Donnie Berkholz › Likes

Lovely to see this kind of analysis. - Cameron Neylon

"In the best of all possible worlds, what you would like is for all papers to be published, just making sure that the conclusions are reasonable given the observations. And then retrospectively assess the impact and importance of the paper." - Björn Brembs from Bookmarklet

That may be true for a fraction of scientists, I don't know the size of that fraction, though. In my experience, many senior scientists are well aware of what should change and how absurd in many instances our current way of doing science is. Maybe much of the inertia comers from "what could I change?" - Björn Brembs

pq: "By the way, $32 billion is exactly the sum that BP has been forced to pay by the US government as a penalty for the Gulf of Mexico oil spill. I don't know whether to laugh at that coincidence or just cry. " - Bill Hooker

Crying is an acceptable response. So is screaming into the night sky. What else can you do? - Mr. Gunn

Hadn't heard this story before. What a thrilling tale of ACS attacking the little guys. - Donnie Berkholz

Charities, not for profits etc can still get engaged in law suits and the associated costs come from the coffers that would generally be applied to other things. This case has being going on for a number of years and in theory is over but may get challenged again. - Antony Williams

"Reanalysis is a direct measure of utility to other researchers, which is the basis for reputation and for a high level of citation. So there is potentially value in Analyses looking at the accessibility of data, the adequacy of metadata and protocols, and the reproducibility of specific results. Such studies—if transparently and responsibly conducted—can be more useful in guiding excellent research practices than any number of standard-setting documents because they directly demonstrate the effects of data formatting, accessibility and precisely described decision making on other researchers' ability to use the published results and data." - Chris Miller

Prior to this label, I wasn't aware that Nature Genetics would think this work within its scope. - Heather Piwowar

Here's the webserver: http://phylogenomics.berkeley.edu/satchmo... - Ruchira S. Datta

There are just a lot of pieces to the pipeline. We need to extract it and package it up. - Ruchira S. Datta

Now available to play with - Rajarshi Guha from Bookmarklet

"One problem that I am facing is convincing colleagues of the utility of an Open Access publication. ... Not everyone operates on large grants. Many lab budgets leave very little room to buy a new laptop, let alone pay for an OA publication (typically the price of two of said laptops)." - Mickey Kosloff from Bookmarklet

Good points here. Proving a rival to current closed-access or setting a precedent to get grant-givers to make line-items for OA publication are good in an abstract/aggregate level, but the individual lab decision-maker is thinking on a lot more concrete terms. Perhaps, some sort of Impact Factor or "open access journal news" to add credence/credibility can substitute? - Benjamin Tseng

I'm glad you've made the point -- I talk about it with students who will have to make these kinds of decisions in the coming years -- and it's a tough one: ideological belief against practical action. Maybe we need a kind of OA investment account where interest can be accrued over the life of a grant. Okay, not realistic...government subsidies, maybe;-)? - Mickey Schafer

Also check out his other post: http://blog.zacharyvoase.com/post... Awesome awesome stuff. Also, I'm more than a little relieved to find out I'm not crazy. Or at least that I have company in crazy town depending on the interpretation. - Paul J. Davis

Nice post, but I don't think it would sell me on using RDF. It's not like you can't agree on syntax and meaning (or even use ontologies) without RDF. Better to show how RDF helps deal with the fact that not all databases are ever going to agree on a single set of non-overlapping concepts for describing their data, and -- more important -- with more fundamental disagreements (such as what an organism even is). - Eric Jain

"like" as in "wtf?" - Bill Hooker

Perhaps that's their undercover advocacy for Open Access to the methods sections? - Daniel Mietchen

Yes! Finally!!! - Alejandro Montenegro

"The acid test: if I see electrons pushed around, it's chemistry" http://scienceblogs.com/terrasi... - Iddo Friedberg

I really want to "like" that comment, but I guess I'll settle with the whole post... - Donnie Berkholz

Imo journals should simply refuse to publish without full M&M details, sufficient for replication. - Bill Hooker

Update: My "Carters" reacted friendly to my friendly inquiry, and we provided each other with more details on the experiments, but it is still next to impossible to reconcile our results, and neither they nor me currently have funds for this line of research - another case where baseline grants would be handy. - Daniel Mietchen

"The Internet has changed scientific publishing in many ways, some good and some bad. No one would deny that it is easier to find papers on a particular subject than ever before. Looking up papers in Index Medicus or by browsing Current Contents has long been replaced by online searches on Medline or even Google Scholar. This has not necessarily improved our understanding of the literature, but it certainly provides a quick way to feel up to date." - Abhishek Tiwari from Bookmarklet

I agree that the ability to track readership and download stats for my papers would be *extremely* valuable. It will probably just become more so as online papers approach the next-gen prototypes so you could even tell which sections and figures are viewed most. - Donnie Berkholz

press release: http://www.sciencenews.org/view... - Michael Kuhn

@Michael: I guess you've seen the list on Wikipedia: http://en.wikipedia.org/wiki... - Michael Kuhn

It's nice to see other journals following the system Biology Direct has. - Alejandro Montenegro

Transparency has to be good... - Peter Murray

"The majority of papers published" - why not all? - AJCann

This is really good! - Björn Brembs

excellent b/c addresses delivery and environment as well as design -- most instructional sites don't do this, though Michael Alley on posters (http://www.writing.engr.psu.edu/posters...) and especially power point presentations (http://www.writing.engr.psu.edu/slides...) are generally excellent, student-friendly guides -- not necessarily humorous, unless you like squirrels. - Mickey Schafer

"What if scientists, instead of rushing to publish or perish, chose to cooperate? Sean Cutler decided to do “a little experiment,” as he calls it, and you can see the results in the forthcoming issue of Science. " - Abhishek Tiwari from Bookmarklet

By determining goals, method of achievement, and providing feedback competition can be designed to encourage cooperation. - Mike Chelen

Obviously sorting isn't the most parallizable test, but sorting on a dual-core machine took nearly twice as long with bashreduce. I probably should test some quad or 8-core machines before passing judgement. - Chris Miller

"What you're doing is very clever, and I see how it's useful, but how is it science?" - Abhishek Tiwari

"It's not. How is your research science?" - Abhishek Tiwari

They don't make it very easy to send a copy online. - Donnie Berkholz

Bother your US friends? - Bora Zivkovic

"The usual N.I.H. research grant is from $250,000 and $300,000 and runs for four years, and each grant supports six or seven full-time or part-time jobs, Dr. Kington said. To provide a quicker economic impact, the institutes may also award two-year grants of $500,000 per year, but soliciting proposals and judging them could take up to a year." - Andrew Su

There is more good news for UC journal authors. The California Digital Library (CDL) and Springer have signed a ground-breaking agreement in which UC-authored articles accepted for publication in most of the 1700 Springer journals will be published using Springer "Open Choice" which brings with it full and immediate access to all readers. This means that UC authors will pay no additional publication fees in order for their articles to be immediately and fully open to all. Under the agreement, articles will be published under a license in which authors retain the right to distribute and re-use their articles freely. - Jason Stajich

To invoke the "Open Choice" option, UC authors will select a UC campus affiliation from a drop-down box that appears on the acceptance screen which authors must complete once an article has been accepted for publication. A message on the acceptance screen will indicate that the Open Choice option is being made available to them at no charge. (The Open Choice publication fee would... more... - Jason Stajich

http://www.universityofcalifornia.edu/news... - Jason Stajich

Do any of you use SciTopics? - Steve Koch

"Now, most scientists are familiar with the “cataloging system” of scientific journals, they’ve been reading them their entire careers. Everyone has their own filters, their own rankings of which journals are more interesting, or publish better work than others. And all kinds of tools are available for filtering things down to just the relevant essentials for keeping up with your own field. But even so, most people that I talk to are left with more useful, relevant articles that they need to read than they have time to get to. These are not articles that should be filtered out. These are important, quality findings of direct relevance to their own work. And there are too many of them without even factoring in a need to keep up with science in general and see what developments in other fields can be applied to one’s own." - Alexey from Bookmarklet

"A company's lawsuit against researchers should not be allowed to intimidate others." Note: free to access online (registration may be required). - Maxine from Bookmarklet