Mendeley users revolt against Elsevier takeover 275 points by pms on Apr 10, 2013 | hide | past | web | favorite | 147 comments

 Mendeley's sale to Elsevier reminds me of this video: http://cs702.wordpress.com/2013/03/20/you-have-to-monetize-y... -- one slide shown in the background, in particular, makes me cringe and laugh at the same time: "Only sell your users to whoever has the deepest pockets."PS. More seriously, I've come to feel that only a non-profit organization can solve the "walled garden" problem in academic publishing. We need something like a "Mozilla Foundation for Science" -- an organization dedicated, not to maximize profits for shareholders, but to keep power over scientific research in people’s hands.
 an organization dedicated, not to maximize profits for shareholders, but to keep power over scientific research in people’s handsThat's why we have governments.No, I'm not being sarcastic. The public sector is there to serve the public good, and this is quite obviously a public good. I'm not anti-privatization either. Private exploitation under public laws and guidelines is a common strategy to solve these issues.What has undermined public/private solutions is not public opinion or political ideology, but greed, lobbying and corruption. A foundation is nothing but a workaround, and foundations have a history of getting corrupted by the greed and delusions of grandure of its administrators.It's time we address the real problem. The legacy of thousands of years of civilization is being stolen from us.
 I appreciate where you're coming from. But do you really trust, say, Sarah Palin to oversee evolutionary biology research? Exxon to have veto power over climate change articles? Todd Akin to be able to interfere in STD epidemiology?The open source movement has shown that there's a third way, and I suspect that that's the way to go. It's fault tolerant: if a group of people are detracting from its mission, the others can very easily go on and continue as is.Science is more expensive than software, though, and therein lies the rub.
 Sarah Palin wouldn't stand a chance in hell in mature democracy that hasn't been corrupted by the power of money.Palin is a sock puppet for those with the money, and the people voting for the likes of her have been deliberately deprived of a decent education. This is a symptom of the same corruption.The open source movement is a workaround, exploiting a flaw in a corrupted system. It should serve as an example of how much better things can be, not as an excuse to never address the problem, especially not when millions are being criminalized by exactly the same copyright system for the simple act of sharing.It's not fault tolerant: changes in the copyright law (the laws bought and paid for) can kill copyleft, and whatever license one may prefer, copyleft upholds some of the essential pillars of the open source ecosystem.Don't get me wrong: I'm all in favor of pragmatically using these workarounds.But I'm also in favor of keeping our eyes on the prize: the knowledge accumulated over millennia should not be allowed to be monopolized and exploited by the few.Open source is not a "third way". It's a necessary detour.
 "...and the people voting for the likes of her have been deliberately deprived of a decent education."I really wish this were the case, but political views remain relatively static in the face of increasing levels of education. (see: http://www.nytimes.com/2012/03/04/opinion/sunday/college-doe... )Unfortunately, even if we sent all the Palin-voters to college, they would still probably be convinced that Obama is a muslim, earth is 5,000 years old, etc etc. It's rather depressing to think about, since there appears to be no cure for it.
 Science is already funded, in very large part, by the federal government (in the US). The research is already subject to political pressures, here we're just talking about the (much smaller) amount that goes towards publications. Federal grants are going to fund research, the results of which are locked up behind the paywalls of proprietary journals (grant dollars even pay for the privilege of publishing in some journals). Publications by federal employees are already required by law to be in the public domain. It's time we look at doing the same for the results of federally funded research.
 This is exactly what I'm working on. Also, publications by federally funded grants are required to be made public as well (for 1 year). However, even doing that, you are still stuck behind the political pressures, journal bias, and the peer review system which...for a lack of a better term, sucks.Science needs to be transparent and made available in real time. This is the whole purpose of science, to freely distribute knowledge for the well being of humanity. I honestly believe that and I'm working to bring that transparency to science as we speak.
 > Publications by federal employees are already required by law to be in the public domain. It's time we look at doing the same for the results of federally funded research.Yes, this needs to happen. NIH already requires that publications arising from NIH-funded research be made publicly available 12 months after publication (http://publicaccess.nih.gov/). Other funding organizations really need to do this. IMHO, they should also require that publications be made publicly available immediately upon acceptance and provide incentives for "gold" open access (where the article is immediately made available on the publisher's website).
 Other federal research orgs are ramping up now -> http://blogs.nature.com/news/2013/02/us-white-house-announce...
 > The open source movement has shown that there's a third way, and I suspect that that's the way to go. It's fault tolerant: if a group of people are detracting from its mission, the others can very easily go on and continue as is.You can't fork funding the way you fork source code though. It's not just more expensive, but fundamentally different.
 You can't fork funding, but I'm thinking that we're talking about forking content. If the Wikimedia Foundation decided to go in a direction people didn't like, it would be possible to fork all of their content and start your own competing wiki (bring your own funding, of course).
 Of course, but that does nothing to take power over research away from the likes of Sarah Palin and Todd Akin.
 > It's time we address the real problem.The real problem is that some companies manage to exploit a monopoly granted to them by the government in ways that are not pleasing to the public. The government is the entity which created the problem. Granted, while solving another but it will still be the government agents who break down your door and arrest you if you build an unauthorized competitor or even just try to release that "legacy" (vide Aaron Swartz), not Elsevier's.It's hard for me to understand how you can blame a company that puts up a paywall more than people using violence (or at least credible threats of it) who enforce the rules stopping others from competing.
 > It's hard for me to understand how you can blame a company that puts up a paywall more than people using violence (or at least credible threats of it) who enforce the rules stopping others from competingBecause we're not 15 year olds who just read Atlas Shrugged?
 So you're arguing that because the government has a monopoly on force, anything bad that happens anywhere in the US is their fault because it's their guns backing up the law?Laws happen because a variety of agents (lobbyists, legislators, public interest groups) push for them. They're not enacted by some amorphous specter of 'government'.
 There's a difference between a for-profit company with a government-backed monopoly, and a not-for-profit organisation with government support (of which there are already many examples).I don't think anyone here blames companies for putting up a paywall or doing something else to maximise their profits; it's why they exist. However, we do recognise that this is not always an ideal state of affairs. A public sector body is one way to remove the profit requirement; private-sector not-for-profit organisations are also a possibility (but have to worry more about where their funding comes from).
 > The government is the entity which created the problem.And it acts as an extension of "the people" as the entity providing oversight and regulation in this example as well. That it doesn't happen in real life is evidence of subversion of an ideal, rather than some inherent truth.
 It's called PLOS:
 Know any donors? I'd love to be involved in a project like this. I wonder if the Wikimedia foundation would be interested--that would do a lot to get over the network effect advantages JSTOR and Elsevier already have.Additionally, I think that until academic publishing has a standard browser-based solution (MathML, MathJax + Pandoc + LaTeX) outside of PDF that the costs will be prohibitively expensive.
 JSTOR is not a publisher. They are also a not-for-profit organization. While it would be awesome if all the material they scanned were open access, I think their hearts are probably in the right place. Scanning millions of journal articles isn't cheap, and there's no obvious alternative way to fund that.
 There seems to be a world of difference between "not-for-profit" and "non-profit" in the ways we are imagining open-access.JSTOR is not a publisher--agreed. They are, however, a central repository who charges an arm and a leg for research that, often, has been funded on the taxpayer's dime.
 In my world, I guess I think of JSTOR as the "good guys." The trustees of its parent organization are real academics (http://en.wikipedia.org/wiki/ITHAKA). Its fees are extraordinarily reasonable, at least compared to Elsevier's. (JSTOR fees for large U.S. universities are on the order of $10,000 annually, whereas my university says they pay about$2 million per year to Elsevier.) Since JSTOR is a not-for-profit, I don't really see where the money would go besides toward the actual cost of making the research publicly available (which in JSTOR's case is non-trivial, since they are scanning a lot of publications instead of converting InDesign files to PDFs).There is obviously a difference between making academic research available to universities at reasonable prices and making academic research available to everyone for free. The latter is obviously better, but to happen, the money would have to come from somewhere. For a publisher, the obvious answer is publication fees (which is what PLoS does). This is not an option for JSTOR, since most of their material has already been published. I suspect that JSTOR would happily make everything in their collection open access if they had a sufficiently large endowment to do so.
 > Since JSTOR is a not-for-profit, I don't really see where the money would go besides toward the actual cost of making the research publicly available (which in JSTOR's case is non-trivial, since they are scanning a lot of publications instead of converting InDesign files to PDFs).I agree with your point. But you are ignoring another major expense that the fees go to:Paying the actual publishers and rights-holders licensing fees. JSTor is not a publisher. Most of what they distribute, there is a copyright holder, usually the original publisher, that will not let them host and distribute without a fee.This is obviously not something JStor has a whole lot of control over.I agree that JStor are the 'good guys'; their fees are more reasonable than most of their for-profit competition, AND their service is _just plain better_ than most of their for-profit competition.It would be interesting to see how much of JStor's budget goes to paying licensing fees to the rightsholders; I don't know if that information is public.
 For the non-free content on JSTOR, I don't see much that another archive could do about it. The main issue is back issues of journals published between 1923 and now-ish. Future content could go open access directly online, in which case JSTOR doesn't even really enter into the picture. And JSTOR has already made all the older, public-domain content freely available. But in between, there is almost a century of copyrighted content controlled by the journals. JSTOR scans the paper journals, but can only make the PDFs available with agreement of the copyright holder. They could try to pressure them more, e.g. by threatening to evict journals from JSTOR if the journal doesn't agree to certain minimum licensing requirements. But they don't ultimately control that content themselves.
 Ask Google to do it. If they can get books scanned, OCR'ed and available online, they should be able to do journal articles as well.
 Try the Public Knowledge Project. You can contribute monetarily, by helping fix bugs in one of their open source software packages, or by finding one of the many open access journals that use their software and contributing articles or editorial support (note: I used to work for them).
 The state of academic publishing is in a truly dreadful state. The same monopolies that created the industry hundreds of years ago have never been pushed out and innovate in the slowest way possible, aqui-murdering even worse than EA when they have to. Online journals and the promise they provide are peddled by high pressure sales pitches who insist on absurdly high prices. For many institutions, when taking usage stats, the price of online access per user often works out to several dollars per search...This is why I've given up trying to work in the field or found a company in the sector... Anyone with an idea and need a technical cofounder? ;)
 I think that there should be something like SO (Stack Overflow) for scientific papers, with anonymous user-generated reviews and ratings of the papers, and reputation being acquired by the users, both based on papers and their reviews. I wrote 'anonymous' because it's a more heavy-weight business than posting and assessing questions about coding. To avoid the situations when scientists get angry because of bad reviews, and try to revenge on their reviewers, it should be at least in the first years anonymous. The reviews would be voluntary, and also would be rated, just like answers to question in SO. I am a scientist, and I know that reviews have very low quality because of many reasons, such system could perhaps help improving the reviews, while keeping the reviewing process automatized, and reducing its cost to the minimum. In fact, costs of storing papers are low (Arxiv), reviews are free (nobody pays to the scientists anyway, they do it for the community and reputation), and the only cost that is high is the cost of managing the reviews. But if reviews could be automatized then we have a system that is as cheap as Arxiv is, and peer-reviewed :)In the long run I see such system emerging and being successful, and eventually replacing everything else. Needless to say it will take a lot of time though to popularize it.What do you think? Could this be done?
 Refereeing papers is an odious chore that you only do to get your back scratched in return in the future. (They call it "giving back to the community", but it's really a protection racket.) You can't replace this with a voluntary system.
 Why not, if you would get reputation points for it? The idea is to review the papers which you want to read anyways, or perhaps you have already read them and you want to express your feelings about these papers, hopefully in a way useful to other viewers of the paper. Nobody tells you to do it, so you do it by heart, this surely would increase reviews quality.
 Well, maybe this could work, but probably it would have to replicate the "coercive" component of the current system. In other words, by reviewing other people's papers you somehow improve the chances of having your own papers reviewed. And if somehow that system manages to also provide an incentive to do the job thoroughly, then that would be a huge improvement on top of what we have now.
 Well, the coercive component is the unified reputation that you gain in this site, just like the reputation that you gain in SO. Obviously, the higher reputation you have, the more recognizable you are and more people read about what you do.
 Coercion comes from the employers (tenure/promotion requirements) not from the publishers.
 I think that could be a successful community, you just have the same problem as any social community, finding users. Especially ones of interest that are open to publishing anonymously and listening to anonymous reviewers.The real tragedy is the general reference, social science, and humanities journal diaspora where the usage and demand has skyrocketed with the increased access online resources allow to lay researchers. The science journal communities are way ahead in self-sufficiency in adapting, and are increasingly open to the corrupt state of publishing and alternate community publishing platforms.
 I think SO is the wrong model and that Hacker News is a better one. There's already reputation/badges/etc for the sort of academic tasks you're describing: look at any CV (eg: conference presentations, referee assignments, etc, and the obvious one is journal publications). So I don't see how replacing the old system with the old system plus usernames is an obvious improvement or a necessary evolution.I'm way more interested in informal discussion of interesting papers and news than anything else.As everyone else has mentioned, the big issue is getting a large community. So what would be really cool would be to figure out how to do something like HN or SO without active involvement by a large community. In my field there's a lot of discussion/review/etc of working papers and published results, but it's all scattered across different blogs and commenting systems. Plus papers build on each other and some are clear replies to other research. If you could take that sort of dispersed discussion and put it into an HN or reddit style threaded view that was available at one spot (or an SO style question and answer format, if you prefer), that would be awesome.edit: typo
 There are a few websites already trying to do this, but as with all networks, it only works if you get enough users.
 Could you give me examples? Thanks!
 Arxiv and marxiv are already working on this.Arxiv even has a paid fellowship, but it is postdoc wages, not professional wages.
 Serious question: why does this need a technical solution? Researchers comprise the editorial staff for these journals, conduct the peer reviews, and submit the papers, all for free (or nearly so). They (we) universally want the papers to be accessible by other researchers (because that means the paper might get cited) and are at worst indifferent to the papers being accessible to the public at large, and by that I mean some people care a lot about that issue, some people don't care very much, but I don't know anyone who is opposed to public access.So there's an ongoing transition now by researchers/editorial boards/etc to move to a system with lower access costs (some of which involves taking back journal ownership, some doesn't). There's some logistical overhead and fixed costs, but those are falling. It seems like in 20 years (conservatively) all new research will be available to whomever wants it no matter what Elsevier or other companies do in the meantime (the papers may not be literally free, but affordable).So, like I said initially, I can see how some software for logistics or communication would be helpful, but the main issues don't strike me as technical.
 One of the many problems with academic publishing is that it's holding on to an antiquated idea behind publishing and not progressing with the way communications are moving now. In a sense, publications are moving at 1970s speed and this hurts science. Hence the technical need to bring it to current times.Is it a "technical issue"? No, but neither is booking your flight via phone, that worked just fine. Could it be made much better, more accessible, cheaper, and overall better via technology. Yes.
 An anecdote: I finished a decent draft of a paper two weeks ago and posted it to my website an hour before submitting it to a journal. The code to replicate it is on github available to anyone who wants to look at it, and the statistical methods I use I've put in a GPL R package. I've already discussed aspects of the paper and some implementation issues with other researchers over email, presented the paper at conferences, and I think people are already writing papers that use the statistic I propose (again, despite the paper having been submitted to a journal for the first time two weeks ago). In the process of discussing the paper (in person, over email, etc) I've already essentially done two rounds of peer review without journal submission.Maybe you could give details about what you mean by "antiquated idea behind publishing" because I'm pretty sure what I described is not 1970s speed. Now, if your point is that what I've described is not common practice, I agree completely. But that means that people need to be persuaded to use existing technical tools -- I can't see a specific step that's going to be a significant pain point (I'll grant that not everyone can/will use github, but uploading a zip archive of the paper's directory to a personal webpage is easy and is almost as good for code and data dissemination).Other anecdotes are blogs that announce and discuss new research:http://johnhcochrane.blogspot.com/2012/10/nber-asset-pricing...http://johnhcochrane.blogspot.com/2012/09/woodford-at-jackso...That is legitimate academic discourse, put out by an extremely established and credentialed economist, almost instantly. On blogger.
 I think it's super awesome that you did all of that! Kudos to you, and I wish more people were doing stuff like that.My viewpoints are limited to life sciences, where people have no idea what FTP means, let alone GIT. Also, what you did is not typical, people (at least in my field of neurobiology) have no intention of doing something like that in fear of being scooped. The antiquated idea behind publishing is the concept of doing an experiment, filtering out all the negative data, and then submitting their positive data to a journal that they think will publish their data. We've been waiting for 7 months now for a paper to get published in PNAS due to this antiquated process. 7 months to do what you did in a few minutes uploading your data online and making it public.
 I'm all about this sort of openness in the research process, but it seems counter to some disciplines' cultures- aren't eg, medicine and chemistry more competitive / secretive prior publication?
 You're doing it vastly different from many academics. Kudos to you!
 A good start would be increased quality of interfaces and abilities to find and connect similar sources; that's all I'm really asking for. There is a huge amount of research published within the Gale-Wilson-ElSevier-JSTOR-Ebsco-Taylor&Francis vaults, properties of immense academic and economic value, yet the tools they charge to access them aren't much more advanced than Yahoo circa '99. Don't even get me started on the transition from physical-copy journal publishing where you always 'own' the copy to a model of journals-as-a-service (the ultimate DRM; they host it) that cost well into the five figure range per year where you lose all access once you let the subscriptions expire.Meanwhile, 'search' as we know it rules the world and is the driving force enabling the entire tech industry. It wouldn't be hard to throw a little effort in building out their platforms, but there's no competition to force further development in their products.
 Not sure you realize, but these companies already are throwing more than a little effort into advancing their platforms.Elsevier in particular is spending ridiculous amounts on internal research & acquisitions for its platform (called SciVerse, http://www.hub.sciverse.com/), following the latest advancements in machine learning and NLP for data mining, etc etc.They also host competitions for start-ups and developers to produce new apps for their platform.These businesses may be unethical and not to everyone's liking, but they are not stupid.
 For most scientific fields, the last decade's research is much less important than the next decade's research. New research is much less locked in than stuff that was written before the internet became ubiquitous, so I'm not as concerned about that issue.
 Well, a technical solution is needed to make changes faster and even better, namely: 1. Provide for the papers a system of transparent reviews and ratings accessible and readable to the public. 2. Provide a recommender system and a search engine based on the reviewed and rated papers available publicly.This would add real value to the scientific publishing and simply help the researchers to find what they need.
 > Provide for the papers a system of transparent reviews... [snipped]I don't think this is a technical issue. Journals make mistakes on which papers to publish all the time, even when the referees work hard and take the review seriously, so this is hard for committed people to do well.
 Sure, but reviews are not transparent, nor accessible to the public. Why not? Wouldn't it be nice to see what other people think about the article before reading it? Currently there are citations, but that's about it.
 My point is only that these are cultural issues, not technological issues; I agree that it might be useful to see referee reports.
 A public review of article X by reviewer Y would often be quite different than a double-blind review of the same article by the same reviewer.There are some arguments for both approaches, but I believe that the double-blind approach is much better.
 I dont know how it is in other fields, but in physics, at least, reviews are only singly blind. The reviewer knows who the author is. Even then, it is often possible to guess at the referrer based on the comments they make. Blinding the author would be nearly impossible due to the small number of workers on most specific topics. That being said, I'm not sure why journals don't at least try (which should benefit newcomers to an area).
 I don't think any journal reviews attempt to be double-blind. I could be wrong, but I've never heard of it in my field. In smaller fields, even single-blind (the author not knowing the identity of the reviewer) is difficult, the other way around would be impossible.
 Yes, I actually do:) Me: Neuroscience PhD at Columbia w/ some a technical background but not a coder.I'm working on going up against academic publishing right now. I have a YC application that is currently being reviewed and I'm in need of a technical cofounder.Project: Very briefly, I'm working on collecting raw data (positive AND negative), indexing it, and making relationships between datasets. For example, my neuroscience study has relationships to cancer biology, so the data presented to the user would include results from both.Re: Publishing, I'm going to provide raw data to scientists and create a venue for them to "blog" about these datasets. I think science needs to move incrementally (at internet speed) and get away from taking 3 years to produce a study and publishing a big paper of only positive data. Also, I'd like for the "peer review" portion to be more transparent, so that we can avoid the insane bias that goes into peer review.Goal 2: Create "big data" by combining small academic science results into a big ass database. Meta data could be the new preliminary data for academic grants.So yeah, if anyone is interested in playing with this, let me know. klg2142 @t columbia.edu
 Aqui-murdering is a consequence of our financial system. When some big company can get bank money at far less than other companies, let's say 3% just as a hypothetical example, they can buy any business with a 6% cap rate and run it poorly so it only makes a 4% cap and still make a profit. This happens all the time. Meanwhile the entrepreneur cannot get money for anywhere near that and has to actually create real value instead of performing financial arbitrage as these companies with access to the cheap money can.
 There was a time when I would've been on board. But I think that time has passed. I have a wife, a new baby, and a nice day job that allows me to enjoy both.A couple years ago, I spent many nights and weekends working on the academic publishing problem. The effort culminated in a massive hypermedia-style XML schema for distributed and inter-connected publishing, referencing, archiving, etc. There were hundreds of elements just in the common metadata model before I even got around to defining content modules.Then something hit me like a ton of bricks. I think it was seeing backbone.js for the first time. I realized how quickly web technology was moving forward, how easy it was becoming, and, by contrast, how absolutely shitty it was going to be to write mountains of XSLT on top of my huge DTD. Even in my attempt to create something really different, my approach was still totally clouded by the prevailing anti-wisdom of the academic publishing technology community.I realized I was on the wrong path. It was a great thought exercise that contributed immeasurably to my day work, but I had to move on.Happy to share more information if you like, though I'd need to dig the files out of deep storage.
 I am working on something that may be of interest. Drop me a line, my email is in my profile
 I know a guy. Shoot me an email, let me know what tech you know, and I'll chat with him to see if he's interested.
 I don't get it. It was absolutely clear that they were using a propiretory software owned by a for-profit company.There a perfectly viable alternatives, Open Source and free to use e.g. Zotero et al.
 While true, it seemed like a fairly pro-openness company, which not only said the right things but seemed to have a lot of employees genuinely committed to improving the state of academic literature.But it does add another example of why we should be wary of even well-meaning for-profit companies, without some kind of more solid guarantee that they won't sell out in the future. For stuff like this, either a nonprofit foundation, or at least a forkable open-source version of the platform, seem like necessary prerequisites if you want to ensure that Elsevier-and-co can't buy it out. I guess a company 100%-owned by a strong open-culture advocate could be reliable also, but it gets more complex when investors are in the mix.Also a reason I don't trust academia.edu compared to, say, the arXiv.
 The difference of Mendeley is that they had a good PR team, and composed of academic, "people like us". And they were everywhere, and this PR team banged on the note that Mendeley was going to be open and "grassroots" academic, because it was made by academics. Now, we know the real answer.
 Your assumption is that now Mendeley is going to suddenly shed it's sheep's clothing and reveal itself to be a wolf. As a Mendeley employee (and a scientist, not a PR person), you may not believe me or you may think I'm just naive but I think you will have to wait and see.Nothing we've done over the past 4 years should give you reason to worry and there's plenty of reason to believe that Elsevier doesn't want to piss off our community.
 All those employees just turned into evil drones this week because of the acquisiton?
 No, they're leaving: http://enjoythedisruption.com/post/47527556151/my-thoughts-o...Choice quote: "For that reason then I co-founded PeerJ, an Open Access journal, with one aim of never being in the position to take shit ever again from a closed publisher."
 They are not leaving. This one person left, a while ago. Correlation or causation, I can't speak for him.
 Maye this person that left knew something like this would happen. The timing is irrelevant, what is relevant is that the ones thst stay are linked to a publisher that has no morals, no ethics.
 This week? No. One, two, or more years down the road? We shall see.I'm not 100% behind the Mendeley hate right now, but they're against all odds. While everything I've heard from the team so far, including on the prominent HN threads, has been reassuring and positive, it's still just words.People are making predictions about the future right now, and no words will be able to sway public opinion. Only action, and time. It seems Mendeley (or, as of now, Elsevier) are betting on the latter, because there has been no action, only PR.
 The same PR team that is flooding social media with the usual spiel will be given maybe a 6-month 1-year contract and will be gone soon.
 All these employees, including the CEO, are no longer in control anymore; the owner, Elsevier, is in control and is not an impartial 'financial investor' but an 'strategic investor' with a larger stake in the industry than the whole of Mendeley.It means that a week ago CEO could make the same promises and be heard seriously, but the same CEO promises right now are not worth the paper they're not written on.Now at any point in the future all the Mendeley 'openness' promises can be easily broken by Elsevier, so they either know that all the promises they're making now are empty (i.e., lying intentionally) or they don't know that (then they're naive and incompetent as general managers).Promises can be made by those in control. Leaders in public companies can be considered in control. Leaders in privately held companies can be considered in control if their public vision and roadmap is aligned with the owner. But if the owner has a clear interest to change the roadmap - then it would be imprudent to rely on such a roadmap. Elsevier has a reputation of intentionally sabotaging projects (say, gov't initiatives) that should bring openness - if they fool you twice, shame on you.
 No, they turned into useful idiots.
 No, but with gradual attrition due to fundamental disagreements with the new management, I imagine the character of the company will change significantly within the year, if not sooner.
 No, they just became employees of a corporation that use unethical tactics in publishing. You end up guilty by association.
 PR is irrelevant to "open". Either the product is or isn't. Academics should be smart enough is it isn't.
 Academics usually like shiny things, specially free. And Mendeley didn't target the old school ones, they targeted students, post-docs, usually the trend-setters in the academic environment. Professors and Senior Researchers are too busy or don't have time to check these things, and they end up using what other people use in their labs.And for broke, internet saavy students, free stuff with a promise of a new groundbreaking trend in science was enough to lure them.
 Still wondering how academia.edu got approved for an edu domain name. Screams scam to me.
 In the early days there wasn't a formal process for .edu approval. There was a bit of netiquette that educational institutions should register under .edu, nonprofits under .org, network providers under .net, and companies under .com.That started being enforced for .edu in 2001, but previous registrants were grandfathered in. The registrar did manage to evict a bunch of the questionable .edus in 2003, by stepping up enforcement of technical requirements, such as the requirement to have accurate whois information, and to be responsive via the whois-registered email address. But presumably academia.edu survived that purge. I can't actually think of any other prominent for-profit company that still retains an .edu. The registrar also now prohibits transferring them, so you can't buy one even if some others have survived (though maybe you could lease it).
 I have personally integrated Mendeley into my process as a student, despite the fact that I should have known better. Sometimes everyone gets distracted by shiny things, I guess. Shame on me.
 Mendeley is not going to stop working all of a sudden. It's still the same tool, developed by the same people, with the same roadmap and vision ahead.
 The keys to the castle have been turned over to the enemy. I'm going to have to migrate eventually, so might as well start sooner rather than later. This is an incredibly sad event for me. But, like I said, I should have known better. Closed-source software can be taken away and turned toward evil purposes and there's nothing the users can do about it.
 Their vision right now has a remote control with a "reverse" button, held by well known enemies of that vision.
 "We are committing to implementing Mendeley’s existing product development roadmap, and giving the company the space to “let Mendeley be Mendeley.”" - http://elsevierconnect.com/elsevier-welcomes-mendeley/
 I'd be rich if I had a penny for each time such promises were publicly made when acquiring a company and broken within less than 12 months.Even right here on HN there have been many posts about such situations some time after acquisitions; and Elsvier reasonably does have practical motivation to interfere here and there.Such arms-length separations are often published in mergers&acquisitions PR and practically never happen in practice, they all get abused - should we really believe that Elsevier is so exceptionally more etchical than most other companies?They have that "remote" in their hands. They have promised not to use it. Will they?
 And from a company with such a reputation of truthful public statements!
 I really like the way Mendeley handles notes, specifically highlighting / annotating PDFs. Do you know of any alternatives that include this? I was planning on writing my own at some point but it might be a bit ambitious.
 You could also submit a feature request to Zotero:https://forums.zotero.org/7/Or build it yourself if so inclined/able:http://www.zotero.org/support/dev/sample_plugin
 check out quicka (spelled qiqqa) http://www.qiqqa.comI chose it a few months ago over mendeley because it allowed me to search in the PDF annotations, which isn't possible with mendeley. I recall mendeley could search notes added to a PDF file (one text area for the whole file), but not within sticky notes attached to specific pages, so it was impossible to search the annotations I made and also have those annotations appear on the relevant part of the PDF.The other thing I like about qiqqa is that it allows us to have a shared library on our local server, instead of having to send all our data to the cloud.Both are great desktop tools for full text search across many PDF files, even those that need OCR. Before I was using google desktop for this function, and qiqqa is definitely a step up.
 This looks great, however Windows only is a bit of a deal breaker. Definitely going to keep my eye on it though.
 Keep an eye on http://hypothes.is. I think they plan to support private annotations, and handle PDFs through pdf.js. It doesn't have an offline document management component, but it could be used as the annotation component in a larger system.
 I spent some time a few months back researching ways to have electronic PDFs which I could annotate and keep on my tablet. Mendeley was far and away the best. Here's hoping someone else figures this out.
 My own personal favourite, Papers (papersapp.com), was recently taken over by Springer too. So far, so good--the original team is still running it and there's no sign anything bad will come of it, but I'm still wary of the future.
 The Springer-Papers and Elsevier-Mendeley acquisitions are indeed interesting because they've happened at about the same time. It seems that the big publishers want to get a better grip on paper search and/or paper reading habits.
 Of course Springer has one of the most onerous paywalls I've come across. I hadn't heard of the Papers acquisition: I use it on my iPad but only because it sucks less than every other solution I've looked at.
 What do you think can be done to improve it? Can you tell me what your ideal reference/citation software looks like?
 Now I'm going to have to e-mail all the friends I advocated Mendeley to, and tell them to consider switching. Serves me right for not looking more carefully at whose interests Mendeley was serving.:-(
 Honestly? It's a for-profit company, whose interests did you think was serving?
 Yeah. My bad. I had a real need and Mendeley's software (which is awesome, by the way) came to my rescue; issues of who controls it and what they might want from me someday seemed very far away at the time.
 This is how capitalism works. Companies (and individuals) try to maximise their own profits; and (ideally) the most profitable course of action is the one which is the most beneficial to the most people. Altruism has no place in it.And yet, people are continually surprised and disappointed when a company takes a profitable course of action, rather than ignoring profits for altruistic reasons.
 It's not a matter of altruism, it's a matter of reputation. I reasonably guessed that Mendeley would not try to screw scientists in the short run in order to preserve their reputation in the long run, all to benefit their own profit. However, Elsevier (1) does not have much of a good reputation to risk and (2) can also coordinate with its publishing arm to further multiply the benefit of screwing scientists than Mendeley could alone. It might have been possible for me to predict this business move, but that's a very complicated calculation. I'm not unreasonable for failing to have done so. You can argue that it would have been more prudent to never trust any company that might be sold, but then you'd be criticizing my risk calculation and not my confusion about altruism.Likewise, I could be surprised that a fancy restaurant replaced all their silverware with disposable plastic. It would maximize their profits that night, but destroy their reputation and hence long-term profits.
 > yet, people are continually surprised and disappointed when a company takes a profitable course of actionI think this is a fairly recent phenomenon, that's gone hand in hand with the development of the Internet.First, we had companies without business plans (or profits) that peaked in the 90s. That bubble burst, but the reputation of "something for nothing" has lingered.Companies have since found new ways to monetize users (e.g. targeted advertising) in a way that's mostly transparent to the users. This has perpetuated the sense of "something for nothing" associated with online products and services.
 > This is how capitalism works. Companies (and individuals) try to maximise their own profitsPlease don't lecture me about capitalism. I had enough of that when I took a degree in economics.
 Companies are implemented over people. They can be non-evil, it's just that all the incentives are against it.
 There's a slight irony that this news story is being posted on a site which is partially owned by Elsevier.
 We've come a long way when a "revolt" means "users post their frustrations on Twitter".
 A long way indeed, and mostly in a terrible direction. :/
 Well then, Elsevier may have won. 70 mil to destroy a viable threat to its monopoly may be a small price to pay in the grand scheme of things.
 Mendeley was not a direct threat to Elsevier's business. They aren't a publisher. PLoS (and PLoS's model) is more of a direct threat. Fortunately they are a non-profit which I think makes them immune from takeover.
 We're here and ready to not be destroyed. From the looks of it at the office, it's work as usual. By that I mean, building a great tool and resource for researchers. :)
 Everything I've read from folks at Mendeley misses the point of the disgust. Most people are not concerned about Mendeley going away, or about development stopping, or about new features not being added. Of course you're continuing to build the tool, at least the for the foreseeable future. Of course Mendeley will continue to be have a free version, etc. Of course Mendeley will continue to add features.But none of that is because Elsevier has suddenly decided to support open access. It's because buying and developing Mendeley is an affordable way for Elsevier to launder its godawful reputation. All the smiling emoticons in the world don't change that.
 Hah, this was exactly the reason I was hesitating to use Mendeley, although it's got great tools. Creating your paper database in such a system is a huge investment in time, it's hard and very frustrating to move between such systems.AFAIK, the open source tools cannot much the maturity of Mendeley, am I wrong? In this age and time, how hard can it be to clone a service like that?
 It depends on what parts you're using. If you're using Mendeley mainly as a personal reference manager, Zotero is as good as Mendeley or better imo. But it doesn't have a web-based social layer like Mendeley does, for people who like that part.
 I think Mendeley had more advantages over Zotero than the social aspect (which I never used). Mendeley could automatically incorporate your folder of orphan PDFs into your library, automatically fetching the bibliographic info. It had a nice dedicated desktop client for searching your library, correctly bib info, and adding notes and whatnot to papers, which just isn't as nice on a browser.
  > I think Mendeley had more advantages over Zotero than the social aspect > (which I never used). Mendeley could automatically incorporate your > folder of orphan PDFs into your library  So can Zotero.http://www.zotero.org/support/retrieve_pdf_metadata > automatically fetching the bibliographic info.  https://github.com/zotero/translatorshttps://github.com/zotero/translation-server(Those two repositories are the greatest things about Zotero, in my opinion. Holy crap.) > It had a nice dedicated desktop client for searching your library  Zotero standalone seems to be listed here very prominently:
 Thanks for the correction. I never downloaded it because it was described everywhere on the web as a browser extension. The existence of the standalone client is not mentioned on the homepage, where in fact it says "It lives right where you do your work—in the web browser itself."Is the standalone client decent? Is the meta-data retrieval as good as Mendeley?
 > Is the standalone client decent? Is the meta-data retrieval as good as Mendeley?I think the standalone client is actually based on Gecko SDK and possibly xulrunner, so calling it standalone might be a little unfair of me. However, it certainly doesn't require Firefox itself...Zotero retrieves metadata directly from a publisher's site with 100s of javascript plugins. Mendeley told me once that they just do OCR with some super-proprietary system they licensed. But I suspect that Mendeley now uses their servers to centralize millions of pdfs and their metadata, and probably uses that to identify and fingerprint the files in your collection... maybe.Here's to hoping that Elsevier wont revoke your pdfs!
 Why the use of the past tense? Mendeley still has all those features and more. :) Also, the open API we provide allows for building third-party applications like Android apps and such. But I digress. :)(Disclosure: I'm part of the Mendeley team)
 The past tense is presumably because the GP doesn't want to use a tool produced by Elsevier, so as far as they are concerned the tool no longer exists.
 Yup. I was already very hesitant to invest a bunch of time in a tool that could be pulled out from underneath me by a for-profit company, and in fact I never integrated it into my work. With Elsevier owning it, I wouldn't consider risking it.
 You might think a lot of things, but your description of Zotero is completely inaccurate. Zotero isn't a browser-based application, and it can do everything you describe.
 No need to be a dick, anyone reading Zotero's homepage comes away with the message that this is a browser-based application only.There is no mention anywhere of any other way of using it except on the download page.The first time I went there I didn't click on the download button because I didn't want a browser-based app.
 Okay, we've tried to remove the implication that Zotero is browser-based from the website. Let us know if you have a suggestion to make things clearer. (Also, sorry stakats is a dick :)
 That's great news, I'm sure Zotero is getting a traffic bump these days.
 You're new here so pro-tip: More concrete details, less snark, or you're gonna downvoted to oblivion.Instead of just telling someone they're wrong, explain why. How is Zotero not a browser-based application, and how does it do everything OP described?
 Sure! Zotero has been available as a standalone application for several years (and even when it only ran within Firefox in the early days, it was still a local application): http://www.zotero.org/download/Zotero retrieves PDF metadata using a Google Scholar lookup, a method that Mendeley later adopted: http://www.zotero.org/support/retrieve_pdf_metadataThis process can also be applied to a watch folder using the third-party add-on ZotFile (Zotero supports extensions): http://www.columbia.edu/~jpl2136/zotfile.htmlZotero has always allowed all kinds of searching of metadata and content: http://www.zotero.org/support/searchingZotero also includes notes (and these notes can be pulled from PDF annotations using ZotFile): http://www.zotero.org/support/notes
 I liked BibDesk better myself, and some of my non-Mac colleagues had success with JabRef.
 With Google Reader recently announcing the shutdown, and now this, closed-source cloud-based solutions for organizing and processing my data have started looking increasingly unattractive to me. I guess the only safe way to retain all of your data and prevent commercial interests from affecting its organization is to organize it using (preferably) open-source tools on your own computers, and use the cloud only for backing up the raw data / generated databases so they can be recovered later.
 Look at JabRef as a front end to bibtex. I had a bit of a learning curve, but was so frustrated with the Microsoft toolchain that I switched to R/Sweave/LaTeX/bibtex/git and am quite happy. Everything is Open Source and in general community support has been better than commercial support. Since all these are text based, they play well with version control (git). Also makes for a reproducible workflow where an entire analysis and report can be reproduced by a single click on a shell script or command file. The same toolchain works on my Linux, MacOSX, and Windows boxes.
 Zotero is unlikely to go the way of Mendeley: may be worth checking out.
 I've been looking at that and thinking about it lately.shoot me an email if you want to chat more (it's in my profile)
 Ideologically I feel like every tax funded researcher (i.e. the vast majority) has an obligation to make all his work publicly accessible.Change will happen once open access journals get A level status. If there's enough that are sufficiently peer reviewed a simple legislative fix (for state funded/supported education which is the case for most forms of education) would be to treat open access publications preferential when it comes to hireing new academic staff.As someone with the long term vision of massive changes in education towards e-learning I think the way to attack this is to actually couple OA initiatives with sites like coursera, edx etc.How deep are the Buffet/Gates pockets, maybe just buying up a bunch of content and freeing it might be the easiest path.
 Buying up a bunch of content? Gates already did that decades ago: http://en.wikipedia.org/wiki/CorbisThere's no sign of freeing it, though.
 While I am not a researcher and have never used Mendeley et al I do know about Elsevier's reputation.As mentioned in this blog it would seem the wisest thing would be to switch for the moment and keep an eye on mendeley.Who knows, maybe they really will change Elsevier, I doubt it but you never know.After all, given the backlash Elsevier know this is their ONE (long-haul) chance to redeem themselves. Screw this up and they are totally beyond hope (For those who might not think they already are)
 Ok, then I'll use Papers!Papers purchased by Sinauer in early 2013... Endnote?part of Thompson-ReutersZotero?free and open, backed by a major non-profit organization
 Taking inspiration from Star Trek, a new impact factor could be invented to teleport the reputation of a known publication to an alternate publication based on the editorial board. If the board of mathematics reviewers agree to move their effort to another platform, then it follows that the reputation follows the people, not the name of the publication.
 mendeley has always been closed source for-profit. They may have gotten a new owner but it isn't like they were ever doing it for altruistic reasons.Hopefully this will be good news for zotero which is open source.And hopefully it will be really bad news for endnote which is one of the worst commercial programs I've ever tried to use.
 It could be that Elsevier is pivoting into an open access model through its other efforts and buying up Mendeley. I won't hold my breath, though. The model, while evolving, could just morph into something else that sucks.It's a real bummer. There's so much good stuff locked up in these publishing houses.
 If Elsivier wants to change its business model, it will need to do it in a way that doesn't completely cannibalize its sales. Adding open research companies to its umbrella would be a way to do that.However, more likely, it wants to be able to say, "See, we are committed to being open", and continue with its primarily closed practices.
 Reminds me of macrobreweries buying microbreweries. The big guys (who make terrible beer) come in and cut costs anywhere they can to increase margins. This includes using cheaper ingredients which decreases the quality of the beer.The same will happen here.
 I am quite disappointed by this - the next target which hasn't been really picked up yet is Academia.edu though it's purpose is slightly different than Mendeley.
 How to export, delete and move your Mendeley account: http://duncan.hull.name/2013/01/18/mendelete/
 revolt, takeover. reminds me of the mutiny post https://news.ycombinator.com/item?id=5525173