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List: bioc-devel
Subject: Re: [Bioc-devel] Use and Usability metrics / shields
From: Henrik Bengtsson <henrik.bengtsson () ucsf ! edu>
Date: 2015-05-20 17:34:54
Message-ID: CAFDcVCRsO6xQ_FREhResVykyjWfGCgifF231twh_NCe9-ibY1g () mail ! gmail ! com
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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@fredhutch.org> wrote:
>
>
> ----- Original Message -----
> > From: "Leonardo Collado Torres" <lcollado@jhu.edu>
> > To: "Dan Tenenbaum" <dtenenba@fredhutch.org>
> > Cc: "Jim Hester" <james.f.hester@gmail.com>, bioc-devel@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@fredhutch.org> wrote:
> > >
> > > ----- Original Message -----
> > > > From: "Jim Hester" <james.f.hester@gmail.com>
> > > > To: "Martin Morgan" <mtmorgan@fredhutch.org>
> > > > Cc: bioc-devel@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@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@r-project.org] de la part
> > > > > > de
> > > > > > Wolfgang Huber [whuber@embl.de]
> > > > > > Date d'envoi : samedi 9 mai 2015 19:57
> > > > > > À : Martin Morgan
> > > > > > Cc: bioc-devel@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@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@r-project.org mailing list
> > > > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > Bioc-devel@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@r-project.org mailing list
> > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > >
> > > >
> > > > [[alternative HTML version deleted]]
> > > >
> > > > _______________________________________________
> > > > Bioc-devel@r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > >
> > >
> > > _______________________________________________
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> _______________________________________________
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