----- Original Message ----- > From: "Leonardo Collado Torres" <lcoll...@jhu.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: bioc-devel@r-project.org > Sent: Friday, June 12, 2015 11:43:09 AM > Subject: Re: [Bioc-devel] Use and Usability metrics / shields > > 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 > >
Cool! Note that some shields will be the same for release and devel; others will differ, such as the "platforms" shield. So since your repos is presumably mapped to the devel version of your package, you should pull the 'platforms' shield from 'shields/availability/devel' instead of 'shields/availability/release'. Dan > 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
