[Denovoassembler-devel] Ray Browser

[Sébastien Boisvert]

Hi !

[I CC'ed denovoassembler-devel as this is a really interesting question]

I am not a legal expert, but read on !

Hey Sébastien,

I only work on open source software projects.

Open-source or closed, someone owns the license to the code.

I think you mean the copyright over the code, not its license.


I am not an employee of my university -- I am a doctoral student. I have no employer-employee
relationship with my university for what I do in my doctoral projects.
I work on whatever I want, which happens to be open stuff in genomics.

Back in 2010, my director wanted Ray to be a proprietary software,
but I convinced him otherwise by describing the pros of doing things this way.
And he's quite happy with that decision now.

Ray and Ray Cloud Browser are licensed under the GPLv3. Ray Platform is licensed under the
LGPLv3. I own the copyright on most source code files since I wrote them, and because I am not an employee
and I have never signed any contracts (or other legal documents) for these projects.

Anyway, copyright does not mean anything
for a GPLv3-licensed program because the point is to not limit copies of the programs so that people
hopefully build on top of that.

To decide what license to release the source code (or to change the license), all copyright holders must
agree. For closed-source programs, the license is not on the source code
(since it's confidential), it's usually a end user license agreement (EULA) that is renewed
with contracts (there can be a EULA over a product based on open source software too, see Red Hat).

For instance, Applied Maths NV. ships Ray in their BioNumerics product

=> http://www.applied-maths.com/news/new-de-novo-assembler-next-generation-sequencing-data-bionumerics


More and more, proprietary software are no longer licensed as a goods (which is bad for the consumers).
Instead, you get a license to use the software (as a service) over a period. If you played Diablo III and got a sword in the game,
you can actually (probably) send a mail to Blizzard and ask them for your license to use the sword.
For each Diablo III item, the player gets a exclusive-from-Blizzard license to use it over the lifetime of his/her character.


I think there is a clear distinction between:

* license for using a software vs. license for distributing source code;

=> GPLv3 covers both of these. GPLv3 tells you that you have the 4 liberties and that you can use the software for whatever use.

* ownership (intellectual property) vs. copyright

=> ownership is usually on ideas (patents), which is ridiculous by definition (see Apple v. Samsung) or brands
(which make sense because a brand is for a product, not for an idea).

=> I think that in the GPLv3 (warning, I am not a legal expert), there is a clause that says that patents can not be
added after releases as open source releases are prior art. Regardless, Everything novel in Ray is not patentable because there's is public
prior art: Ray source code files and scientific papers describing methods.
Furthermore, this prior art is easily demonstrated with git source code logs and publications.


-Séb

That is the
part I was asking about.
Best,
Manoj

[Sébastien Boisvert]

Hi Sébastien,
Thank you for the detailed response. Yes, I meant 'copyright' in my
original question. In US, graduate students and post-docs are usually
employees of the institutions, and sign various legal contracts giving
away their patent/copy rights. As a result, someone interested in
licensing their work needs to deal with both the inventor and the
university. The second part can get very bureaucratic, and that is why I
asked.

Anyway, copyright does not mean anything for a GPLv3-licensed program
because the point is to not limit copies of the programs so that people
hopefully build on top of that.

That is not true. Being the copyright owner allows you to change mind on a
later date, or issue different license for 'preferred clients'. If your
brother asks for a proprietary copy of your GPLv3-licensed Ray code from
you, you can release it to him, because you are the copyright owner. I
cannot create a proprietary copy of Ray for my brother :)

What I meant here is that even if all the copyright holders decide at some point that
the product should now be proprietary, previous releases keep their respective license
arrangements.

And it's all or nothing -- you can not release SoftwareX v1.2.3 as proprietary software
and as GPLv3-licensed software because that would infringe the GPLv3 license, and it does
not make sense.

I agree about what you said on patents. Whole patent thing is legacy of
feudal society of Europe, where the large guilds could buy monopoly rights
from the kings.

Yes. I believe in brands, but patents are just silly.

You probably know that US patent law is changing next month from 'first to
invent' to 'first to file'.
http://www.preti.com/major-patent-law-changes-2013
http://www.forbes.com/sites/robertjordan/2012/11/13/the-new-patent-law-end-of-entrepreneurship/

Correct me if I am wrong, but this is a bad thing for everyone except patent trolls, right ?

In my opinion, the competition for market share should occur on the "battlefield" with
customers, not in patent offices where there is no product and no customer.

Competition is good for customers, it increases the quality of products and it lowers the
prices of goods.

Best,
Manoj

Hi !
[I CC'ed denovoassembler-devel as this is a really interesting question]
I am not a legal expert, but read on !

Hey Sébastien,

I only work on open source software projects.

Open-source or closed, someone owns the license to the code.

I think you mean the copyright over the code, not its license.
I am not an employee of my university -- I am a doctoral student. I have
no employer-employee
relationship with my university for what I do in my doctoral projects.
I work on whatever I want, which happens to be open stuff in genomics.
Back in 2010, my director wanted Ray to be a proprietary software,
but I convinced him otherwise by describing the pros of doing things this way.
And he's quite happy with that decision now.
Ray and Ray Cloud Browser are licensed under the GPLv3. Ray Platform is
licensed under the
LGPLv3. I own the copyright on most source code files since I wrote them,
and because I am not an employee
and I have never signed any contracts (or other legal documents) for these projects.
Anyway, copyright does not mean anything
for a GPLv3-licensed program because the point is to not limit copies of
the programs so that people
hopefully build on top of that.
To decide what license to release the source code (or to change the
license), all copyright holders must
agree. For closed-source programs, the license is not on the source code
(since it's confidential), it's usually a end user license agreement
(EULA) that is renewed
with contracts (there can be a EULA over a product based on open source
software too, see Red Hat).
For instance, Applied Maths NV. ships Ray in their BioNumerics product
=>
http://www.applied-maths.com/news/new-de-novo-assembler-next-generation-sequencing-data-bionumerics
More and more, proprietary software are no longer licensed as a goods
(which is bad for the consumers).
Instead, you get a license to use the software (as a service) over a
period. If you played Diablo III and got a sword in the game,
you can actually (probably) send a mail to Blizzard and ask them for your
license to use the sword.
For each Diablo III item, the player gets a exclusive-from-Blizzard
license to use it over the lifetime of his/her character.
* license for using a software vs. license for distributing source code;
=> GPLv3 covers both of these. GPLv3 tells you that you have the 4
liberties and that you can use the software for whatever use.
* ownership (intellectual property) vs. copyright
=> ownership is usually on ideas (patents), which is ridiculous by
definition (see Apple v. Samsung) or brands
(which make sense because a brand is for a product, not for an idea).
=> I think that in the GPLv3 (warning, I am not a legal expert),
there is a clause that says that patents can not be
added after releases as open source releases are prior art.
Regardless, Everything novel in Ray is not patentable because
there's is public
prior art: Ray source code files and scientific papers describing methods.
Furthermore, this prior art is easily demonstrated with git source
code logs and publications.
-Séb

That is the
part I was asking about.
Best,
Manoj

[s***@homolog.us]

Post by Sébastien Boisvert
And it's all or nothing -- you can not release SoftwareX v1.2.3 as proprietary software
and as GPLv3-licensed software because that would infringe the GPLv3
license, and it does not make sense.

Yes you can, and that was the business model for MySQL. MySQL distributed
their database program for free under GPL license, and that resulted in
wide deployment of their program. However, GPL meant anyone doing
derivative work had to release all their own code as well, and that was
not acceptable for many software companies. However, those companies could
buy proprietary licenses for open source MySQL so that they could bundle
their own proprietary programs.

http://stackoverflow.com/questions/620696/mysql-licensing-and-gpl


I used to think like you before, but was corrected by two readers in our
blog. Please check here -

http://www.homolog.us/blogs/2012/10/19/software-licenses-in-bioinformatics-programs-and-their-legal-implications/

http://www.homolog.us/blogs/2012/10/26/more-on-gpl-licensing-of-bioinformatics-programs/

[Sébastien Boisvert]

Post by s***@homolog.us

Post by Sébastien Boisvert
And it's all or nothing -- you can not release SoftwareX v1.2.3 as proprietary software
and as GPLv3-licensed software because that would infringe the GPLv3
license, and it does not make sense.

Yes you can, and that was the business model for MySQL. MySQL distributed
their database program for free under GPL license, and that resulted in
wide deployment of their program. However, GPL meant anyone doing
derivative work had to release all their own code as well, and that was
not acceptable for many software companies. However, those companies could
buy proprietary licenses for open source MySQL so that they could bundle
their own proprietary programs.
http://stackoverflow.com/questions/620696/mysql-licensing-and-gpl
I used to think like you before, but was corrected by two readers in our
blog. Please check here -
http://www.homolog.us/blogs/2012/10/19/software-licenses-in-bioinformatics-programs-and-their-legal-implications/
http://www.homolog.us/blogs/2012/10/26/more-on-gpl-licensing-of-bioinformatics-programs/

Wow !

I have read these two links with great interest.

Thank you.

[s***@homolog.us]

Hi Sébastien,

Thank you for the detailed response. Yes, I meant 'copyright' in my
original question. In US, graduate students and post-docs are usually
employees of the institutions, and sign various legal contracts giving
away their patent/copy rights. As a result, someone interested in
licensing their work needs to deal with both the inventor and the
university. The second part can get very bureaucratic, and that is why I
asked.

Anyway, copyright does not mean anything for a GPLv3-licensed program
because the point is to not limit copies of the programs so that people
hopefully build on top of that.

That is not true. Being the copyright owner allows you to change mind on a
later date, or issue different license for 'preferred clients'. If your
brother asks for a proprietary copy of your GPLv3-licensed Ray code from
you, you can release it to him, because you are the copyright owner. I
cannot create a proprietary copy of Ray for my brother :)

I agree about what you said on patents. Whole patent thing is legacy of
feudal society of Europe, where the large guilds could buy monopoly rights
from the kings.

You probably know that US patent law is changing next month from 'first to
invent' to 'first to file'.

http://www.preti.com/major-patent-law-changes-2013
http://www.forbes.com/sites/robertjordan/2012/11/13/the-new-patent-law-end-of-entrepreneurship/


Best,
Manoj

Hi !
[I CC'ed denovoassembler-devel as this is a really interesting question]
I am not a legal expert, but read on !

Hey Sébastien,

I only work on open source software projects.

Open-source or closed, someone owns the license to the code.

I think you mean the copyright over the code, not its license.
I am not an employee of my university -- I am a doctoral student. I have
no employer-employee
relationship with my university for what I do in my doctoral projects.
I work on whatever I want, which happens to be open stuff in genomics.
Back in 2010, my director wanted Ray to be a proprietary software,
but I convinced him otherwise by describing the pros of doing things this way.
And he's quite happy with that decision now.
Ray and Ray Cloud Browser are licensed under the GPLv3. Ray Platform is licensed under the
LGPLv3. I own the copyright on most source code files since I wrote them,
and because I am not an employee
and I have never signed any contracts (or other legal documents) for these projects.
Anyway, copyright does not mean anything
for a GPLv3-licensed program because the point is to not limit copies of
the programs so that people
hopefully build on top of that.
To decide what license to release the source code (or to change the
license), all copyright holders must
agree. For closed-source programs, the license is not on the source code
(since it's confidential), it's usually a end user license agreement (EULA) that is renewed
with contracts (there can be a EULA over a product based on open source
software too, see Red Hat).
For instance, Applied Maths NV. ships Ray in their BioNumerics product
=>
http://www.applied-maths.com/news/new-de-novo-assembler-next-generation-sequencing-data-bionumerics
More and more, proprietary software are no longer licensed as a goods
(which is bad for the consumers).
Instead, you get a license to use the software (as a service) over a
period. If you played Diablo III and got a sword in the game,
you can actually (probably) send a mail to Blizzard and ask them for your
license to use the sword.
For each Diablo III item, the player gets a exclusive-from-Blizzard
license to use it over the lifetime of his/her character.
* license for using a software vs. license for distributing source code;
=> GPLv3 covers both of these. GPLv3 tells you that you have the 4
liberties and that you can use the software for whatever use.
* ownership (intellectual property) vs. copyright
=> ownership is usually on ideas (patents), which is ridiculous by
definition (see Apple v. Samsung) or brands
(which make sense because a brand is for a product, not for an idea).
=> I think that in the GPLv3 (warning, I am not a legal expert),
there is a clause that says that patents can not be
added after releases as open source releases are prior art.
Regardless, Everything novel in Ray is not patentable because
there's is public
prior art: Ray source code files and scientific papers describing methods.
Furthermore, this prior art is easily demonstrated with git source
code logs and publications.
-Séb

That is the
part I was asking about.
Best,
Manoj