----- Original Message ----- > From: "Leonardo Collado Torres" <lcoll...@jhu.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Jim Hester" <james.f.hes...@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 > <dtene...@fredhutch.org> wrote: > > > > ----- Original Message ----- > >> From: "Jim Hester" <james.f.hes...@gmail.com> > >> To: "Martin Morgan" <mtmor...@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 > >> <mtmor...@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-boun...@r-project.org] de la part > >> >> de > >> >> Wolfgang Huber [whu...@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 > >> >> <mtmor...@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 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
