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
