yes, this is a much better article even if I don't agree with him. - Pedro Beltrao

The article is mostly just a statement of facts about what PLoS has achieved on the business side, versus what they set out to achieve. It looks to me like an exceptionally useful document to OA advocates - OA journals need sustainable business models, and Timo is dead right that the best way to achieve this is open discussion. - Michael Nielsen

Much better than the original. Still I think Timo misses the larger point -- see esp. comments by Bjoern Brembs -- it's time to do away entirely with the *whole concept* of "high-end" journals. Journal-level metrics (impact factor, rejection rates, perceived prestige) simply do not work as a way to rank and evaluate projects, ideas or scientists. Let peer review do what it can do -- weed out the obvious crap -- and let search and database software and the research community do the rest. - Bill Hooker

It also amuses me to see Nature folks with their lace hankies pressed to their horrified mouths over the "kneejerk backlash" and "internet outrage". The original piece was outrageous -- I think most of the responses have been quite calm and reasonable. I guess it all depends whose ox is being gored, no? - Bill Hooker

I'd like to see a publication discussing the economics of scientific publishing in detail. It's clear that there are ways to sustain open publishing. I'd like to get a better understanding of the cost structure, esp in a purely internet publishing environment. - Deepak

Yeah Pedro, I would like to see the post-publication review on PLoS ONE, i.e. the comments on the papers, to be emphasized more. That's a killer feature that is under utilized. Similarly, I often link up PLoS ONE articles on my blog and never once have my trackbacks worked... strange, given that PLoS ONE is one of the only journals I know that allows commenting and trackbacks on articles, but the trackbacks don't work. - Kambiz Kamrani

There was also the little interesting remark (from an unidentifiable source) stating that BMC is already profitable and for sale. It will be interesting to see if this is really true, who ends up buying BMC and what will happen to BMC in the future regarding their publishing policies. - Pedro Beltrao

PLoS ONE serves a valuable function; it publishes "sound science". Not amazing or ground-breaking, but solid and worthy of attention. The kind of work that the majority of us do, I imagine. Disclaimer: my boss is an academic editor and I'm a reviewer. I don't think "not ground-breaking" equates to "lower review standards". Didn't Bora mention on his blog that 50% of submissions are rejected? - Neil Saunders

I really don't get the negative spin on the good financial results. NPG is also diversifying a lot with a growing list of Nature branded journals that include for example Nature Protocols (an experimental lower tier version of Nature Methods?) along with many other journals that do not carry the Nature name (http://www.nature.com/siteinde...). - Pedro Beltrao

PLoS ONE++ - j1m

I've just read the comment thread to the Nature news story. There is outrage about the "slurs" the commenters feel are cast upon PLOS but no factual responses to the facts presented in the article. I'd be more impressed if one of the commenters pointed to a factual problem with the article, rather than the usual "internet outrage" reaction because something is published that the commenter happens to disagree with but can't be bothered to support rationally. - Maxine

By the way, my disclaimer (comment above): I am an editor at Nature, the journal. - Maxine

A journalist writes: grass is green, sun is yellow, sky is blue. Declan writes: grass is green and that is BAD, sun is yellow and that is REALLY BAD, sky is blue and that is REALLY, REALLY BAD. He may have gotten all the facts right but he painted them in puking green in a way that suggests that good is bad, up is down and we are now in war with Eastasia. - Bora Zivkovic

Maxine, Paul Peters commented on the original, making a point that many have made (NPG has its own stable of "second-tier" journals). That's a fact, but you chose to obscure it in your response to Paul by focusing on the "Nature Whatever" group, which makes up about 1/3 of the ~60 journals published by NPG. It's not even (see Bora, above) a criticism of either publisher -- where did this idea come from that publishing solid science was bad? - Bill Hooker

Further, Butler seriously misrepresents the PLoS ONE review process, skirting the edge of disinformation in an attempt to paint it as somehow less rigorous than other journals. PO reviewers do not "only check for serious methodological flaws" as Butler claims. This is a petty smear, carefully worded to keep lawyers at bay but clear in its intent. - Bill Hooker

Sorriest (and most blatantly wrong) attempt I've seen by a for-profit publisher to debase the open-access movement. Incidentally, I do think there are reasons to have a different pricing structure for open-access than PLoS, but the attack on the review process at other PLoS journals while touting the lesser Nature journals rings hollow. Incidentally, it was a slanderous and misguided enough attempt to get me to join the commenting section of Nature and this website to talk about how bad it was. - Evans B

I've confused by your point about my reply to Paul Peters, Bill. I thought it was clear enough and it contained the URL (not a live link) to the numbers in question. I didn't "choose to obscure" anything, I am not that kind of person, I was correcting an error of fact that this commentator made. - Maxine

Bora, the news story didn't say green is green, etc, it had numbers in it. I haven't looked at the comments on the Nature site since this afternoon, but when I did, they were mostly of the "shock horror, Nature has run a news story about another publisher" variety. We often run news stories about scientific publishing/publishers. Do we need to write that we are one do you think? - Maxine

Sounds like it's all tits-up for toll access - Graham Steel

Yeah, no conflict of interest here. are Nature commentaries peer-reviewed research? - Timothy Driscoll via Alert Thingy

Maxine, thanks for the responses. Do the editors at Nature really miss the subtext of the following lines? "PLoS stays afloat with bulk publishing", "bulk, cheap publishing of lower quality papers", "PLoS One uses a system of 'light' peer-review to publish any article considered methodologically sound." The subtext is clear, that things are different in a bad way from how things are at Nature ... so where's that graph of Nature's financials? - Evans B

As a followup, are we really to believe that Nature recently added all the new NPG titles for any other reason than to capitalize on the very thing you condemn PLoS for doing? - Evans B

Yeah, sorry Maxine, didn't mean to say it quite like that. Mea culpa, I apologize. - Bill Hooker

My point, more carefully phrased, is that Paul's comment (though he made an error which I think effectively obscured the larger point) is just an example of a point that many have made: NPG has, indeed most publishers have, their Glamour Mags and their workhorses. Declan makes it sound somehow heinous to do this, but it's a standard business model. - Bill Hooker

What I'd like to see is a PLOS ONE with 0$ cost to the authors, where the light review puts it at a different level (counts for tenure points) from Nature Proceedings, but it still is free - community based - open access. The PLOS ONE reviewers don't get paid anyway right? So the only cost would be only for computing infrastructure, and a few people for organizing/moderating peer-review (infrastructure can be covered from donations, people can donate time). Imagine if this thing picked up like Wikipedia... - Ntino

factual points for maxine: a) the live link you (maxine) gave us only shows the impact factors of the "nature xxx" journals, not those of the >40 other lower impact factor journals that npg publishes. the PLOS accounts are public, and nature is entitled to publish the results of its sleuthing, but for the analysis to be convincing or useful, a comparison with the publishing models of other groups (or at least that of NPG) is essential. b) how exactly is evaluating a paper for methodological soundness "light" review ? and how does adding on a subjective assessment of potential impact somehow makes the review "heavy" (or "rigorous") ? more on all this in the original nature thread ... - mad -

Since not everyone has access to nature, I'll re-post my comment here: Why do we, with today's technology, still have about 20,000 different 19th century journals around? Nature Neuroscience editor Noah Gray points it out: "Nature Neuroscience aims to send 30-35% of papers out to review, so getting past that stage is the biggest hurdle." http://network.nature.com/foru... Why does this step come *before* peer-review? Shouldn't this come afterwards? Why is this considered "non-light"? : - Björn Brembs

Let scientists decide what is good science in their field and then have ex-scientists which usually are smart, knowledgeable, experienced and eloquent decide what is "hip" right now? Let's exaggerate our current system slightly: "non-light" peer-review is mainly a review by ex-professional scientists (either voluntary or involuntary ex-) for popularity. Publication in such journals usually decided who gets grants, tenure, a life. So basically, we have a system going in which ex-members (either members who left or didn't cut it) decide which members get promoted and which get fired. How many corpporate managers do you think would want to implement that in their company? Conflict of interest statement: I have published in Science and PLoS One; I volunteer as academic editor for PLoS One. - Björn Brembs

Thanks! No native Linux yet though. I don't do Wine :) - Neil Saunders

Seems it might be on the way. Meanwhile, Wine it must be. - Ricardo Vidal

I begged for an invite in your comments to ensure you have my email :) - Andrew Perry

@Andrew invite sent :) - Ricardo Vidal

Danke ! - Andrew Perry via fftogo

Here's me begging as well. I signed up, so hopefully I'll be able to distribute some myself. - Mr. Gunn

Mr. Gunn, just sent your invite :) - Ricardo Vidal

Got it. The comparison to MP3 sharing is apt, with all the implications that entails. A hot feature for them would be online backup integration, so you're not limited to running it from one PC and so people could share references without having to actually mail the PDF. - Mr. Gunn

I want in too. If possible ... obrigado. - PauloNuin

Ah, reading the license terms: "You may (at your option) use our Software to make a regular back-up copy of your Academic Papers to our servers so that you can access your Academic Papers using the World Wide Web and you hereby grant to us a limited licence to upload, copy, store, use, modify, display and reproduce your Academic Papers for the sole purpose of providing our back-up service to you." I like this very much. - Mr. Gunn

We may from time to time provide interactive services on our Site, including, without limitation: "facilities for the uploading and sharing of users’ and members’ Academic Papers with other users or private user groups you have created" This is perfect! The social networking angle of the online service, linking people via authorship, looks really nice and pretty much kills SciLink. - Mr. Gunn

Don't mean to live-blog my reading of the license here, but I should include: "You may use our Site and our Software only for lawful purposes. You may not use our Site or our Software: to send, knowingly receive, upload, download, use or re-use any academic papers or articles without the permission of the copyright owner." - Mr. Gunn

Finally, "You may link to any of our publicly available pages, provided you do so in a way that is fair and legal and does not damage our reputation." I'm going to blog my review, just as I have with 2collab and Connotea. I hope they don't close my account because I say something too critical. - Mr. Gunn

Mr. Gunn, how about a blog post about the license terms? Sounds like you have some opinions about them. - Ricardo Vidal

That's coming, once I get some hands-on time with it. The import from Connotea is putting the doi in the notes field instead of the doi field, which is apparently Connotea's fault. Two killer features I hope they add soon: automatic download of PDF once metadata is added and adding to library via bookmarklet. If they don't have the second feature, I'll probably still use Connotea or something and periodically update Mendeley, provided. It needs to be easier to select a range of papers in Connotea by date - Mr. Gunn

Mr. Gunn - "I hope they don't close my account because I say something too critical." We sure as hell wouldn't! We know that we still have a lot of work to do, so our technology as well as our license terms are far from perfect - both will be modified based on our users' feedback. Any ideas are appreciated! Just one remark regarding the current license terms: As you can tell from the language, they were largely written by our lawyers with the main intention to protect us from lawsuits... - Victor

The license terms quite strangely resemble readable prose, so props for that! I'm still trying to find an import format that works 100% for Connotea/2collab -> Mendeley. I takes about 20 sec on my machine to import 550 records. It's becoming apparent to me, and probably has been for a while to Ian et al, that RIS kinda sucks. Every app seems to expect things like DOI and URL and notes to be in a different field. - Mr. Gunn

Thanks - we tried to intervene and rephrase where possible, but our lawyers were adamant on some points! To be honest, we hadn't planned with a Connotea/2collab import specifically; we just tried with BibTex and RIS files generated by Google Scholar and EndNote XML... If you feel so inclined, it would be enormously helpful if you entered any import/field mapping problems into our bug tracking system: http://mendeley.com/trac?compo... - Victor

I tried it yesterday. I think I imported around 400 articles. There were several errors in import but these are understandable. However I wanted to go through the errors and add tags etc but it was a bit to slow so working on it was a bit frustrating. Is it just me or is it slow for other people as well ? - Pedro Beltrao

Hey Victor, any way to get an invite? Thanks ... - PauloNuin

I second Paulo's question for an additional invite.. - Daniel Jurczak

Paulo, Daniel - I feel rotten for having to turn down your request, but unfortunately, we can't currently invite new testers. Sincerest apologies! The reason is that we've got our hands full fixing the bugs and implementing the feedback brought up by the current testers. I know it seems arbitrary, but there's also a waiting list of people who signed up on our website (www.mendeley.com). May I ask you to register there? You'll be notified first thing we go public beta... - Victor

So, that was true, life exists beyond Paris... Can't be true. - Pierre

This, and the Discovery Channel commercial ( http://www.youtube.com/watch?v... ) , make me want to travel sooo bad. - Eva

Yeah, I had the same reaction. Hadn't seen the Discovery Channel commercial - it's pretty cool. - Michael Nielsen

Found a translation of the Bengali lyrics here (see "Stream of Life) - http://www.schoolofwisdom.com/... - "The same stream of life that runs through my veins night and day runs through the world and dances in rhythmic measures. It is the same life that shoots in joy through the dust of the earth in numberless blades of grass [...]" - Michael Nielsen

I also deleted any previous answers that had been entered so far, because I wasn't clear about how the data would be used. So if you've filled out the survey once, and are happy about your data being released, you'll need to do it again. - Michael Barton

re-posted the form on my blog. - Pierre

http://en.wikipedia.org/wiki/D... should be enough to figure if you're covered. Data is anonymous and if everyone who takes place understands the data is to be released, not sure what the problem would be - Daniel Swan via twhirl

Cheers Dan. :) - Michael Barton

Michael, for Nationality, should I put "American" or "United States"? "American" is geographically (though not practically) ambiguous. Too bad those fields aren't drop-down boxes so the input is standardized and idiot proof. :-( - Chris Lasher

re-posted the survey as well. - Pedro Beltrao

I've only studied bioinformatics briefly but should be eligible to fill out the survey and I may be able to forward this to some researchers I know - Julian Baldwin

Science Progress is amazing. I subscribe to only the best posts via AideRSS, which I can't recommend highly enough for those of us without enough time: http://www.aiderss.com/rss/gre... - Donnie Berkholz

We are so screwed. :-( - Bill Hooker

"Like" as in "I like that someone noticed this and is still pushing the issue". - Andrew Perry

Well, if it's tre that the odds of someone getting a tenure track position by 35 are only 7%, there's only one solution: make PhD programs a mandatory two decade ordeal! That should get most people past 35! - Todd Harris via twhirl

"In 2007, two hundred scientists received six or more NIH grants, and a single investigator won 32 grants, while many others got close to ten." This sounds ridiculous. It is clear that this investigator cannot be coordinating closely all those projects. - Pedro Beltrao

It's a classic catch-22. Increasingly, funding consists of large grants to established researchers with stellar track records. However, to become established and build a track record, you need funding - which you can't get. I'd actually like to see postdocs desert academia en masse; let's see where the big bosses would be without their slave labour. - Neil Saunders

I've always wondered how science would work with a more active 'union' for PhD students and/or PostDocs .... if they went on strike how would things pan out ... it's not like public transport employees or a big building project with tight deadlines ... the 'general public' probably wouldn't notice for years. Hence the level of exploitation that occurs (not saying every student/postdoc is exploited, but many are, and I think the lack of any power in a stop-work is a large part of it). - Andrew Perry

I still get a little bugged by the assumption that PhD = career in academia - Deepak

Yeah, I've often wondered how long it would take for anyone to notice if academic researchers went on strike :) - Neil Saunders

Thing is, the rules are different in academia. Basically, if you're not independently-funded, you don't count and are not free to pursue your own agenda. So we end up working for successful group leaders and furthering their careers, rather than our own. I personally think it's wrong that senior researchers get credit for minimal input, solely because they hold the grant, but that's how it is. - Neil Saunders

Neil ... one of the many reasons I wasn't interested in academia. In a good company, you get recognized (as does your manager) when you do well. In academia, it seems like the managers (PIs) get undue credit ... nothing wrong with academic science. I quite envy the freedom from time to time, but there's a lot more - Deepak

@Neil: don't disagree with you, but just to play DA: it's brutal to get and hold onto a lab as a PI, and once you're there it takes all your time and energy just to hang on. (Unless you're one of the silver-spoon Big Shots, but there are a lot more small, struggling labs than big fat ones.) So there's a PI catch-22 as well: you have to take credit for what your lab does, or you get no credit at all. I keep wondering whether Pawel and his freelancing ideas might not be a viable alternative model... - Bill Hooker

@Bill - don't disagree with you either. In theory, a PI is rewarded for their previous hard work, skills in organisation, directing research, mentoring and so on. Sometimes, it even works out like that :) However, I do think we've entered an era where the system actively favours established researchers and actively discriminates against young, early-career scientists. I think it's untenable and would like to see it proved so by people voting with their feet and getting out. - Neil Saunders

I think there's definitely a "rich-get-richer" thing going on. I also think that competition has reached the point -- 7%! -- where we might as well draw names out of a hat. (Sneaky self link: http://3quarksdaily.blogs.com/...) There's not much correlation any more between smarts+hard work and success. Something's gotta give. - Bill Hooker

@deepak: One problem is that academic training is done by academics. That's all they know. They aren't prepared to train people for careers in other environments. And as for grad students striking, it's been done, and doesn't really work for reasons mentioned below. Besides, aren't we all in it for the love of discovery? Are you really going to go on strike when your killer experiment you've spent a year setting up is coming to fruition, your bunnies need a bleed, or you need to read galleys? - Todd Harris via twhirl

Todd, I wouldn't disagree with that, but there are more than enough PhDs who move on to industry, where quite frankly I enjoyed the science I did. I think the stike that Neil refers to is people choosing industry over academia - Deepak

That is indeed the action I meant. The whole notion of striking PhDs/postdocs is ridiculous! If your job (any job) is really making you so unhappy, then look elsewhere. I'm acutely aware of "whinging postdoc" syndrome when we explore these issues. I have no time for those "life is so hard in academia" style of blogs. It really isn't. - Neil Saunders

Well, the strike I was referring to was a real strike, not a shift out of academia, but for reasons Todd (and I) have already stated, it wouldn't work, it would have to be a pretty bad situation before things came to that, and despite problems overall most junior scientists do love their work to much to do it. Because of this, it's one less bargaining chip that they have to improve their situation, unlike some other industries. So in reality, I guess a move to industry is a good alternative to a strike ... - Andrew Perry

Especially since it's often a pretty good alternative, and you get to build stuff and often, esp in a small company, get to do some very interesting research - Deepak

I came to this discussion late (ironically because I'm writing yet another grant) but thought I add anyway. I train people in my lab for academics or industry. Most have gone on to industry as it turns out. Since I've worked in both settings its easy for me to make the training fit either option. I try to give the person the chops for either and then let them pick. - Maureen

Since we are talking about alternative career paths it could be worth mentioning that scientific publishing is still growing at a strong pace. I think if I was not happy with research in academia publishing would be the place I would look for an alternative. - Pedro Beltrao

Postdocs: A 1960s invention because they didn't have enough professorships. Lame. Lame. Lame. - Mitchell Tsai

Comments came back today for a .au funding round. A comment directed at a senior researcher with 10 000+ citations was "very good track record but very no recent first author papers". Also last year the Platypus was not exciting, this year the reviewers are so excited they are creaming their pants. Two questions. Who are the idiots who review these grants (I hope it isn’t those who hold 10+ grants)? Are the only things that get funded something that's been big in the media? It appears very short-term hype focused vs long term vision - Mitchell J Stanton-Cook

This is the logical outcome of poorly synchronized boom-bust cycles in funding, training and the availability of scientific careers in any given place. On top of this, since science is now a transnational career possibility, problems are being exacerbated by even more short-sighted policies in other countries. Some interesting comments here: http://bigpicture.typepad.com/... - Heather

Reading this has rather put me off continuing in academia. I like doing research, but I'm not sure if I fancy spending most of my time writing grants if I become successful. Success in research = do less research ? - Michael Barton

Michael, I do think that to an extent it's a choice. I know a few PIs who still write their own code. Even in industry you can choose your track (technical vs. management). Most of my friends are still in the technical track and at least managing large projects if not right in the middle of them. - Deepak

"Success in research = do less research?" Depends in part on the field. A few years ago I started going to occasional math and philosophy meetings (I'm a physicist). I noticed the senior mathematicians and philosophers were a much more interesting and happy bunch than the senior physicists, on average. My eventual theory was that the relatively low level of funding in mathematics and philosophy was actually a boon for these people. Most senior physicists are machines for turning coffee into grants. - Michael Nielsen

I just don't get people. It's not like anyone is saying that ONS is the only way of doing science. It's "a" way, and a perfectly fine one if someone so choose, but then if anyone equates science to just wet lab work is hopelessly lost - Deepak

Yeah, I don't get the animosity either. I do know it's very common in science though, and I don't understand why that should be. Shouldn't researchers be both *curious* and *positive* about new things? - Bill Hooker

I am not sure it is even worth responding anymore. The whole strategy of that blog seams to be to irritate people enough to comment and come back to the "discussions". - Pedro Beltrao

I take back this last comment. Whoever writes the blog does have interesting and useful blog posts in there. I don't get it why once in a while he/she has those posts full of insults that clearly look like flame bait. Just for the fun of it here is a link to a rinsed version of the RSS feed of DrugMonkey (http://www.feedrinse.com/servi...) - Pedro Beltrao

There's an art to using a combative, abrasive style in this way. Personally, I think RPM at ScienceBlogs has it and this guy doesn't. I just find it very tedious and go elsewhere. - Neil Saunders

@Neil: absolutely agree there's an art to it, but I like PP and think RPM should dial it back a few notches, because he has lots of good stuff to say but just doesn't have the gonzo style down. - Bill Hooker

On a related note --- what do people recommend for electronic lab notebooks in general - either the closed kind or the open kind? I am trying to move my lab to all electronic notebooks with the long term goal of posting a lot of stuff openly but I need to start with a good electronic notebook ... - Jonathan Eisen

@Jonathan - can of worms, mate! There is no good, free/open-source, one-size-fits-all ELN solution. Most people here are using wikis, blogs or a combination (blikis). - Neil Saunders

One to keep an eye on though, as an online solution is SmartNote: http://smartnote.miraibio.com/.... Good if you do mostly DNA sequence stuff. - Neil Saunders

@Bill - question of personal taste, I guess. I'm not a fan of science bloggers who feel the need to project a contrived writing style. It just obscures the message for me. - Neil Saunders

Thanks Neil. The problem with the wiki/blog option is getting non techno people to use it. We have a lab wiki. Still hard to get everyone to use it for lab notebook stuff. Will check out smartnote - Jonathan Eisen

Jonathan - as you know I'm still a big fan of the general purpose wiki as lab notebook. One of the advantages of Wikispaces is that it has a decent visual editor and a highly simplified WikiText. But not matter what you use it will take more than technology to get your group members to enthusiastically use it. - Jean-Claude Bradley

Agree, Jean-Claude and Jonathan. My attempts, even with a visual editor and a training course, have failed to encourage lab members to edit our internal lab wiki. It was set up initially to only share our small sequence datasets, with the idea that this could be a pathway toward lab members using the wiki for protocols, and maybe even migrate to an open space like OWW eventually. It seems to be a real difficulty for the non-techno crowd, and it seems that they won't even try. - Andrew Perry

We get some use from our lab wiki and a LIMS that I hacked together, but only under great duress - basically the boss demands participation. Unwillingness to try is a source of continual frustration and incomprehension to me. The benefits are clear (I hope), the users are not stupid (I hope), nor computer-illiterate (if they can set up and manage Facebook, they can manage a wiki). It's either not a priority for them or else they're just lazy. - Neil Saunders

The problem we are having is integrating multiple formats - handwriting (e.g., lab notes), pictures (e.g., non digital images), digital images, analysis, etc. It is not that people are technically fearful, it is that getting people confortable with the idea of doing everything on the computer and changing practices (e.g, taking notes on the computer not by hand) will take some time. - Jonathan Eisen

I use the exact same approach for writing papers as Jason; works very well. - Neil Saunders

If I haven't invested yet in Connotea, can I import old Endnote libraries into CiteULike? - Heather

Heather: if you export your Endnote as RIS or BibTeX, you sure can. Just not the nasty, proprietary, good-for-nothing, binary EndNote (.enl) files. - Neil Saunders

I started my library with connotea but I think I would use citeulike now just for the pdf uploading tool.. I use this scientific-social-boorkmarking tool because they understand the DOI or the pubmed-id's. However, once a month, I transfer all my bookmarks from connotea to http://del.icio.us because, at the end, its 'network" option is the best tool for knownledge discovery : http://del.icio.us/network/lin... - Pierre

Duncan also takes indecent liberties with the Bioperl paper to describe buggotea: http://www.nodalpoint.org/2006... - Jason Stajich

"Liking" this to remind me to try CiteULike. - Bill Hooker

Google Trends shows that CiteULike is more popular. Both could have better group features. - Martin Fenner

Pierre - Just today I was thinking again how Nature could try to combine Nature Network with Connotea to provide a page in NN for paper recommendations (based on the contacts libraries in Connotea). Also maybe analyze the papers published by the user to give recommendations based on a search for related papers (automated query to pubmeds related papers ?). To be a bit fancy they could give some options to filter them. Hide some of the users contacts or pick a selected group of journals to filter etc. - Pedro Beltrao

@Jason "Indecent liberties with the bioperl paper", I like it! I think citeulike is better, but only just and agree with Martin that they could both be better. Been using http://www.scopus.com a lot recently, and this plays nicely with citeulike, dunno about connotea though... - Duncan Hull

You may want to try http://2collab.com/ too - Rafael Sidi

I'm going to try CiteULike soon. I tried it soon after launch and didn't have a good experience, but I understand it's come a long way. The only thing keeping me with Connotea is inertia, and the fact that I think citeulike is the dumbest name ever. Sorry, Mr. Cameron. I tried 2collab http://synthesis.williamgunn.o... but there are all kinds of weird design decisions that just don't make any sense to me and the import and export still need work. - Mr. Gunn

I use Connotea, but the problem with online ref. managers is when you try to access articles from journals that require subscription. Which has me going all the way around to login through the university library's proxy and then retrieve the article. The middle way I've found is by saving the pdf's locally through Zotero, and then uploading the references to Connotea via .ris or .bib file export from Zotero... So I get pdfs right there in my hands to read right away, and saving the refs online for Web 2.0 - Ntino

My impression is that 2collab is more of a social bookmark/discovery tool for papers than a bibliography manager. I liked Zotero a lot initially, but abandoned it in my quest to move as much stuff online as possible. When it supports synching to online repositories, I might come back to it. - Neil Saunders

Thanks, all. Giving citeulike a shot. - Chris Miller

I used to be a Connotea guy but this thread got me curious to check out CiteULike. Verdict: I like. The UI could be improved, I had a hard time figuring out how to edit the citations I submitted, but it works and I love the PDF uploading -- beats me having to email myself the PDF or carry around a memory stick when I find papers I wanna read. I also like the tagging the items either as "read." "to read." - Kambiz Kamrani

Funny, the tagging by importance of reading is my least favourite feature of CiteULike. I guess it's supposed to function as a recommendation - only the default is "might read" and everyone leaves it as that (go on, check the library of almost any user!) If I make the effort to save it, I assume that I either have read it or plan to at some point. Useless feature, for me anyway. - Neil Saunders

All I want is the webbyness of citeulike combined with the iTunes like interface of Mekentosj Papers, but cross-platform, rather than Mac only. - Duncan Hull

Why not combine Connotea and Nature Network? I see a lot of synergy. - Martin Fenner

You should ask Ian Mulvany http://friendfeed.com/ianmulva... if they've considered doing this - Duncan Hull

Pedro has pushed the NN-Connotea integration at NN and other forums. Don't know if it's under consideration. Perhaps the priority is fixing Connotea first. - Neil Saunders

In related news, the long (January) overdue update to make Endnote work with Word 2008 for Macintosh was just announced. - Martin Fenner

http://www.plos.org/embargo/ http://www.plos.org/journals/e... - Jason Stajich via twhirl

They have done that unofficially in the past, so looks like they are formalizing part of that process - Deepak

@Neil Yeah, you can't blog about it until after the embargo date has passed. - Euan

This is great. Levels the field for bloggers wanting to work as science journalists. - Pedro Beltrao

I think we're still working out the etiket here as well - but overall share other people's posts if you like them (or don't but think they're important) but don't stream the whole lot. It does appear as 'Heather posted a message on ####' - Cameron Neylon

What a game! Okay. I figured out how to remove the feed. That wasn't obvious to me. I don't follow blogs in Google Reader but might get around to it... meantime, I'll give the imaginary friends thingy a shot. -