[Bioc-devel] question on bioconductor/package citation

Martin Morgan martin.morgan at roswellpark.org
Sat Mar 4 17:02:47 CET 2017

On 03/04/2017 09:13 AM, Dwivedi, Bhakti wrote:
> Hi,
> I have a few general questions. With such a rigorous peer-review
> process in place for new package submissions in Bioconductor, I was
> wondering if there is a way to assess the package acceptance rate?

One could summarize the number times the '3a. accepted' (118) tag is 
associated with closed issues, versus '3b. declined' (9; packages are 
sometimes marked as 'declined' for reasons not related to the review 
process; packages reviewed in the same issue, e.g., software and 
experiment data packages, are only counted once).


We (I) view the review process as an opportunity to improve the 
technical quality of submitted packages (the output of the review 
process is a technically better package than the input), rather than to 
pass judgment on scientific merit or impose an absolute threshold on 
technical quality. I'm not sure how this fits with standard measures of 
academic contribution.

> The reason I asked, I want to include the Bioconductor package
> citation in my NIH bio-sketch; however, given the format
> requirements, I cannot provide a URL and the unfortunately the
> release citation is not recognized similar to a citation for a
> typical journal article. Have anyone thought of a Bioconductor
> software journal? Is there a better way to cite a package that I am
> unware of? Would appreciate your help and suggestions.

Not sure what you mean about 'cannot provide a URL' but in case it's not 
known the url https://bioconductor.org/packages/<YourPackageHere> always 
points to the current release version of your package or, if a new 
package and only available in devel, the devel version.

The F1000 Bioconductor channel represents one publication venue, with 
the emphasis there on utility of the package within the overall 
Bioconductor ecosystem.


> Also, I am really interested in becoming a Bioconductor
> member/participant and volunteering as a code/documentation reviewer
> or contributor to a part of a project. Is there someone I can contact
> to achieve this or get an idea of what may be required to get there?

We would like to enable more widespread community participation in the 
review process, and will try to provide an update in the not too distant 

Martin Morgan

> Thank you.
> Regards,
> Bhakti
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