[BioRuby] [pjotr.prins at gmail.com: Revitalizing SciRuby]

Wed Apr 19 10:54:04 EDT 2023

Hi all, I believe the various Bio* mail lists are all active and still hosted by OBF, but very low traffic.  We just discussed in the OBF Board meeting whether it would be better to move to a forum-based platform for discussions (discourse or biostars, the latter which is used by the Bioconductor community).  It would be great to have some feedback from Bioruby developers on this.

Best

Chris

PS: Pjotr, I should come see you when you are in Tennessee next time!

From: BioRuby <bioruby-bounces at mailman.open-bio.org> on behalf of Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp>
Date: Wednesday, April 19, 2023 at 8:07 AM
To: bioruby at mailman.open-bio.org <bioruby at mailman.open-bio.org>
Subject: Re: [BioRuby] [pjotr.prins at gmail.com: Revitalizing SciRuby]
Hi,

In recent years, data science libraries including data frame libraries
are actively developed in the Red Data Tools project.

https://urldefense.com/v3/__https://red-data-tools.github.io/__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxqxn7Netg$<https://urldefense.com/v3/__https:/red-data-tools.github.io/__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxqxn7Netg$>

RedAmber, a new data frame library that internally uses Apache Arrow,
is developed by Hirokazu SUZUKI (@heronshoes)
The development is partially financially supported by Ruby Association.

https://urldefense.com/v3/__https://www.ruby.or.jp/en/news/20221027__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxq7Wp-_ww$<https://urldefense.com/v3/__https:/www.ruby.or.jp/en/news/20221027__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxq7Wp-_ww$>

@ankane (the author of https://urldefense.com/v3/__https://ankane.org/new-ml-gems__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxpwbyDO7Q$<https://urldefense.com/v3/__https:/ankane.org/new-ml-gems__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxpwbyDO7Q$>  )
have been actively developing data science libraries.

Polars Ruby is a new data frame library that internally uses
Polars DataFrame library.
https://urldefense.com/v3/__https://github.com/ankane/polars-ruby__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxrniSAd1A$<https://urldefense.com/v3/__https:/github.com/ankane/polars-ruby__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxrniSAd1A$>

Rover is also a data frame library developed by @ankane.
https://urldefense.com/v3/__https://github.com/ankane/rover__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxrF1RcTZA$<https://urldefense.com/v3/__https:/github.com/ankane/rover__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxrF1RcTZA$>

I think that the development of Ruby data frame library is very active,
but I also think there is no de-facto standard nor recommended stable one.

PS.
By the way, I'm not aware that the mailing list is still alive
and I'm sorry that recent release announcements of BioRuby
have not been sent here. New version of BioRuby will soon be released.

Thanks,

Naohisa Goto

On Tue, 18 Apr 2023 09:46:25 +0900
"MISHIMA, Hiroyuki" <missy at be.to> wrote:

> Hi all,
>
> It is great to hear that the SciRuby project continues to be active.
>
> The use of a common dataframe structure for some of the BioRuby/BioGems functionality would be highly beneficial. The dataframe structure could resemble that of Python's Pandas or R's dplyr/Tidyverse, and personally, I would prefer the latter.
>
> Hiro,
>
> pjotr.public14 at thebird.nl wrote (2023/04/18 6:51):
> > We may want to merge SciRuby and BioRuby initiatives. Who is
> > interesting in discussing such a topic?
> >
> > Pj.
> >
> > ----- Forwarded message from Pjotr Prins <pjotr.prins at gmail.com> -----
> >
> > Date: Mon, 17 Apr 2023 23:48:28 +0200
> > From: Pjotr Prins <pjotr.prins at gmail.com>
> > To: sciruby-dev at googlegroups.com
> > Subject: Revitalizing SciRuby
> > User-Agent: NeoMutt/20170113 (1.7.2)
> >
> > On matrix we have been talking about giving SciRuby a new boost.
> >
> > People may be tired of Python now and there are some ML initiatives of
> > interest. E.g.
> >
> > https://urldefense.com/v3/__https://ankane.org/new-ml-gems__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxpwbyDO7Q$<https://urldefense.com/v3/__https:/ankane.org/new-ml-gems__;!!DZ3fjg!_E2Ynz0_FOxvywAlwAINVjLxQWtaoe9CpIFMX_G1pAvzkuq8e-lKZtawYCxONR634-u2DPTf-LmI9fYFWaAOGxpwbyDO7Q$>
> >
> > Who here would be interested in participating in a zoom meeting to
> > discuss Ruby options? I know there are some Daru users and good people
> > programming Ruby. And it is still one of my favorite languages -
> > together with Lisp and Zig.
> >
> > Pj.
>
> --
> MISHIMA, Hiroyuki, DDS, Ph.D.
> Assistant Professor
> Department of Human Genetics, Nagasaki University
>
> _______________________________________________
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