[Biopython] Bioinformatics node-red module based on BioPython

[Ferran Fàbregas]

Thanks for the feedback,

I will check the http://biojs.net/ project.

With node-red, each module is divided in nodes, and each node gives some
specific functionality, the idea is about creating one or more modules with
several (dozens maybe) of individual nodes.

My main problem is trying to avoid 'reinventing the wheel' and find
something useful to do. This is hard because  galaxy is a very big and
flexible project, but, in the end, I think that node-red can give to the
user useful and unique features like:

- +3000 pre-packaged modules with almost any functionality you can imagine,
especially in data interchange and data transformation. Not in
Bioinformatics, of course, this will be my job :)
- A flexible and customizable dashboard functionality, allowing to
transform any workflow into an interactive online web application for the
user.
- The workflow architecture can be useful for some users.

I've a video showing a concept demo of the biotools module for node-red.
The audio is in spanish but the UI is in english and it's pretty easy to
understand the concept viewing the video (5min)

https://youtu.be/k7WsIQNgz8o

Hope you find it interesting,

F


On Mon, Jan 31, 2022 at 4:16 PM Jocelyne <jocelyne at gmail.com> wrote:

> 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
>> _______________________________________________
>> Biopython mailing list  -  Biopython at biopython.org
>> https://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20220131/66abd774/attachment-0001.htm>