[Bioc-devel] Use and Usability metrics / shields

Martin Morgan mtmorgan at fredhutch.org
Thu May 14 16:47:28 CEST 2015

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 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?

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.
> Wolfgang
>> 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
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>> Bioc-devel at r-project.org mailing list
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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

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