[Bioc-devel] Use and Usability metrics / shields
----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu> To: "Dan Tenenbaum" <dtenenba at fredhutch.org> Cc: bioc-devel at 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.hester at 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.bengtsson at 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 <dtenenba at fredhutch.org> wrote:
----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu> To: "Dan Tenenbaum" <dtenenba at fredhutch.org> Cc: "Jim Hester" <james.f.hester at gmail.com>, bioc-devel at 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 <dtenenba at fredhutch.org> wrote:
----- Original Message -----
From: "Jim Hester" <james.f.hester at gmail.com> To: "Martin Morgan" <mtmorgan at fredhutch.org> Cc: bioc-devel at 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 <mtmorgan at 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-bounces at r-project.org] de la part de Wolfgang Huber [whuber at embl.de] Date d'envoi : samedi 9 mai 2015 19:57 ? : 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?
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 <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
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