[Bioc-devel] Use and Usability metrics / shields

Dan Tenenbaum dtenenba at fredhutch.org
Thu May 14 16:42:35 CEST 2015 


----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Wolfgang Huber" <whuber at embl.de>
> Cc: bioc-devel at r-project.org
> Sent: Thursday, May 14, 2015 7:33:04 AM
> Subject: Re: [Bioc-devel] Use and Usability metrics / shields
> 
> 
> 
> ----- Original Message -----
> > From: "Wolfgang Huber" <whuber at embl.de>
> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> > Cc: bioc-devel at r-project.org
> > Sent: Thursday, May 14, 2015 4:03:54 AM
> > Subject: Re: [Bioc-devel] Use and Usability metrics / shields
> > 
> > 
> > 
> > Can it be that the “in Bioc” shield is incorrect?
> > For instance, it says “9.98 years” for vsn but the first commit was
> > in Oct 2002
> > Curiously “9.98 years” is stated for many old packages - surely we
> > can use R for more precise date arithmetic?
> > 
> 
> It is not counting from the first commit (as it says in the tooltip
> text) but from the day of the first release in which the package
> appeared.
> 
> So it does not count the time that the package is in devel only.
> 

Actually, it turns out that I don't have data for packages committed prior to BioC 1.6. I was using the release manifests (and associated release dates) to calculate "years in bioc"; I'll switch to using svn logs.

Thanks,
Dan


> Dan
> 
> 
> 
> 
> > 	Cheers
> > 	Wolfgang
> > 
> > > On May 13, 2015, at 21:36 GMT+2, Dan Tenenbaum
> > > <dtenenba at fredhutch.org> wrote:
> > > 
> > > 
> > > 
> > > ----- Original Message -----
> > >> From: "Henrik Bengtsson" <henrik.bengtsson at ucsf.edu>
> > >> To: "COMMO Frederic" <Frederic.COMMO at gustaveroussy.fr>
> > >> Cc: bioc-devel at r-project.org
> > >> Sent: Wednesday, May 13, 2015 12:28:54 PM
> > >> Subject: Re: [Bioc-devel] Use and Usability metrics / shields
> > >> 
> > >> Sweet; you went live with the badges/shields, e.g.
> > >> 
> > >>  http://bioconductor.org/packages/release/bioc/html/affxparser.html
> > >> 
> > >> A positive side effect is that now there's a link from the
> > >> package
> > >> page to to the package's check results, which I always wanted :)
> > >> 
> > > 
> > > That was there before (and still is, see the bottom of the
> > > Details
> > > section). But yes, it was not very visible.
> > > 
> > > Dan
> > > 
> > > 
> > >> Thanks for adding this
> > >> 
> > >> /Henrik
> > >> 
> > >> 
> > >> On Sun, May 10, 2015 at 11:39 AM, COMMO Frederic
> > >> <Frederic.COMMO at gustaveroussy.fr> 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?
> > >>> 
> > >>> 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
> > >>> 
> > >>> _______________________________________________
> > >>> 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
>

More information about the Bioc-devel mailing list