[Biopython] Bioinformatics node-red module based on BioPython

[Jocelyne]

Hi Ferran,
I personally only use biopython as a library and would rather build my
workflow in a python based language, outside of biopython.
I'd be cautious about workflow building. There seems to be 101 (figurative)
existing languages (nextflow, snakemake, wdl come top of mind) with many
different preferences. I think it's a decision best left to user. But I
might not be understanding the intent of the feature well enough.
Jocelyne

-- sent from phone

On Mon, Jan 31, 2022, 02:01 Ferran Fàbregas <ferri.fc at gmail.com> wrote:

> Hi all,
>
> Based on the feedback you gave me a few weeks ago I've been thinking about
> leaving the GUI for BioPython and focusing on a BioPython-based workflow
> tool.
>
> I'm aware that the Galaxy project also has a workflow tool, but I've been
> thinking of using something more modular, flexible and cross-functional
> from an IT point of view, so I think node-red could be a great option.
>
> https://nodered.org/
>
> Using node-red you could integrate a new bioinformatics module based on
> BioPython with thousands of workflow nodes of all kinds, allowing almost
> everything you can ever need, from access to any database engine, to using
> an API of anything you can imagine.
>
> For example you can implement, without the need for programming and using
> only the workflow interface, applications such as a public Telegram
> bioinformatic bot (maybe not very useful, but surely fun).
>
> But node-red is based on node.js, not Python :( Although I have been doing
> some research, and it is possible to run python scripts from node-red.
>
> Maybe another option would be to port BioPython to Javascript,
> facilitating the integration with node-red infrastructure.
>
> What do you think about using BioPython as a backend for a bioinformatics
> module for the node-red workflows?
>
> I also created a ultrabasic test module package for node-red using npm
> (using native JS)
>
> https://www.npmjs.com/package/node-red-contrib-biotools
>
> Kind regards,
>
> F
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