[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: 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
<dtenenba at fredhutch.org> wrote:

----- 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

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

--
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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