[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)

Hi Simon,

On Tue, May 05, 2020 at 03:24:12PM +0200, zimoun wrote:
> > I wonder how users of that software are dealing with this.
> Personally, I am using on the top of Debian the package manager GNU
> Guix with custom channels for installing these non-free software.  It
> helps because it is easier to travel through the history tree of the
> packages and because ``profiles`` allow to install several versions
> side-to-side.

I admit installing several versions side by side.  That's pretty
orthogonal to the fact whether some software is free or non-free, right?
> The presentation "seeing Debian through a Functional lens" by Joey
> Hess at DebConf14 helped me to catch the point about ``functional
> package manager``.
> BTW, thank you for all the hard packaging work you are doing.  I am
> still using Debian (med) packages for the ones I care less; my motto
> is: if it is not planned to be in Debian, then it is not really
> useful. ;-)

We will love hints about enhancements anyway. ;-) 
> > That's a strong point actually.  However, we will face more and more
> > problems of this nature.  Mo's attempt to write a deep learning policy
> > might help here a bit.
> Note that considering the Guppy case -- because it is non-free and the
> structure of the neuronal network is thus not know -- there is no
> point at all. :-)
> However, I think the "problem" of Deep Learning is not new.  Probably
> not the right place to discuss that.

Not really under this topic on this list - but I think it could be
discussed in Debian anyway.
> 1. Trying to state if the weights are part or not of an free licensed
> application does appear to me relevant.  It is part of the application
> as any icon image can be part of some application.  Because the
> application is free, the structure of the network is known and so any
> other weights can be provided (yes they will be probably irrelevant).
> The only question could be, IMHO, in which format the weights are
> stored
> 2. The weights are simply data resulting of one (big) processing.
> This process can be well-describe or it cannot be.  The tools used can
> be free or cannot be.  It does not matter; the only point is the
> license of such data.  For example, an aligner needs a genome for
> reference.  No one argues that all the data used -- notebook,
> discussion for the consensus, etc. -- to build this reference has to
> be released under free licenses.  It is the same for annotations.
> Another example is all the default values, e.g., the ones in
> scikit-learn; they are based on training data set and it is not
> necessarily available.  It happens more than often that software use
> the data resulting of a process of other (training) data.  And the
> only concern about user freedom is the license of the resulting data.
> 3. The access of the training data set is not about freedom but about
> (reproducible) science.  Is the weights considered "scientific" if
> they are not available?
> From my point of view the Mo Zhou's policy melds free software and
> (real) Science, or say reproducibility.  There are bridges between
> both and part of the same big picture.

Since you mention Mo Zhou's policy:  That's the perfect place to
discuss issues like this.

> > Once I've started packaging deepbinner[1] which is stalled as long as we
> > do not have python3-tensorflow.  But may be that's at the horizon since
> > bazel packaging sounded quite promising.
> That's sound awesome!

I guess Olek Wojnar who is busy packaging bazel and who is making
great progress would probably welcome any help. ;-) 
> > > Altogether, I think that we will best serve our users by making sure
> > > that Free basecallers are easy to install on Debian, providing the
> > > standard tools for downstream analysis (we are quite good at this), and
> > > adding value by supporting bioinformatics workflow systems.
> >
> > That's exactly my opinion here.
> Really cool!  That's why Debian rocks!

... and why we on the one hand need opinions like yours as well as
active contributions from people like you. 
> Thank you for all the work that helps a lot to get thing done more easily.

You are welcome and thanks for your opinion



Reply to: