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?
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. 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
