[Bioc-devel] Use and Usability metrics / shields
james.f.hester at gmail.com
Thu May 14 16:53:03 CEST 2015
The common shield convention is to use blue or orange when the information
is not qualitatively good or bad, but the color choice is just subjective
in the end.
On Thu, May 14, 2015 at 10:47 AM, Martin Morgan <mtmorgan at fredhutch.org>
> On 05/10/2015 11:39 AM, COMMO Frederic wrote:
>> Dear Martin,
>> All of these suggestions sound good.
>> Wolfgang's suggestion regarding possible associated papers might be also
>> 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?
> Thanks for these suggestions.
> I like the idea of linking into the scientific literature, initially as
> part of the 'Citation' section on each landing page rather than as a shield
> (maybe a shield in the long term). As Wolfgang mentions it is a little more
> challenging than a one-liner to match the information available from a
> CITATION file (or automatically generated) to an appropriate search in
> PubMed, and because citations are an important formal metric it seems
> important to get this more-or-less right.
> For what it's worth the more-or-less continuous stream of papers citing
> 'Biocondcutor' are listed at
> The links in the 'Literature Search' box query various resources for use
> of the term 'Bioconductor'.
> We have so far kept the distinction between 'available' and 'build',
> partly because builds sometimes fail for transient (e.g., connectivity)
> reasons or, in devel, because of an incomplete check-in that does not
> compromise the end-user availability and functionality of the version
> available via biocLite().
> It's kind of amusing that (a) most of the information was already
> available, often on the landing page (like the links to build reports that
> Henrik mentions, or years in bioc), so the shields are serving just to
> emphasize these; and (b) the 'green' implies some-how 'good', but many of
> the shields (e.g., years in Bioc, posts, commits, downloads) are actually
> never not green. Maybe these shields should be white?
> Thanks again for the feedback; initial response seems to be positive.
> 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>
>>> 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.
>>> 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
>>> - Support forum activity -- questions and comments / responses, 6 month
>>> - 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
>>> 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
>> Bioc-devel at r-project.org mailing list
> 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
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