more... - Andrew Perry
some more comments here: and I agree with Andrew .. thats why we should fight against even the language that is used (i.e. "quiting science") - Pedro Beltrao
Mr. Gunn
DNA sequencing for the masses : Nature News [this is awesome stuff, if it works well] -
Konrad Förstner
You can contribute to an open paper about #GWAS that might be published in Nature Genetics #WikiGenes
I thought part of the idea behind Wikigene is that a paper can be improved steadily. So publishing one version of it in NG contradicts this concept. - Konrad Förstner
Andrew Su
Survey: How many scientific articles do you estimate that you read per year? (really read, not just skim...)
Maybe a couple of dozen (not including reviews -- I probably do 20-25 of those a year, and each requires at least one close reading). I probably skim 5 or 10 times as many as I really read, where "skim" = glance through intro/discussion and take a reasonably close look at the results, usually to pull out some particular piece of evidence for my own use. - Bill Hooker
3000/500/100 (read abstract and saved for later/skimmed/read carefuly) - Pawel Szczesny from iPhone
(Remember, Pawel is The Man Who Reads Everything. Mere mortals should not be judged by this standard.) :-) - Bill Hooker
10-15 across all fields these days. When I was still in the field probably half a Pawel - Deepak Singh
Really read in-depth? Probably a dozen. For most articles, I just skim and take the most relevant parts. - Chris Miller
carefully read: 200 (I have time-slots devoted solely to reading ~10h/week), re-do the math: 20 - marcin
From 1997 to 2007 I saved 1350 PDFs on my hard drive. So 135/year. I think I read all of them fairly carefully. In the 20th century I also read actual paper copies so more, maybe about 200. Now I read less and skim more, no paper copies at all, lots of abstracts by RSS feed. - Dave Lunt
Read carefully - several dozen per year. Skim/read selectively - hundreds. - Mickey Kosloff
I'd say I was around 1000/500/100 when I was in grad school - Mr. Gunn
@MrG -- what about now? I 'fessed up, now it's your turn! - Bill Hooker
Not just skim? Title to references? Less than a dozen, certainly. - Björn Brembs
527/277/108 according to Papers (sort by date of import/sort by last opened/count ratings) over the last year. I do read some via Mendeley, ordinary pdf readers or online. Of the papers whose abstracts I read (mostly via RSS), about one fourth ends up in Papers. - Daniel Mietchen
When I was a phD student and postdoc at least 1 a day, now about 1 a week if I am lucky - Kubke
really, really read: 6 a year. - Andrew Lang
Should this convo worry me and/or folks interested in the peer review process? How many papers of those folks *really* read are ones they have reviewed? (Perhaps they aren't counted in these estimates..) What level of reading should be taking place in the peer review process? - Carmen Drahl
None ... that's a separate list - Deepak Singh
Review requires a close reading, but I think everyone has done the same as Deepak and I, that is, considered the two separately. - Bill Hooker
Thanks for the input. I guess I was feeling sensitive this week because I just wrote about a prominent retraction where details in figures and supp info came under fire: - Carmen Drahl
Carmen, that's not to say that peer review actually *does* in practice what it is supposed to in theory; for instance, I suspect that many of the reviews I see as AE at PLoS ONE and BMCRN were written after skimming at best... - Bill Hooker
Sigh. That's a shame. But I'm not sure what to do about that as schedules get busier and journal articles to review get more numerous... - Carmen Drahl
I'm along the Miller/Saunders lines, not counting reviews though - Attila Csordas
600/150/30 = (skim,add to Mendeley / read & discuss > 1hr, add notes to Mendeley / read & re-read carefully, favorite in Mendeley) - Carl Boettiger
Interesting. We seem to be coming up with roughly similar numbers from a fair range of people. I wonder if we all understand the same thing by "close reading" (I suspect we do), and whether there is some kind of cognitive limit on how much of that kind of effort you can put out. - Bill Hooker
I don't know about cognitive limit, but time is certainly limiting. I'm skimming about one per day on average, discussing about 80, and reading and reviewing about 50 or so. - John Hogenesch
Well, I actually was including reviews in my numbers, but it wouldn't skew the numbers much. Bill - I read more web pages and less PDFs these days, maybe a tenth as many PDFs, but those I do read I read more thoroughly, so maybe 100/50 or thereabouts - Mr. Gunn
Y'all might be itnerested in King and Tenopir's work on how much scientists read, and and lots of others. - Joe
Ha, Joe! I was just coming back here to post that! Average researcher reads 250, apparently, mostly found via search & browsing, NOT citation graph (but that could partly be due to poor tools). - Mr. Gunn
Thanks for the link on the jisc article. Don't think I have seen this one before. - Joe
Lars Juhl Jensen
PROMISCUOUS: a database for network-based drug-repositioning -
Michael Kuhn
Announcing Google Refine 2.0, a power tool for data wranglers - Google Open Source Blog -
if you've ever received an Excel sheet with ever so slight inconsistencies in the columns (trailing spaces, misspellings) then this will make you cry for joy (if it holds the intro video's promise) - Michael Kuhn from Bookmarklet
@Neil: grumpy old man? ;-) seriously, lots of these things you could do with your standard grep/sed/awk tool chain, but for one-off clean up operations, this might be more comfortable. Plus, you can also store the transformations, if you need them again. - Michael Kuhn
I'm a reporter at Nature and looking to compile a list of biological wikis, along with some numbers on readers, editors, etc -- basically an update of a list Andrew Su put together: Any ideas? Thanks, Ewen
That list is a bit mixed - not all wikis actually. If you want to include other knowledgebases, I would add PathGuide, Pathway Commons and Reactome among others. Also, you may want to contact the organizers of as they are focusing on biological wikis - Shannon McWeeney
I wonder if someone would be interested in automating the edit/editor counts. The numbers in the old spreadsheet were filled in by hand, but one can imagine writing a simple program using the MediaWiki API to get that info. Might even be a cute application note (BMC Research Notes, PLoS One) that creates a historical and continuously-updated report of wiki activity... - Andrew Su
Thanks for pushing this! Ewen - ewencallaway from email
Ewen -- Hah! you overestimate my ability to "push". Lots of smart people lurking here, so I'm just throwing out a random thought to see if it sticks. Usually an effective filter for good ideas... - Andrew Su
Why would we do free work for Nature? - Bill Hooker
Bill, only if you thought it were personally interesting or beneficial I suppose... - Andrew Su
Eh, sorry, ignore me, that was uncalled-for. The benefits of maintaining such a list are obvious and if Nature is promoting it that's even better. My bad. - Bill Hooker
I agree the list is worth maintaining, but it's just a pain to keep current. (The numbers there now are almost two years old.) Anyway, perhaps a fun little project (for those around here who like that sort of thing)... - Andrew Su
Neil, are you sure a Wiki is the right tool for this? ;-) - Cameron Neylon
Hi, Dan Bolser has kindly created a wiki to collect data on biological wikis:, so if you have anything to add, please put it there! Ewen - ewencallaway from email
Ideally the maintainers of these wikis could supply this info. Perhaps the thing to do is to write/find a mediawiki plugin that would expose this data automatically - then the source wikis would simply have to install the plugin and everything would/might/might sometimes 'just work'. - Benjamin Good
I did a list of life science wikis this summer - Mary Canady
Andrew Su
Deepak Singh
Egon Willighagen
Shared: @petermurrayrust If you are still looking for data storage take a look at Google Data: 100Gb free & RESTful service
Limited to a selection of US developers... but surely also SciFoo-ers, not? - Egon Willighagen
myKaryoView: First Open Source Visualization Software for 23andMe Data
Peter Binfield
Welcome to PLoS Blogs - our new blog site featuring an outstanding lineup of bloggers :)
Where are full text RSS feeds? - Pawel Szczesny
Pierre Lindenbaum, a free open-source menu-driven file-sharing and Cloud-Computing web-service for computational biology. -, a free open-source menu-driven
file-sharing and Cloud-Computing web-service for computational biology.
Been looking through source code available at and also programmer's guide - Mike Chelen
Chris Miller
Rare Sharing of Data Leads to Progress on Alzheimer’s - -
"The key to the Alzheimer’s project was an agreement as ambitious as its goal: not just to raise money, not just to do research on a vast scale, but also to share all the data, making every single finding public immediately, available to anyone with a computer anywhere in the world. No one would own the data." - Chris Miller from Bookmarklet
To those who are skeptical, he says, “My answer to them is ‘get over it.’ ” - joergkurtwegner
Great story. Also featured on Derek Lowe's blog at - Matthew Todd
Roderic Page
Mendeley API: we'll bring the awesome if you bring the documentation -
HI Roderic, We hear you loud and clear. I think our developers have responded to your questions on twitter, the Google Group, and private email. If not, please let me know. We would have loved if you had participated in our beta API program to help spot some of these bugs. The duplicates you are seeing are actually not a bug in the API, but rather part of the process in how we clean... more... - Jason Hoyt
@Jason: can the API also be used without registering an app? - Egon Willighagen
Jim Hardy
BBC News - Vaccine patch may replace needles -
BBC News - Vaccine patch may replace needles
the real point: 'If proven to be effective in further trials, the patch would mean an end to the need for medical training to deliver vaccines and turn vaccination into a painless procedure that people could do themselves. It could also simplify large-scale vaccination during a pandemic, the researchers said. Although the study only looked at flu vaccine, it is hoped the technology... more... - Attila Csordas
Lars Juhl Jensen
Dissecting spatio-temporal protein networks driving human heart development and related disorders. -
Jim Hardy
Largest study of genomes and cancer treatments releases first results -
Mr. Gunn
Biotech start-up wins Google's attention--and money - FierceBiotech (via phidias51) -
Luke Jostins
We just launched a new group blog about personal genomics, with bloggers, scientists, lawyers and public health experts:
Michael Kuhn
Going to speak at the EBI Computational Drug Repositioning Workshop in three weeks, along with FriendFeeders @jscheiber and @sjcockell :-) [ / ]
Excellent! See you there... - Simon Cockell from iPhone
hey guys, would be good to meet with you - Attila Csordas
Hi guys, we've got coffee breaks today at 15:30 and tomorrow at 11:15... or you drop by around 6 today. Would be great to meet you. We're in the EBI IT training room - Michael Kuhn
I try to be around the coffee break (listening to Simon now). - Attila Csordas
Mr. Gunn
Peer review provides £209,976,000 public subsidy to commercial publishers - Boing Boing -
"The Open University's Martin Weller looks at the Peer Review Survey 2009's numbers on free participation by UK academics in the peer review process for commercial science journals and concludes that 10.4m hours spent on this amounts to a £209,976,000 subsidy from publicly funded universities to private, for-profit journals, who then charge small fortunes to the same institutions for access to the journals." - Mr. Gunn from Bookmarklet
I would still love to see a model where my reviewing work would get me credit for 1) a free submission; 2) a free OA (gold) publication. - Egon Willighagen
While I chose not to respond, the very first comment is one that always bothers me: The society publisher justifying high library subscription prices because those subscriptions pay for the rest of the society's budget. In times when libraries lack adequate funds, that's simply not an acceptable argument, but it sure does keep popping up. - walt crawford
I'm with Walt. If the society will die without the journal, then hurry up and die already. - Bill Hooker
The only OA journals that charge bunches of money to publish, far as I can tell, are in fields where there's bunches of public funding sloshing around. Why does it have to cost so much when so much is done for free and distribution online costs close to zero? (Even scientists with complex formulas and images do their own layout fer crying out loud!) I'd love to get a group of libraries... more... - barbara fister
"Why does it have to cost so much?" -- that's the question, innit? Of all the publishers out there, I think PLoS is probably the best guide to what it actually costs to compete in the current system, since they have an incentive to charge not the most the market will bear (like a for-profit does) but the least that they can make do with. Since I think the "prestige journal" concept... more... - Bill Hooker
I'm thinking of humanities journals published by small societies formed around the interest of a handful of like-minded scholars - which publish three or four issues/year, five or six articles per issue, unpaid editor and board; why should it take more than 2 FTE to run that baby? The U of MN press, which has 50+ books in its fall catalog and publishes six journals appears from its... more... - barbara fister
What I've seen of BePress looks pretty simple - not cheap for an annual subscription, but cheap if it meant it actually worked without a lot of effort. Haven't looked too closely, though. 'Cause then I'd just cry that we can't afford it. - barbara fister
Who cares about typesetting in an online publication? or by typesetting do you mean tagging the content in SGML fashion? (the author should be doing that anyway) - Aaron the Librarian
Oh, I'm sure they know the difference between SGML and their elbows. - DJF
The author should be doing proper SGML? Interesting. Boy, am I glad I don't write scholarly articles... and I think Dorothea's right in general: Presentation at a level appropriate for scholarly papers isn't a gimme. (OK, so I rarely argue with Dorothea where production etc. are involved. Big surprise there.) - walt crawford
Specially Gruesome Markup Language? Sure, I can write that. - Bill Hooker
Considering I'm barely literate in the HTML subset of SGML, I'm not saying I expect the author to produce valid SGML, I'm saying in a SGML fashion (using Word (shudder) as an example: the title is labeled Title, section Headings are Header [n], etc etc. - Aaron the Librarian
Dude, HTML isn't a subset of SGML. The only thing they have in common is all the annoying angle-brackets. - DJF
@DJF see what I mean? :) - Aaron the Librarian
Speaking as an author who has relied on conversion peasants without even, at the time, knowing such folk existed -- D0r0th34's right. You'll never get authors to stick to even a simple layout that could be readily auto-converted into markup. So my question is, how much does care and feeding of a conversion peasant cost? The question at the end of that rainbow is, of course, how much of what publishers charge is necessary and how much is profit? - Bill Hooker
I would like see a comparison of the production costs of Nature, a commercial venture that sells advertising (probably at a very high rate considering its impact and the cost of the items being advertised to a specialised market), to the production costs of The Economist, a commercial venture that sells advertising (ditto), but also has to pay for all of the original content that it produces every week. - DJF
Another society journal, running on less than the PLoS ONE charges: . Apparently sustainable - they (European Geosciences Union) continue to expand their portfolio. Also interesting is that the typesetting issue is factored into the pricing - this provides for an incentive to use TeX or at least to care about layout standards. - Daniel Mietchen
+1 DJF - it would be interesting to compare Nature with a similar outfit that has to pay for all its content. - Mr. Gunn
As far as the cost to run a small publishing house, would it make sense to add some money to pay people for their peer-review time as well? - Mr. Gunn
Let me ask the question in a different way: If you took all subscription fees in every library on this planet, how much of that money would be needed to sufficiently staff and equip each library to publish all the papers from their own institutions themselves? My guess is that the subscription costs would easily cover everything and then some, because libraries don't need to make a... more... - Björn Brembs
Doing journalism and publishing what might be the most prestigious science journal (I'm not sure about the various flavors of Nature, because I'm not familiar with them, but the mothership itself) are different, but in some ways not so much. A large part of Nature is staff-written news, opinion, commentary, both online and in print, and with a much higher frequency than most scholarly... more... - barbara fister
Thanks, Dorothea, for the under-the-hood look. It seems as if there should be a standard word processor for academics that does what it takes to make papers look good. (TeX works for scientists, but then ... they passed organic chem.) When I say "how hard is it, really?" I'm thinking of the smaller society journals, published infrequently, that turn to commercial publishers to manage... more... - barbara fister
As someone with, er, intimate knowledge of one particular humanist's interaction with technology, I can say anecdotally that Dorothea speaks truth. - Catherine Pellegrino
Yeah, but twenty years ago our college had a typing pool because some of the older faculty needed someone to type up their handwritten book manuscripts; typing wasn't part of their job. (Yes, I am ancient.) The tools will get easier and the faculty less afraid of them, and someday typesetting will as expected as coal scuttles and the maids it took to haul them away. I should start the legal process of changing my name to Pollyanna soon.... - barbara fister
*stands up and applauds* Dorothea, I love you. It goes without saying, of course, but after your comment, I had to say it. - Ordinarybug Heather
So many traditional journals also offer crap typesetting that there's gotta be a niche there just RIPE for taking over... - Marianne
Sorry, pure ignorance on my part. I'm trying to learn. (You and Walt can probably go halfsies on a hitman for me.) I guess given that the most interesting stuff I read these days is not typeset, I am wondering what I'm missing. Then again, I have ranted about how ugly most e-books are because they all look alike, have no page design, and are are mass converted to look all alike. Then... more... - barbara fister
Without wading into an argument about whether humanities authors could/should handle markup languages (for the record I think if you've got a PhD in anything, well... markup isn't brain science or rocket surgery) -- the fact remains that at every OA journal I've seen, people who submit BEAUTIFULLY PRE-TYPESET docs in LaTeX STILL get charged as much as people who send crapulous Word docs. </rant> ... which is about the one thing about OA that still really bugs me, we do their work, they get paid - Andrew Clegg
Yes. That's the point, they send you a template, you produce a PDF that's basically print ready (apart from it has crop marks etc.) - Andrew Clegg
I reckon :-) I get on better with LaTeX than I do with any word processor I've met, but it stil takes longer... - Andrew Clegg
PS belated +1 for Egon's idea waaaay up there about getting a free pub. in exchange for your review - Andrew Clegg
@ Andrew - such differential charges were mentioned in the link I posted above (here again: ). This is just one of multiple journals published by that are handled in the same way. - Daniel Mietchen
Didn't spot that -- thanks. - Andrew Clegg from twhirl
@ D0r0th34 - a good example for excellent typesetting (in my view) of an OA book is at . All TeXed, complete with embedded videos. And even in terms of content, it is one of the best physics textbooks that I know. - Daniel Mietchen
Google to employees: 'Mac or Linux, but no more Windows' -
Ami Iida
Pierre Lindenbaum
Awesome find. I wonder how this stacks up against something like a nested containment list. - Paul J. Davis
Daniel Mietchen
Science 2.0 Pioneers § SEEDMAGAZINE.COM - From open-access journals to research-review blogs, networked knowledge has made science more accessible to more people around the globe than we could have imagined 20 years ago. -
Science 2.0 Pioneers § SEEDMAGAZINE.COM - From open-access journals to research-review blogs, networked knowledge has made science more accessible to more people around the globe than we could have imagined 20 years ago.
"Surely you’ve noticed: The scientific community is undergoing a research-and-data-sharing sea change. Perhaps slower to take to Web-based dissemination than some professions, science—the endeavor for which the World Wide Web was developed—has gradually been adopting new online methods for distributing knowledge. Some say the changes could accelerate scientific progress." - "To be sure, some changes are easier advocated than adopted." - Daniel Mietchen from Bookmarklet
Ruchira S. Datta
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction
Congrats! I have a question about your alignment -- how come you didn't compare it to the best stuff out there, like ProbCons/ProbAlign? Was it the tradeoff between accuracy and speed? - Donnie Berkholz
Nevermind, I just got to the Future Work section. =) - Donnie Berkholz
Donnie, thanks for your interest. In fact, the accuracy of SATCHMO-JS is competitive with ProbCons in accuracy, while taking much less time. These results are not yet published (we've submitted them). - Ruchira S. Datta
Could the server source code be made available? Looks like a great utility. - Mike Chelen
Mike, thanks for your interest. We do plan to make SATCHMO-JS available as downloadable software--we have a very small group, though, so it's taking some time. - Ruchira S. Datta
That is great to hear! Open source makes the software more accessible for both implementation and learning by examination. What are the challenges in releasing the code? Knowing that the group intends to do so makes waiting patiently much easier :) - Mike Chelen
There are just a lot of pieces to the pipeline. We need to extract it and package it up. - Ruchira S. Datta
Pierre Lindenbaum
My new position at INSERM/UMR915 -
Congratulations Pierre. Best wishes for your new position. - Khader Shameer
thank you all :-) - Pierre Lindenbaum
Congratulations Pierre! - Farhat
Find the cheese gene in the French genome! - Bosco Ho
Congratulations Pierre! I will look forward to your forthcoming paper entitled "Why the French are the way they are, and how they became that way" ;-) - Lars Juhl Jensen
Congrats, Pierre! - Björn Brembs
Conratulations from me too Pierre ! - Ian Simpson
Congratulations! - Rajarshi Guha
Conratulations! Hope you will like it there :-) - Darek Kedra
Congrats! - Ruchira S. Datta
Pierre++ - Egon Willighagen
thank you all (again) :-) - Pierre Lindenbaum
Congratulations to INSERM on their excellent new hire. :-) - Bill Hooker
Congratulations! - Andrej Kastrin
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