[Biopython] Bioinformatics node-red module based on BioPython

[Peter Cock]

Hello Ferran,

You might want to look at BioJS, http://biojs.net/ - although I think they
are dormant now.

To my mind you wouldn't be writing one module for such a workflow system,
but dozens or more. For example, you could have a sequence file format
converter (e.g. SFF to FASTQ), a multiple sequence alignment file format
converted (e.g. PHYLIP to FASTA), a protein statistics tool (FASTA to TSV
table), etc. Some of those would be quite simple, others would be lots of
work for the person linking the Python code to the workflow interface.

That's my impression based on having written quite a few Galaxy tools in
Python - I would be surprised if this was dramatically different in any
other workflow tool. For Galaxy I would start by defining a task as a
command line tool written in Python using Biopython, then for Galaxy
integration it is like wrapping any other command line tool.

Peter

On Mon, Jan 31, 2022 at 10:01 AM 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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