[Bioc-devel] Use and Usability metrics / shields

[Dan Tenenbaum]

----- Original Message -----
> From: "Leonardo Collado Torres" <lcollado at jhu.edu>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: bioc-devel at r-project.org
> Sent: Thursday, June 11, 2015 9:26:13 PM
> Subject: Re: [Bioc-devel] Use and Usability metrics / shields
> 
> Is it ok if we use the Bioconductor shields elsewhere? For example,
> in
> a github repo landing page or in our website listing the software
> we've contributed to.
> 
> In particular, I'm thinking of adding
> http://www.bioconductor.org/shields/posts/derfinder.svg (and the
> other
> shields) to https://github.com/lcolladotor/derfinder to go along the
> Travis CI shield I use right now.
> 

Feel free, that was part of the idea.

Dan


> On Thu, Jun 4, 2015 at 11:22 AM, Jim Hester
> <james.f.hester at gmail.com> wrote:
> > Henrik,
> >
> > While I proposed the idea for the shields/badges Dan gets all the
> > credit
> > for the implementation.
> >
> > As far as your (implied) idea of a coverage badge, the thought had
> > occurred
> > to us!
> >
> > Jim
> >
> > On Wed, May 20, 2015 at 1:34 PM, Henrik Bengtsson
> > <henrik.bengtsson at ucsf.edu
> >> wrote:
> >
> >> So, lots of things are happening in a few months: Jim Hester
> >> starts
> >> working at Bioconductor, we get Bioc shields/badges, Jim's covr
> >> package is released on CRAN, snare drum, ...  am I to eager if I
> >> already now start wishing for a hi-hat as well?
> >>
> >> /Henrik
> >>
> >> On Tue, May 19, 2015 at 12:47 PM, Dan Tenenbaum
> >> <dtenenba at fredhutch.org>
> >> wrote:
> >> >
> >> >
> >> > ----- Original Message -----
> >> >> From: "Leonardo Collado Torres" <lcollado at jhu.edu>
> >> >> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> >> >> Cc: "Jim Hester" <james.f.hester at gmail.com>,
> >> >> bioc-devel at r-project.org
> >> >> Sent: Tuesday, May 19, 2015 12:37:18 PM
> >> >> Subject: Re: [Bioc-devel] Use and Usability metrics / shields
> >> >>
> >> >> Regarding the 'posts' tag, I can see that it includes a "closed
> >> >> questions" component. For example,
> >> >> http://www.bioconductor.org/packages/release/bioc/html/derfinder.html
> >> >> is 3/1/9/0 right now meaning that 0 questions are closed. From
> >> >> https://support.bioconductor.org/info/faq/, only moderators can
> >> >> close
> >> >> questions. That seems like quite a bit of work for the
> >> >> moderators. So
> >> >> maybe it would be best to drop the "closed questions"
> >> >> component. Or
> >> >> alternatively, can the author of a package moderate the posts
> >> >> that
> >> >> have a tag corresponding to their package?
> >> >>
> >> >
> >> > Perhaps the wording is wrong; what 'closed' is supposed to mean
> >> > is that
> >> the original poster has accepted an answer. I'll change 'closed'
> >> to
> >> 'accepted'.
> >> >
> >> >
> >> >> As for 'build: warnings', it seems like it will show for some
> >> >> devel
> >> >> packages all the time. For example,
> >> >> http://www.bioconductor.org/packages/devel/bioc/html/regionReport.html
> >> >> always has a warning in the Windows build machine due to a
> >> >> mismatch
> >> >> in
> >> >> the version of Rtools installed.
> >> >
> >> > This is a bug in devtools and may have already been fixed (but
> >> > not yet
> >> propagated to CRAN).
> >> > IMO this should be reflected in the build shield.
> >> >
> >> > Dan
> >> >
> >> >
> >> >>
> >> >> I do like these changes and the addition of shields =)
> >> >>
> >> >>
> >> >> On Thu, May 14, 2015 at 10:56 AM, Dan Tenenbaum
> >> >> <dtenenba at fredhutch.org> wrote:
> >> >> >
> >> >> > ----- Original Message -----
> >> >> >> From: "Jim Hester" <james.f.hester at gmail.com>
> >> >> >> To: "Martin Morgan" <mtmorgan at fredhutch.org>
> >> >> >> Cc: bioc-devel at r-project.org
> >> >> >> Sent: Thursday, May 14, 2015 7:53:03 AM
> >> >> >> Subject: Re: [Bioc-devel] Use and Usability metrics /
> >> >> >> shields
> >> >> >>
> >> >> >> 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.
> >> >> >
> >> >> > It does seem though that we should indicate the non-changing
> >> >> > nature
> >> >> > of these shields with some kind of color change. Perhaps we
> >> >> > can
> >> >> > come up with one that works with the other design elements on
> >> >> > the
> >> >> > page.
> >> >> >
> >> >> > BTW, the 'posts' tag does change color; if there are 0 posts
> >> >> > tagged
> >> >> > with a package name, the shield is yellow; otherwise it's
> >> >> > green.
> >> >> >
> >> >> > Dan
> >> >> >
> >> >> >
> >> >> >>
> >> >> >> On Thu, May 14, 2015 at 10:47 AM, Martin Morgan
> >> >> >> <mtmorgan at fredhutch.org>
> >> >> >> wrote:
> >> >> >>
> >> >> >> > 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
> >> >> >> >
> >> >> >> >   http://bioconductor.org/help/publications/
> >> >> >> >
> >> >> >> > 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.
> >> >> >> >
> >> >> >> > Martin
> >> >> >> >
> >> >> >> >
> >> >> >> >  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
> >> >> >> >>>
> >> >> >> >>> _______________________________________________
> >> >> >> >>> Bioc-devel at r-project.org mailing list
> >> >> >> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >> >> >>>
> >> >> >> >>
> >> >> >> >> _______________________________________________
> >> >> >> >> Bioc-devel at r-project.org mailing list
> >> >> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >> >> >>
> >> >> >> >>
> >> >> >> >
> >> >> >> > --
> >> >> >> > 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
> >> >> >> >
> >> >> >>
> >> >> >>       [[alternative HTML version deleted]]
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> Bioc-devel at r-project.org mailing list
> >> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >> >>
> >> >> >
> >> >> > _______________________________________________
> >> >> > Bioc-devel at r-project.org mailing list
> >> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>
> >> >
> >> > _______________________________________________
> >> > Bioc-devel at r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>