Awesome! Here's the code in case others want to add the shields to their github readme files. https://gist.github.com/lcolladotor/de2e0b67fbf33518b922
derfinder example (software package) https://github.com/lcolladotor/derfinder derfinderData example (experiment data package) https://github.com/leekgroup/derfinderData On Fri, Jun 12, 2015 at 12:32 AM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > ----- Original Message ----- >> From: "Leonardo Collado Torres" <lcoll...@jhu.edu> >> To: "Dan Tenenbaum" <dtene...@fredhutch.org> >> Cc: bioc-devel@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.hes...@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.bengts...@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 >> >> <dtene...@fredhutch.org> >> >> wrote: >> >> > >> >> > >> >> > ----- 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 >> >> >> >> _______________________________________________ >> >> 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