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Publicly Funded Research Should Be Publicly Available

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Re: Publicly Funded Research Should Be Publicly Available

#71

Post by dalke »

liviu- wrote: post #38
ashitlerferad wrote: post #32

Earlier quoted context omitted.

Bioinformatics is close.

Could you please elaborate for those unfamiliar with their community?

It's tricky to pinpoint exactly when modern "bioinformatics" started. Some notable times are 1979 when the Los Alamos Sequence Database started, 1982 when that became GenBank, and certainly by 1990 when the Human Genome Project started.

GenBank is "an open access, annotated collection of all publicly available nucleotide sequences and their protein translations" (https://en.wikipedia.org/wiki/GenBank ). Most journals now require that sequences be entered into GenBank before publication.

I'll add a few historical observations. The early work at Los Alamos was on Sun machines running Sybase (1987, according to https://en.wikipedia.org/wiki/Sybase ). These are serious Unix fans, who quickly took to perl when it came out. I think some of the support for SybPerl came from bioinformatics; the SybPerl, OraPerl, and other *Perl systems helped create the extension system for perl5. (I am not able to verify that, though the author of SybPerl, Michael Peppler, consulted in the mid-1990s for "Research Genetics" http://www.peppler.org/resume.html .)

Unix people in the early 1990s were serious perl fans. The most popular perl4 library for CGI programming was cgi-lib.pl, by Steven Brenner, a computational biologist/bioinformatics researcher. It was replaced in perl5 by CGI.pm, by Lincoln Stein, another bioinformatics researcher.

This gives a hint that bioinformatics has not only a close connection to the technologies needed for the first dot-com era, but also that the field itself tends towards open resources.

("Tends towards" != "always". See point #3 of https://liorpachter.wordpress.com/2015/07/10/the-myths-of-bi... .)

Re: Publicly Funded Research Should Be Publicly Available

#73

Post by ThomPete »

AnthonyMouse wrote: post #70
ThomPete wrote: post #31

Earlier quoted context omitted.

The IP laws are based on greed/capitalism/profit. No one besides the big corps want this just ask Mickey Mouse.

> The IP laws are based on greed/capitalism/profit. No one besides the big corps want this just ask Mickey Mouse. I believe that's the point. "Big corporations lobbying government for rent-seeking legislation" isn't capitalism , it's corruption .

Lobbyism is legal so no.

Re: Publicly Funded Research Should Be Publicly Available

#74

Post by coolnow »

chias wrote: post #68
NotOscarWilde wrote: post #42

Earlier quoted context omitted.

There are a lot of steps a university can take, even without a risk of getting sued: * Cut 25% of your journal subscriptions to the worst offenders and keep cutting every year with some smaller percent. * Publicly recommend to all scientific boards that the hiring process should judge applicants by the merit of their publications, not by their journal's ranking. * Promote open-access submissions by your researchers:…

> Promote open-access submissions by your researchers: a small monetary bonus would probably suffice. Simply paying for open-access submissions would probably suffice. I'm a scientific researcher myself, but most of my work gets published non-open-access: publishing open-access costs ~$500, and as a grad student as much as I think open-access should be the de-facto standard, I'm not in a position to be paying that my…

Is it possible for you to release a PDF/LaTeX source via other means?

Re: Publicly Funded Research Should Be Publicly Available

#75

Post by atom-morgan »

ThomPete wrote: post #47
atom-morgan wrote: post #39

Earlier quoted context omitted.

True. Point is I think the government should be the focus here, not the players who take advantage of the rules they create.

I think both should be at the focus as they are often two pieces of the same part.

Think of segregation/separate but equal. Nothing can really stop someone from choosing not to associate with another person because of their race or gender. And that's generally okay. But the second it becomes law of the land, through government, it's a problem. IP is no different.

Re: Publicly Funded Research Should Be Publicly Available

#76

Post by dubbel »

coolnow wrote: post #74
chias wrote: post #68

Earlier quoted context omitted.

> Promote open-access submissions by your researchers: a small monetary bonus would probably suffice. Simply paying for open-access submissions would probably suffice. I'm a scientific researcher myself, but most of my work gets published non-open-access: publishing open-access costs ~$500, and as a grad student as much as I think open-access should be the de-facto standard, I'm not in a position to be paying that my…

Is it possible for you to release a PDF/LaTeX source via other means?

Then you are running into problems with the commercial journals, and you need their peer-review.

Re: Publicly Funded Research Should Be Publicly Available

#77

Post by AnthonyMouse »

ThomPete wrote: post #73
AnthonyMouse wrote: post #70

Earlier quoted context omitted.

> The IP laws are based on greed/capitalism/profit. No one besides the big corps want this just ask Mickey Mouse. I believe that's the point. "Big corporations lobbying government for rent-seeking legislation" isn't capitalism , it's corruption .

Lobbyism is legal so no.

Corrupt doesn't mean illegal, it means dishonest, disloyal, lacking in integrity, etc.

Re: Publicly Funded Research Should Be Publicly Available

#78

Post by acomjean »

NIH has a Public Access Policy already[1], so anything NIH funded is public. Lots of stuff is already available (https://www.ncbi.nlm.nih.gov). Other agencies have public data to AHRQ, CDC, FDA, HHMI, NIST, VA (see link for acronym clarification)[2]

This FASTR proposal shouldn't be a big deal, since a lot of funding sources already have that requirement. I'm not sure why some funding gets not to be public.

(part of my job is uploading data to pubchem)

[1]http://publicaccess.nih.gov/ [2]http://www.ncbi.nlm.nih.gov/pmc/about/public-access/

Re: Publicly Funded Research Should Be Publicly Available

#79

Post by infogulch »

chias wrote: post #68
NotOscarWilde wrote: post #42

Earlier quoted context omitted.

There are a lot of steps a university can take, even without a risk of getting sued: * Cut 25% of your journal subscriptions to the worst offenders and keep cutting every year with some smaller percent. * Publicly recommend to all scientific boards that the hiring process should judge applicants by the merit of their publications, not by their journal's ranking. * Promote open-access submissions by your researchers:…

> Promote open-access submissions by your researchers: a small monetary bonus would probably suffice. Simply paying for open-access submissions would probably suffice. I'm a scientific researcher myself, but most of my work gets published non-open-access: publishing open-access costs ~$500, and as a grad student as much as I think open-access should be the de-facto standard, I'm not in a position to be paying that my…

How much is the department paying for those journal subscriptions?

Just redirect that cut journal subscription money that GP suggested into the open-access submission fee.

Re: Publicly Funded Research Should Be Publicly Available

#80

Post by amelius »

ThePhysicist wrote: post #11

Personally, I think civil disobedience is more effective at changing the status quo than e-mail campaigns, although they can help to increase awareness. What I would really like to see is a big institution / university take a stand and build something like Scihub to provide free and unlimited access to all of their own papers, even those that are stuck behind a paywall for "historic" reasons. It would be interesting…

This sounds a lot like the civil disobedience of Google when they started Google Books.
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