Re: Adding you as Nanopore team account to access the resource
On 25.10.20 15:26, Jun Aruga wrote:
>> Could you prepare the draft text to post to [4]? Then we can polish and post it.
> Hi I prepared the text to post to the Nanopore feature request page. I
> considered simple text to be read by people easily.
> Could you review it? I am going to post it this week if there are no objections.
>
> ###
>
> Subject: ONT software to be more open
"Why?" - they will ask. How about:
Provide redistributable Open Source pipeline for ONT raw data
This will give some basic scientifically grounded motivation:
reproducibility.
> Body:
> The current situation for the ONT software with limited distribution
> targets, limited CPU architectures and manual downloading challenges
> us for the usage. Therefore we would like to see the ONT software to
> be more open. We are maintaining Debian, RPM and Bioconda Medical
> packages.
That is secondary. Reproducibility is key. Without availability it is not
reproducible, though.
> ONT might have a concern to be more open. The good news is we can see
> MongoDB [1] and Redis [2] cases for their license. It's great to see
> ONT already distributed the source of the EPI2ME Command Line Agent on
> the ONT download page.
>
> There are ONT's benefits from our experiences and [1][2], that are
> partly duplicated with the ones of another feature request [3].
>
> * Ease of install
> * Better hardware (GPU, CPU) compatibility, accelerating the user-driven tests.
> * Unlimited distribution targets and CPU architectures by both ONT and users.
> * A stronger community
> * A robust and secure software
>
> We think there are the following possible ways for ONT software to be more open.
>
> * Having ONT's own package repository or redistributable ONT binaries
> for distributions (Ubuntu/Debian/CentOS/Fedora).
> Docker is a good example of their own package repository.
> * Partly Open Sourcing. The non-critical or machine related layer
> parts of the implementation could be open sourced.
> * Fully Open Sourcing with a protected license. ([1], [2])
>
> If ONT takes actions to be more open, we appreciate it.
>
> [1] MongoDB: https://www.mongodb.com/licensing/server-side-public-license/faq
> [2] Redis: https://redislabs.com/blog/redis-labs-modules-license-changes/
> [3] Official Docker images for Nanopore software:
> https://features.nanoporetech.com/ideas/ALGS-I-20
IMHO this is all too much text. I would like to summarize this as:
The Nanopore is a new disruptive technology for which the interpretation of
its raw data is key. That is done in software and we yet do not have the
means
to redistribute both software and raw data to our scientific peers
for their review and the reproduction of our findings. While the
software redistributed
under the ONT license on github is fine, essential tools like GUPPY are
not redistributable [do we have more?].
We suggest to completely open a default pathway for the analysis of the
raw data as generated by the sequencers. The Linux distributions
(Ubuntu/Debian/CentOS/Fedora) will do their part to ease everybody's
experiences with the installation. Such an effort will also help
the docker images.
> ###
For the moment I am not sure that all the tools need to be Open Source.
They need to be redistributable, though. And for that, Open Source
definitely helps technically. And .. it is a good scientific practice,
obviously.
Best,
Steffen
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