[Vp-integration-subgroup] "Models are not consistently licensed"

Tue May 25 05:39:02 PDT 2021

Ok William,

You really want to go into details, so let us do so. - and I will try to be
brief, because it is an endless topic and I can really go on for a long
time. Although brief is relative.

You write that:
"The claim that we can’t make software out of pieces with different
licenses is demonstrably false."
This is not entirely false, you can indeed combine different pieces in some
conditions, yet your code can become so messy and problematic to transport
that many times you may be better not reusing some piece of code. And in
any case, you have multiple restrictions and many times cannot distribute
the code together.

And abandoned code is really a problem, this is why public domain licenses
started appearing in the last decade and copyleft licenses are not used as
much as they used to - open source was pretty good idea at a time a lot of
code was proprietary, yet the problems of copyleft and code that needed
relicensing started appearing and there was a need for a new solution. It
took about a generation for public domain licenses to appear - and we are
just starting to experience it.

You write:
"The claim that we can’t use software abandoned by the original authors is
also false."
The issue is that you are confined to a specific license that may not be
compatible with what you want to achieve and if you integrate a library
into your code and build upon it for a long time, this becomes a
technological debt you have to carry. The problem becomes much harsher when
you try to do something that interfaces with the commercial world that
imposes requirements on licenses - if you have abandoned code you
integrated - you may be stuck since you cannot change the license. This is
also true if code was not abandoned and just has many collaborators - you
need to trace them all and ask them all to agree to a different license -
the more contributors you have , the more problematic it is - this
eventually can make some code practically unusable in some circumstances.
And in situations like this COVID pandemic where you need to act fast to
achieve results and some licensing problem appears - believe me, it is not
an easy situation when there is time pressure. If you use a public domain
license - all this disappears and you can innovate quickly. Also a lot of
the bureaucracy disappears - making life so much easier.

As for patents, those exist and will be used by commercial and scientific
entities alike - Many university faculty members hold patents - and
Universities sometimes have departments that support and encourage the
creation of patents - so those will exist as long as law supports it. In
fact, if you look at NIH policy, you will find out that it allows patents
and assigns intellectual property rights arising from grants to the
awardees. There were several attempts at making research products free and
accessible by the public in the US, yet those did not catch on so far. I
can write about those in a different email - yet I am trying to stay on
point here. So like it or not, people will restrict what you can do. And
even an open source license does not protect you from an orthogonal legal
restriction. However, licenses like CC0 at least inform you about it and
remove at least one restriction - which is more than many other licenses
do.

And as for attribution - nothing says you cannot attribute the work when
using CC0 - in fact CC0 mentions the entity releasing the code to the
public - it is just that you are not demanded to do so. You can always give
credit - you are just not required - so scientific practice is not
disrupted by "public domain" licenses - it is just made easier. Also, you
can release the same work under multiple licenses - one that demands
attribution and one that waives copyright restrictions and let the user
choose which one they wish to propagate. So if you think about it, once you
can release it to the public domain, any other license is just a
restriction on the party trying to reuse your work regardless of how
liberal you think the license is.

And you mention BSD/MIT licenses - remember, those are still forms of
protection of intellectual property - copyright based. Regardless of how
liberal you describe them to be, you are still tied to the original
contributors if you need anything changed in the license due to some
incompatibility which leads us back to the original issue of license
compatibility.

Also, when a license is copyright based it depends on who the registered
owner is and as you may have seen in our discussion on this mailing list,
different institutions have different policies on ownership. So it becomes
messy again - there is really no uniformity - it is all situational and
based on interests of the owners.

And you mention OSI - it is only one organization that catalogues open
source licenses. There are also Creative Commons,  Free Software
Foundation,  and the Open Knowledge Foundation. And they have different
perspectives and I must add that OSI is behind in adopting the new
generation of public domain licenses, so perhaps it is better to choose
another entity like Creative Commons for licenses. In fact, we both know of
one COVID modeling platform that is released now under Creative Commons
license rather than the traditional licenses.

I agree with you that releasing a model/code without a license is
problematic - it is actually a strong copyright restriction that equals
"all rights reserved". So this is highly non recommended unless you really
want to restrict.

The reason this discussion is taking place is because we have a section
about it in the paper and we do mention public domain licenses.

In fact Biomodels, the repository where many biological models are stored,
made the correct choice of license and stores models under CC0 - this means
that those models can be reused much easier.

I don't know what led to this decision by BioModels - perhaps Sheriff can
tell us the story, yet I believe their decision was smart and correct.
There are currently over 1,000 curated models in that repository and
hopefully this number will grow quickly so we will have a large public
repository that allows model reuse with an easy to use license interface.

Think about it long term, if you really want modeling technologies to be
widely adopted, you need to make them very accessible and if you want to
integrate them, you want to remove as much bureaucracy as possible. Think
about a future where hundreds of those models will have to be automatically
merged together in ensembles by machine in attempts to explain observed
biological phenomena. We are still far from that point, yet if we resolve
the problems we listed in the paper we wrote together we will be closer to
such a future solution. And fortunately BioModels resolved our need to
worry about license compatibility issues.

I thank you for taking the time to look at my video and the discussion, and
I hope that this response explains well the need to remove licensing
restrictions from integrating models.

            Jacob

On Tue, May 25, 2021 at 5:18 AM William Waites <wwaites at ieee.org> wrote:

> Dear Jacob,
>
> I did watch your video and understand what you are saying. I’m also pretty
> well-informed about licenses and patents as they relate to software and
> data having been engaged with that topic in different countries (i.e.
> different legal contexts) since the mid-1990s.
>
> There are several problems with your analysis.
>
> 1. It is perfectly well possible to compose together software with
> different licenses. We do this all the time, and very successfully. We
> would not have Linux distributions if this were not possible, and most of
> the large programs written in Python or Java or whatever with a ton of
> libraries that we use for scientific computing would not exist. Different
> communities have different cultural ideas about which kinds of licenses
> they prefer. Broadly, there are BSD/MIT style licenses that some like that
> basically only require attribution, and there are copyleft GPL style
> licenses that others like that additionally require derived work to also be
> free. This is, to a very large extent, a solved problem. As I say, most of
> modern computing would not be possible if we hadn’t already solved this.
>
> 2. Abandoned code is not a problem if it is properly licensed in the first
> place. You are perfectly free to take any GPL or MIT or BSD licensed
> software that has been abandoned and continue to use it and develop it.
> Nothing stops you. Nothing at all. You are not free to change its license
> without the involvement of the original authors, but why should you want to?
>
> The claim that we can’t make software out of pieces with different
> licenses is demonstrably false.
>
> The claim that we can’t use software abandoned by the original authors is
> also false.
>
> It is perfectly fine to use CC0. As I said, in the USA that is equivalent
> to putting the software in the public domain. Not every country has the
> concept of public domain in the same sense, so CC0 is designed to emulate
> it in those cases. This is unusual, most people do not do this because they
> require attribution at the very least. Attribution is the norm in
> scientific work so it seems like public domain/CC0 is not really the best
> match to established practice.
>
> I understand very well what you are doing with patents and you have been
> nothing but up front about it. I understand very well what patents are and
> how they work. I still think it’s a bad idea to propose using patents for
> scientific models. It’s also a pretty fringe idea. I often like fringe
> ideas but I don’t like this one.
>
> It is possible to get into trouble if you try to use code released under a
> GPL-style copyleft license with something proprietary. This is by design,
> it is not by accident or ignorance. If we want to discourage this (I don’t,
> personally) then we can recommend the more liberal MIT/BSD style of license.
>
> It is a very big problem when people release code with no license at all.
> That means we can’t do anything with it at all. I suggest that we drop the
> discussion about patents and simply say that it is important that model
> code is released under some license. The OSI maintains a decent list of
> appropriate licenses: https://opensource.org/licenses
>
> Best wishes,
> -w
>
> > On 24 May 2021, at 19:06, Jacob Barhak <jacob.barhak at gmail.com> wrote:
> >
> > Thanks William,
> >
> > A good debate is reasonable regarding licensing. So it is welcome.
> >
> > I can write a lot about it and in fact I have been having this
> conversation on several channels.
> >
> > There are many forms of restrictions on what you can do. Even open
> source licenses are despite their name are based on copyright law which is
> a form of legal restriction. Both copyright and patents are forms of legal
> restrictions. And if you want a comparison and a longer discussion, I
> suggest you look at the table the presentation I made for COMBINE last year:
> >       • Jacob. Barhak, Open Source and Sustainability, COMBINE 2020
> October 5-9. Video:
> https://drive.google.com/drive/folders/1actGnx6FwvoCcPrrF3qbnO0AmHt10WN6
> starting from minute 13:10. Presentation:
> https://jacob-barhak.github.io/COMBINE2020_OpenSource_upload_2020_10_04.odp
> >
> > Many people are unnecessarily worried about patents. I assume many times
> without understanding the details. I repeat again my conflict of interest,
> since I do hold patents. So I may be biased in your mind, yet please do
> check out my arguments in the presentation.
> >
> > Note that just like software licenses are not always compatible with
> each other, patents are not always compatible with some licenses and with
> intentions of all parties involved - this is many times the source for
> misunderstanding. Many restrictions are orthogonal to each other and need
> to be cleared before use.. In many cases, some work may need multiple
> licenses and permissions so you can use it.  It depends on many factors,
> including jurisdictions, time, etc.
> >
> > Specifically for CC0 - CC0 is the most unrestricting license I am aware
> of since it waives copyright and therefore highly compatible with many
> others - this is why it was mentioned as a good solution and indeed it has
> been widely adopted . Moreover, it resolves issues of abandoned software or
> with software where multiple contributors cannot agree on. So it gives life
> to code and provides incentives to improve progress.
> >
> > If I am about to integrate a new model or a new work, I may be
> restricted by many restrictions, and those are coming from potentially
> multiple sources, especially if I am integrating multiple models. So
> eliminating copyright and making things compatible helps a lot. It may not
> be sufficient since there are still orthogonal restrictions, yet it's a
> good start. This is why it was recommended and indeed more and more
> entities are using CC0 to release work or to accumulate it in a repository.
> >
> > You mentioned CC licenses family - yes, those are nice licenses, yet
> some still hold restrictions and are not even compatible with each other.
> Here is the compatibility chart within CC license family:
> > https://wiki.creativecommons.org/wiki/Wiki/cc_license_compatibility
> >
> > And yes, in some cases for some entities some licenses will not match
> their intentions - it depends on the situation - yet if you have to bridge
> many intentions, it's a good idea to remove as many restrictions as
> possible.
> >
> > Hopefully you find these explanations sufficient for now.
> >
> >               Jacob
> >
> >
> >
> > On Mon, May 24, 2021 at 8:19 AM William Waites <wwaites at ieee.org> wrote:
> > I am hesitant to get involved in this particular aspect of the paper and
> have long since timed out on software licensing discussions. However…
> >
> > The point that there are inconsistent licenses (or even absent licenses
> which is legally the most restricted since that defaults to “all rights
> reserved” essentially) and this can cause problems when assembling
> composite models is accurate and fair. This is a challenge that we need to
> address. We want to maximise the impact of the public funding of much of
> the kind of work that we do, which means that others need to be as free as
> possible to reuse our work.
> >
> > It is debatable whether CC0 is appropriate. It is meant to emulate the
> public domain in places that do not have a legal concept of public domain.
> It does not require attribution, which is the normal standard for academic
> work. The other CC licenses that require attribution are not designed for
> software. Insisting on using the public domain for software and then
> asserting the ability to control use using patents is a novel idea, but I
> don’t think it is a very good one. It is also not possible in many
> jurisdictions that do not allow software patents.
> >
> > Standards bodies also typically have patent policies which range from
> “disclose your patents” to “if you contribute patented stuff you must agree
> to never try to enforce it”. We can reasonably expect that if we produce
> patent-encumbered standards, nobody will use them. From a standards
> development point of view, this needs addressed as well.
> >
> > There is also a ton of well-developed literature on free and open source
> software licensing and compatibility among licenses.
> >
> > Best wishes,
> > -w
> >
> >
>
>
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