[Bioc-devel] Short URLs for packages?

[Gabe Becker]

On Mon, Mar 23, 2015 at 9:25 AM, Tim Triche, Jr. <tim.triche at gmail.com>
wrote:

> I guess my problem is that there is even an "if" at the beginning of that
> sentence.  That's not an attack on you, I know that the above reflects the
> current state of affairs, I'm simply saying that perhaps Bioconductor, as a
> project, can help/encourage people to do better.
>
>
> Quite true.  Perhaps that could be emphasized as part of adding the
> redirect rules.  I am always delighted when people cite the version number
> of a package, as it shows that they care about the quality of their work,
> and the stability of its conclusions.
>
> People rarely do what they know is right; they do what is convenient, then
> repent.  (Bob Dylan pointed this out a while ago...)
>

I agree. That is why I am somewhat leery of making more convenient to do
the "wrong" thing (or to not do the right one).


>
> Thus it is more likely that a person will do the right thing if it happens
> to be the most convenient thing IMHO. Anything to advance this strategy
> would be a step in the right direction
>

Bioc core team: This may be getting a bit off topic,  but has there been
any discussion of working with an organization like http://zenodo.org/ to
get DOIs assigned to Bioc packages on release? This could be for every
release or only for the initial inclusion in a Bioc release, but if they
are  version specific they would make citing, etc easier and more rigorous.
We could have a biocCite or figure out how to get citation to do the right
thing.

~G




>
> Best,
>
> --t
>
>
> ~G
>
>
>>
>> --t
>>
>> > On Mar 23, 2015, at 8:38 AM, Gabe Becker <becker.gabe at gene.com> wrote:
>> >
>> > On Mon, Mar 23, 2015 at 8:05 AM, Fischer, Bernd <
>> > b.fischer at dkfz-heidelberg.de> wrote:
>> >
>> >>
>> >> During the production process of the paper we want to link to the
>> >> accompanying
>> >> BioC package that is in devel, but not yet in release. Before the first
>> >> release, the
>> >> link (e.g. www.bioconductor.org/<packagename>) should go to the devel
>> >> version
>> >> (maybe with an additional warning that it is only available in devel),
>> >> before the
>> >> first release of the package and should go to release afterwards.
>> >
>> > I understand the appeal of this, but decoupling publications from the
>> > actual, exact versions they discuss or use seems like a relatively large
>> > step backwards in terms of reproducibility. At the very least, I think
>> > there is some nuance here that warrants careful consideration before we
>> > adopt a single-silently-changing-link-per-package paradigm.
>> >
>> > ~G
>> >
>> >
>> >
>> >
>> >>
>> >> Bernd
>> >>
>> >>
>> >>> On 23.03.2015, at 11:45, Sean Davis <seandavi at gmail.com> wrote:
>> >>>
>> >>> Just so we don't lose the thoughts that have come before, here is a
>> link
>> >> to
>> >>> a similar proposal from last year.
>> >>>
>> >>> https://stat.ethz.ch/pipermail/bioc-devel/2014-February/005292.html
>> >>>
>> >>> Sean
>> >>>
>> >>>
>> >>>
>> >>>> On Mon, Mar 23, 2015 at 6:17 AM, Wolfgang Huber <whuber at embl.de>
>> wrote:
>> >>>>
>> >>>> I wonder whether it’d possible to have the website understand URLs
>> like
>> >>>>       http://www.bioconductor.org/<pkgname>
>> >>>>
>> >>>> This could resolve to
>> >>>> http://www.bioconductor.org/packages/release/bioc/html/
>> <pkgname>.html
>> >>>> or
>> >>>> http://www.bioconductor.org/packages/devel/bioc/html/<pkgname>.html
>> >>>> depending on whether the package was yet released.
>> >>>>
>> >>>> This could be handy in papers or grants that mention packages.
>> >>>>
>> >>>> Wolfgang
>> >>>>
>> >>>>
>> >>>> ----
>> >>>> Wolfgang Huber
>> >>>> Principal Investigator, EMBL Senior Scientist
>> >>>> Genome Biology Unit
>> >>>> European Molecular Biology Laboratory (EMBL)
>> >>>> Heidelberg, Germany
>> >>>>
>> >>>> T +49-6221-3878823
>> >>>> wolfgang.huber at embl.de
>> >>>> http://www.huber.embl.de
>> >>>>
>> >>>> _______________________________________________
>> >>>> Bioc-devel at r-project.org mailing list
>> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>>
>> >>>      [[alternative HTML version deleted]]
>> >>>
>> >>> _______________________________________________
>> >>> Bioc-devel at r-project.org mailing list
>> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> >> _______________________________________________
>> >> Bioc-devel at r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>> >
>> >
>> > --
>> > Gabriel Becker, Ph.D
>> > Computational Biologist
>> > Genentech Research
>> >
>> >    [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> Gabriel Becker, Ph.D
> Computational Biologist
> Genentech Research
>
>


-- 
Gabriel Becker, Ph.D
Computational Biologist
Genentech Research

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