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
