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Mendeley users revolt against Elsevier takeover

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Re: Mendeley users revolt against Elsevier takeover

#61

Post by snowwindwaves »

hemmer wrote: post #49
1337biz wrote: post #4

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.

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.

check out quicka (spelled qiqqa) http://www.qiqqa.com

I 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.

Re: Mendeley users revolt against Elsevier takeover

#62

Post by bmalee »

spindritf wrote: post #47
onemorepassword wrote: post #43

Earlier quoted context omitted.

an organization dedicated, not to maximize profits for shareholders, but to keep power over scientific research in people’s hands That'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.…

> 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 r…

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).

Re: Mendeley users revolt against Elsevier takeover

#63

Post by pms »

Evbn wrote: post #38
pms wrote: post #23

Earlier quoted context omitted.

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 review…

Arxiv and marxiv are already working on this. Arxiv even has a paid fellowship, but it is postdoc wages, not professional wages.

Sounds really good. Could you link me to some material about this?

Re: Mendeley users revolt against Elsevier takeover

#64

Post by Radim »

hack_edu wrote: post #57
pseut wrote: post #40

Earlier quoted context omitted.

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 m…

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…

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.

Re: Mendeley users revolt against Elsevier takeover

#65

Post by omnisci »

Thrymr wrote: post #56
scarmig wrote: post #51

Earlier quoted context omitted.

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…

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 jour…

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.

Re: Mendeley users revolt against Elsevier takeover

#66

Post by drewfrank »

hemmer wrote: post #49
1337biz wrote: post #4

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.

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.

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.

Re: Mendeley users revolt against Elsevier takeover

#67

Post by tomrod »

simonster wrote: post #52
tomrod wrote: post #44

Earlier quoted context omitted.

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.

Re: Mendeley users revolt against Elsevier takeover

#68

Post by simonster »

Thrymr wrote: post #56
scarmig wrote: post #51

Earlier quoted context omitted.

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…

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 jour…

> 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).

Re: Mendeley users revolt against Elsevier takeover

#69

Post by mjn »

Evbn wrote: post #41
mjn wrote: post #9

Earlier quoted context omitted.

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 nonprofi…

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).

Re: Mendeley users revolt against Elsevier takeover

#70

Post by pseut »

omnisci wrote: post #48
pseut wrote: post #40

Earlier quoted context omitted.

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 m…

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…

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.

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