Re: Adding you as Nanopore team account to access the resource
Hi Steffen,
Thanks for your summarized thought! Sorry for my late response.
Let me comment one by one.
> > As we may know, we had a discussion about Guppy to be open source
> > licensees [1]. Guppy is a base calling software by the company Oxford
> > Nanopore Technologies, used in the pipeline of COVID-19 analysis.
> > Guppy has only limited access for Nanopore product purchasing people.
> >
> > I bought MinION [2] recently, the company's product, and there is a
> > feature to other people as a member of the team [3]. That means if you
> > are added as a member to the team, you can access the following pages.
> > And if you like, I can add you to my team "Jun's team" used to
> > communicate Open source communities with Nanopore Technologies.
> >
> > * Community page [4]
> > * Downloading page to download software [5]
> > * Feature request / vote page: [6][7]
> > * Learning (online training) page [8]
> > * Knowledge base [9]
> >
> > The feature request / vote page is a place where we can post our suggestions.
> > In my opinion, we might be able to just ask them for a free license.
> > However if there is no benefit for them, there is no reason they will
> > change their current strategy for the license.
>
> I kept thinking about what we could offer. To tell a quick tale from my
> current ad hoc problems, we are about to order new machines for our
> compute cluster and these should be compatible with the Nanopore
> infrastructure. Now, what accelerator (which is needed) should I go for?
> The 1080Ti or 2080s are no longer sold, the 3080 is not yet known if
> compatible. The V100 seems like a safe bet but is the A100 is what one
> would like to buy, which now needs a more recent version of CUDA and
> having tested a few CUDA tools on an A100, it is not guaranteed that
> these run.
>
> If ONT would be a bit more open then compatibility tests could be flying
> back to the developers much more quickly. Maybe they even make it into a
> few benchmarks for these cards.
>
> Also, if guppy would be redistributable, then it would also be far
> easier to install for the average Joe biologist. Regular Linux distros
> are compatible with biologists, and so would be an "apt install guppy".
Very good points! I agree on the benefits of being more open are
* Accelerate hardware (GPU, CPU) compatibility
* Easy to install. (You can see the guppy's current install steps on
Ubuntu 18 here [1])
MongoDB and Redis's buisiness model is a "open core model" [2]. I
think sharing their thoughts to ONT is useful for them. Here are the
URLs (MongoDB [3], Redis [4]). I want to put the URLs in our
suggestion to ONT. Their open core model's source is open. But we
(Linux distribution) can not redistribute it by packaging. According
to [3], there are the following benefits of open too.
* A software robust and secure software
* A stronger community
> > But if our suggestion is "win-win" between us and Nanopore, if both we
> > and Nanopore have benefits, we will see a better situation for us.
>
> I can understand that ONT may be particularly nervous these days. So,
> maybe they don't need to make a full transition to Open Source for
> everything but we can offer some paths towards a
> Linux-distro-redistribution that is less of a full monty. A principle
> for Debian is that there should be no Debian-specific solution. I
> describe a few points of discussion below. At the moment I do not have a
> complete overview about how the tools are organised, so this needs some
> joint revision - but, let's start with something, and these scenarios
> are not mutually exclusive:
>
> Aim: Full Nanopore infrastructure redistributed with Linux distributions
> Implementation: ONT declares all their binaries to be redistributable
> Would we like that: That is as good as the Nvidia drivers that Guppy
> depends on, except that for anything sciency we are more sensitive to
> inspect the methods and hence would like it as Open Source. But yes, we
> would like that as a start.
Let me name this as aim [a].
> Aim: ONT complements the infrastructure with their own repository for a
> series of distributions
> Implementation: ONT prepares Debian/Ubuntu/etc repositories, maybe as
> easily as by hiring a few of us
> Would we like that: This is both better (getting ONT closer to the
> distribution than by us just redistributing their binaries) and possibly
> worse (NDA? We don't have it.)
Let me name this as aim [b].
> Aim: Partial Open Sourcing of Guppy (and other tools alike)
> Implementation: Any non-critical parts of the implementation (whatever
> that is) would be Open Sourced, other parts would hide behind libraries
> that remain non-free, but are also redistributed
> Would we like that: Sounds like a strategy to me.
Let me name this as aim [c].
> Aim: Full Open Sourcing of critical Nanopore infrastructure
> Implementation: ONT separates the key tools for handling their machines
> (which they may decide to keep closed source) from tools for the
> analysis and Open Sources the latter.
Let me name this as aim [d].
Okay. Thanks for clarifying the scenarios! According to this ONT
community page [5] about distributing official docker images for ONT
software, they are positive. Here is their comment on the page.
> December 12, 2019 13:30
> Yes - there are a few external permissions that have to be cleared in order for this to go through so unfortunatley we're waiting on those to make this happen
So, ONT is positive for [a]. Allowing redistributing binaries makes
users test the hardware compatibility. [b] is like what Docker CE
does. We can share the case to ONT. The [c], [d], the partly open
sourcing can be fair. I agree on your scenarios from [a] to [d]. I
just want to add the above 2 additional benefits of open and citing
MongoDB [3] and Redis [4] cases to our suggestion.
Could you prepare the draft text to post to [4]? Then we can polish and post it.
Thanks!
[1] https://community.nanoporetech.com/protocols/Guppy-protocol/v/gpb_2003_v1_revt_14dec2018/linux-guppy
[2] https://en.wikipedia.org/wiki/Open-core_model
[3] MongoDB license thought:
https://www.mongodb.com/licensing/server-side-public-license/faq
[4] Redis license thought:
https://redislabs.com/blog/redis-labs-modules-license-changes/
[5] Official Docker images for Nanopore software:
https://features.nanoporetech.com/ideas/ALGS-I-20
[4] https://features.nanoporetech.com/
--
Jun | He - His - Him
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