Re: Adding you as Nanopore team account to access the resource
Hi Jun,
On 26.09.20 13:29, Jun Aruga wrote:
> Hello everyone in Debian Med.
>
> I have good news to share with you.
>
> 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".
> 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.
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.)
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.
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.
I am rather busy these days but will help as good as I can next month.
Best,
Steffen
> So,
> if you like to access the Nanopore's pages being a member of the team,
> please let me know with your name (first and last name), and your
> email.
> I am very happy to add you. And let's take a look at the Nanopore
> pages, then think about our better "win-win" suggestion to post.
>
> If you are considering buying Nanopore products by yourself, accessing
> the learning material in advance might also be useful for you.
>
> By the way, currently the team name is "Jun's team". But I am thinking
> of changing the name to "Open Bioinformatics Foundation" by applying a
> process to use the name [10]. Stay tuned.
>
>
> [1] Help for asking upstreams about free licenses urgently needed
> (Was: Help: Seeking source code of guppy base caller)
> https://lists.debian.org/debian-med/2020/04/msg00272.html
> [2] https://nanoporetech.com/products/minion
> [3] Add member page:
> https://drive.google.com/file/d/1H6MxgY3AAq1iA5p350uKYl5nlomekKEE/view?usp=sharing
> [4] https://community.nanoporetech.com/
> [5] https://community.nanoporetech.com/downloads
> [6] https://features.nanoporetech.com/
> [7] Feature request / vote page:
> https://drive.google.com/file/d/1nZwGVBEYNXP0RjjRQsPD3ihiwy2G-fkP/view?usp=sharing
> [8] https://community.nanoporetech.com/nanopore-learning
> [9] https://community.nanoporetech.com/knowledge
> [10] https://github.com/OBF/obf-docs/blob/master/Affiliated-Project-Policy.md
>
> Cheers,
> Jun
>
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