[Bioc-devel] Why should Bioconductor developers re-use core classes?

[Michael Lawrence]

Good points. I think Levi hit on the direct reuse argument (via inheritance
and composition), and, you're right, interoperability is another big one.

On Wed, Oct 18, 2017 at 10:26 AM, Ryan Thompson <rct at thompsonclan.org>
wrote:

> I think the main reason for reusing/subclassing core classes that users can
> appreciate is that it makes it much easier for users to integrate multiple
> packages into a single workflow. Only the most basic of pipelines uses just
> a single Bioconductor package. For instance, an "edgeR" pipeline obviously
> uses the edgeR package, but it likely also uses several other packages,
> like sva, RUV, variancePartition, etc. The more these different packages
> operate on the same core data structures, the less work the user has to do
> to use them together. And to bring that back around to an incentive for
> developers, making your package interoperate with other packages more
> easily means that users will be more likely to use your package.
>
> On Tue, Oct 17, 2017 at 4:55 PM Levi Waldron <lwaldron.research at gmail.com>
> wrote:
>
> > I'm putting together a presentation with a demo on why Bioconductor
> > developers should re-use and extend core classes whenever possible. It
> > includes a demo of some real-life consequences from two packages I use a
> > lot, metagenomeSeq and phyloseq. These are far from the only examples,
> many
> > Bioconductor packages have created new classes from scratch, and I think
> as
> > a community we should greatly reduce that practice. I would welcome any
> > feedback:
> >
> > https://www.slideshare.net/LeviWaldron/why-reuse-core-classes
> >
> > (sorry the slides are a little Frankenstein - in the interest of speed I
> > made part of it in Powerpoint and part in Beamer, and used pdftk to
> > concatenate these! In practice I would do the Beamer part as a live-demo,
> > and take advantage of some animations in PPT)
> >
> >
> > --
> > Levi Waldron
> > http://www.waldronlab.org
> > Assistant Professor of Biostatistics     CUNY School of Public Health
> > US: +1 646-364-9616 <(646)%20364-9616>
> >        Skype:
> > levi.waldron
> >
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> >
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> >
>
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