From owner-chemistry- at -ccl.net Wed Oct 19 21:25:00 2011 From: "David A Mannock dmannock*_*ualberta.ca" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45708-111019183934-804-I0n5Hm8VsIH6pEEkWXOe1A\a/server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=001485f44bf0c5803604afae82d4 Date: Wed, 19 Oct 2011 16:39:19 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock]|[ualberta.ca] --001485f44bf0c5803604afae82d4 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Andy, you have made many good points here. I wonder if the solution, given that many academics have access to online resources through their universit= y libraries, would be to allow access to institutions with licences to commercialized code and to those with their own local licence. No licence = =3D no access. Just an idea. It would also exclude the great unwashed from the equation, although it would not prevent piracy. Dave On Wed, Oct 19, 2011 at 3:38 AM, Andrew Dalke dalke a dalkescientific.com < owner-chemistry~~ccl.net> wrote: > > Sent to CCL by: Andrew Dalke [dalke^^^dalkescientific.com] > On Oct 18, 2011, at 4:17 PM, Adri=E0 Cereto Massagu=E9 adrian.cereto,+, > gmail.com wrote: > > I don't think the manifesto is at odds with FSF. GPL'd software can be > sold at any price, but its source code must be available for those who ow= n > the software at no further cost. And someone who has bought some GPL > software is allowed to redistribute it for free, so researchers using it = for > a paper would be able to provide the software to reviewers and readers of > the paper at no cost. > > Abstract: How much can the paper authors ask for access to the > source code? How much can the curators charge? What should the > curator do if the curated software contains a license violation? > > > If I write a paper which depends on software for its analysis, > and others should have access to the software as part of effective > peer review, then how much can I charge others to get access to > the software? US $1 billion? > > The FSF says I can charge as much as you want, and that freedom > is one of the core freedoms of free software. > > The philosophy that others need access to my source code to > provide good peer review has the implicit assumption that I > will provide the software at a non-prohibitive cost. > > There is clearly a tension between these two viewpoints. This > manifesto says nothing of what that cost might be, nor even > that it might be an issue. > > > What should be the cost to get access to source code from the > author, or from the curator? Does the curator get no-cost access > to it as a condition of publication? Doesn't any limit on cost > curtail what the FSF says is my freedom to charge as much as > I want? > > Remember, the FSF encourages software freedom. I argue that > scientific communication has overlapping but different goals. > Science communications needs to have a low cost so that many > people can get access to it. The FSF is only concerned about > what happens *after* someone gets access to software. > > > This is of course similar to (most) scientific papers. There > the author gives the curator the right to redistribute the paper > without paying royalties, and the curator can charge effectively > any price for it. Most paper publishers want to maximize revenue, > and therefore set high but not prohibitive prices. The software > author may have other concerns. > > > Interestingly, the software curator takes on a more difficult challenge > than a paper curator. The authors of a paper (with a few exceptions > usually well-covered by fair use exceptions) are the only copyright > holders of a paper. More often though, the accompanying software has > many more copyright holders. That can lead to problems. > > Consider the CDK chemistry toolkit. The package contains many > copyright holders, including those from third-party libraries > which it incorporates. A few years ago the CDK was in minor > violation of the LGPL requirement of some of those libraries. > (It omitted the credit required by those licenses.) This was > quickly fixed once pointed out. I can easily imagine cases > where it can't be easily fixed. > > The curator takes on the risk that someone else, who is a > copyright holder to the software in question but not a paper > author, may challenge the right of the curator to distribute > the software. How does the curator resolve the violation, > especially if the original author doesn't want to be involved? > Does the curator remove the software in question? > > If so, and if you insist that the software must be available in > order to do correct peer review, then should the corresponding paper > also be withdrawn? > > As I said before, these are solvable. I bring them up because > I encourage people to distribute their source code along with > the paper, and to be aware that it's not a simple, clear issue. > > > Andrew > dalke:+:dalkescientific.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001485f44bf0c5803604afae82d4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Andy, you have made many good points here. I wonder if the solution, given = that many academics have access to online resources through their universit= y libraries, would be to allow access to institutions with licences to comm= ercialized code and to those with their own local licence. No licence =3D n= o access. Just an idea. It would also exclude the great unwashed from the e= quation, although it would not prevent piracy. Dave

On Wed, Oct 19, 2011 at 3:38 AM, Andrew Dalk= e dalke a dalkescientific.com <owner-chemis= try~~ccl.net> wrote:

Sent to CCL by: Andrew Dalke [dalke^^^dalkescientific.com]
On Oct 18, 2011, at 4:17 PM, Adri=E0 Cereto Massagu=E9 adrian.cereto,+,gmail.com wrote:
> I don't think the manifesto is at odds with FSF. GPL'd softwar= e can be sold at any price, but its source code must be available for those= who own the software at no further cost. And someone who has bought some G= PL software is allowed to redistribute it for free, so researchers using it= for a paper would be able to provide the software to reviewers and readers= of the paper at no cost.

Abstract: How much can the paper authors ask for access to the
source code? How much can the curators charge? What should the
curator do if the curated software contains a license violation?


If I write a paper which depends on software for its analysis,
and others should have access to the software as part of effective
peer review, then how much can I charge others to get access to
the software? US $1 billion?

The FSF says I can charge as much as you want, and that freedom
is one of the core freedoms of free software.

The philosophy that others need access to my source code to
provide good peer review has the implicit assumption that I
will provide the software at a non-prohibitive cost.

There is clearly a tension between these two viewpoints. This
manifesto says nothing of what that cost might be, nor even
that it might be an issue.


What should be the cost to get access to source code from the
author, or from the curator? Does the curator get no-cost access
to it as a condition of publication? Doesn't any limit on cost
curtail what the FSF says is my freedom to charge as much as
I want?

Remember, the FSF encourages software freedom. I argue that
scientific communication has overlapping but different goals.
Science communications needs to have a low cost so that many
people can get access to it. The FSF is only concerned about
what happens *after* someone gets access to software.


This is of course similar to (most) scientific papers. There
the author gives the curator the right to redistribute the paper
without paying royalties, and the curator can charge effectively
any price for it. Most paper publishers want to maximize revenue,
and therefore set high but not prohibitive prices. The software
author may have other concerns.


Interestingly, the software curator takes on a more difficult challenge
than a paper curator. The authors of a paper (with a few exceptions
usually well-covered by fair use exceptions) are the only copyright
holders of a paper. More often though, the accompanying software has
many more copyright holders. That can lead to problems.

Consider the CDK chemistry toolkit. The package contains many
copyright holders, including those from third-party libraries
which it incorporates. A few years ago the CDK was in minor
violation of the LGPL requirement of some of those libraries.
(It omitted the credit required by those licenses.) This was
quickly fixed once pointed out. I can easily imagine cases
where it can't be easily fixed.

The curator takes on the risk that someone else, who is a
copyright holder to the software in question but not a paper
author, may challenge the right of the curator to distribute
the software. How does the curator resolve the violation,
especially if the original author doesn't want to be involved?
Does the curator remove the software in question?

If so, and if you insist that the software must be available in
order to do correct peer review, then should the corresponding paper
also be withdrawn?

As I said before, these are solvable. I bring them up because
I encourage people to distribute their source code along with
the paper, and to be aware that it's not a simple, clear issue.


=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Andrew
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0dalke:+:dalkescientific.com



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