[Bioc-devel] Use and Usability metrics / shields

COMMO Frederic Frederic.COMMO at gustaveroussy.fr
Sun May 10 20:39:06 CEST 2015

Dear Martin,

All of these suggestions sound good.

Wolfgang's suggestion regarding possible associated papers might be also great.

Another useful information would be to point to other publications where a given package was used, and cited.
I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts.

Frederic Commo
Bioinformatics, U981
Gustave Roussy

De : Bioc-devel [bioc-devel-bounces at r-project.org] de la part de Wolfgang Huber [whuber at embl.de]
Date d'envoi : samedi 9 mai 2015 19:57
À : Martin Morgan
Cc: bioc-devel at r-project.org
Objet : Re: [Bioc-devel] Use and Usability metrics / shields

Dear Martin

great idea.
"Current build status” could perhaps be wrapped with "Cross-platform availability” into some sort of “Availability / Accessibility”?

I wonder how informative it would be to make metrics such as
(i) citations of the associated paper
(ii) full-text mentions e.g. in PubmedCentral
actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list?

PS  Martin you’ll like Fig. 2 of their paper.


> On May 9, 2015, at 19:15 GMT+2, Martin Morgan <mtmorgan at fredhutch.org> wrote:
> Bioc developers!
> It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews.
>  http://bioconductor.org/packages/release/
> We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include:
> - Cross-platform availability -- biocLite()-able from all or only some platforms
> - Support forum activity -- questions and comments / responses, 6 month window
> - Download percentile -- top 5, 20, 50%, or 'available'
> - Current build status -- errors or warnings on some or all platforms
> - Developer activity -- commits in the last 6 months
> - Historical presence -- years in Bioconductor
> Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability.
> We initially intend to prominently display 'shields' (small graphical icons) on package landing pages.
> Thanks in advance for your comments,
> Martin Morgan
> Bioconductor
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Bioc-devel at r-project.org mailing list

More information about the Bioc-devel mailing list