Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
Hi Ben,
On Tue, Apr 28, 2020 at 03:16:56PM +0200, Ben Tris wrote:
> I am willing to ask about guppy first,
Thanks a lot.
> but what address could I use best?
May be you can check out the links Michael has given. Does anybody
have some other points of contact? I personally have no idea, sorry.
> And I'm afraid that I will not be that convincing, don't know the
> exact use and needs for having guppy freed.
I'd start with the fact that guppy is on our list of software that
is relevant to fight COVID-19. At the end of our wiki page
https://wiki.debian.org/DebianMed/SoftwareLiberation
is a nice link about kallisto featuring good arguments.
Hope this helps
Andreas.
> On 28-04-20 15:11, Andreas Tille wrote:
> > Hi Ben,
> >
> > would you volunteer to contact the authors about this?
> >
> > Thanks a lot in advance
> >
> > Andreas.
> >
> > On Tue, Apr 28, 2020 at 03:01:51PM +0200, Ben Tris wrote:
> >> I was referring to the flappy license, that is mozilla like
> >> maybe they are willing to change to MPL-2.0 that is GPL compatible
> >> if that research only is a problem, but I think (guess) there are
> >> enough escapes in the license.
> >>
> >> I still think there should be a confirmation
> >> that guppy will not be available with a free software
> >> license. Because I think it is developed with
> >> contributions from the community.
> >>
> >> Otherwise it is indeed non-free.
> >>
> >> Based on the flappy license, should asked to release guppy with MPL-2.0?
> >>
> >> Someone mentioned chiron, maybe that is the only good alternative at
> >> this moment?
> >> (the Basecalling-comparison contains some additional advice on chiron
> >> settings)
> >>
> >> On 28-04-20 10:11, Andreas Tille wrote:
> >>> Hi Michael,
> >>>
> >>> thanks a lot for the links. Any volunteer to start some discussion?
> >>> As I said: If we do not try nothing will change. People with no
> >>> technical skills could contribute by doing so to take some workload
> >>> from packagers.
> >>>
> >>> I'll offer a $DRINK at next Debian Med sprint for every attempt to
> >>> change a license. ;-)
> >>>
> >>> Kind regards
> >>>
> >>> Andreas.
> >>>
> >>> On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote:
> >>>> The guppy binary license is
> >>>> https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf
> >>>> No source code is provided. No competitors of the company may use the
> >>>> software. Must be for "research use only".
> >>>>
> >>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> >>>> "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to
> >>>> license some of their "source available" software
> >>>> Only permits "research purposes", violating DFSG guideline #6 "No
> >>>> Discrimination Against Fields of Endeavor"
> >>>>
> >>>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla
> >>>> Public License and is DFSG compatible
> >>>>
> >>>> On Mon, Apr 27, 2020 at 6:40 PM Ben Tris <benattris@gezapig.nl> wrote:
> >>>>
> >>>>> Sorry to pop in.
> >>>>> I think this license should be reviewed,
> >>>>> unless sure it is not a free license.
> >>>>> To me it looks like a free software license.
> >>>>> Although not understand most.
> >>>>>
> >>>>> What is making this license non-free?
> >>>>>
> >>>>> On 27-04-20 17:06, Jun Aruga wrote:
> >>>>>> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <tille@debian.org> wrote:
> >>>>>>> Hi again,
> >>>>>>>
> >>>>>>> this brings up again my point: We *really*, *really* should take the
> >>>>>>> chance right now to ask upstreams for free licensing. The time is good.
> >>>>>>> We just need somebody who is really doing this.
> >>>>>> For us, the free licensing is good. But for the company nanopore
> >>>>>> technologies it is their core competency.
> >>>>>> I am not sure we can make it happen, but it might be worth trying to ask.
> >>>>>>
> >>>>>>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> >>>>>>>> Extracting the linked deb, one finds a binary and a very restrictive
> >>>>>>>> license. I do not believe that guppy source code is available nor it is
> >>>>>>>> likely to become available any time soon.
> >>>>>>>>
> >>>>>>>> While some of their other basecallers have source code available, I
> >>>>> would
> >>>>>>>> not call the license OSS:
> >>>>>>>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
> >>>>>> I found guppy client software that might be an alternative to use
> >>>>>> guppy's function.
> >>>>>> https://github.com/nanoporetech/pyguppyclient
> >>>>>>
> >>>>>> As Michael mentioned, checking other basecallers for nanopore, then
> >>>>>> communicating the nf-core/nanoseq project using the alternative base
> >>>>>> caller optionally.
> >>>>>>
> >>>>>> I found an interesting document about the basecallers.
> >>>>>> https://github.com/rrwick/Basecalling-comparison
> >>>>>>
> >>>>>> Performance of neural network basecalling tools for Oxford Nanopore
> >>>>> sequencing
> >>>>> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
> >>>>>>> In this study, we tested four basecalling programs developed by ONT –
> >>>>> Albacore, Guppy, Scrappie and Flappie
> >>>>>>> ...
> >>>>>>> We also tested Chiron (https://github.com/haotianteng/Chiron), a
> >>>>> third-party basecaller still under development that uses a deeper neural
> >>>>> network than ONT’s basecallers [3].
> >>>>>> The third party basecaller Chiron's license is Mozilla Public License,
> >>>>> v. 2.0.
> >>>>>> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
> >>>>>>
> >>>> --
> >>>> Michael R. Crusoe
> >
> >
> >
>
--
http://fam-tille.de
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