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

Francesco Napolitano franapoli at gmail.com
Thu Oct 19 12:16:08 CEST 2017

I just converted my gene set data structures to GSEABase::GenSet
class. I think that one major advantage is that I just transferred the
burden of staying up to date with gene set formats to people working
specifically on that. If the file formats from the MSigDB change,
someone will work on updating the methods that import them to GeneSet

In general, there's someone in charge of a software module, and I'm
using both his original work, and his maintenance work.
P.S. the dark side: if they fail to maintain their code, yours will
fail too. I have been there.


On Wed, Oct 18, 2017 at 1:54 AM, 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                                           Skype:
> levi.waldron
>         [[alternative HTML version deleted]]
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