[Bioc-devel] Creating a menu driven list of packages

Seth Falcon sfalcon at fhcrc.org
Thu Aug 2 06:15:32 CEST 2007

Hi Jonathan,

"Jonathan Nowacki" <jnowacki at gmail.com> writes:
> There is a menu driven list of packages here:
> http://www.bioconductor.org/packages/2.0/Software.html

We call that BioC Views.  There is a controlled vocabulary of terms
defined in the biocViews package.  Each BioC package lists one or more
of these terms in the 'biocViews' field of its DESCRIPTION file.

The menu you see is a collection of static pages generated from the
package repository meta data.

> The IU Medical School would like to at minimum mirror this list on a
> University server.  However our real goal is to improve the interface and
> increase it's transparency.  Is this list stored in a SQL database?  If so,
> is there any way I can gain FTP access to the database in order to
> automatically download copies of updates?  Rehosting the packages as an
> official mirror is not a problem.

Nothing is stored in a DB.  At present the repository HTML files are
all statically generated by our build system.  The biocViews package
contains the code for generating the HTML.

We generate and post a special meta data file that is used by the
biocViews package to generate the pages.  You can find the VIEWS file
for devel here:


So you could parse that and build a more dynamic site.  In fact, a
while ago I did just that and built a small Django web app that parsed
the VIEWS file and provided a searchable entry point into the BioC
package collection.  The demo is offline at the moment, but I'd be
happy to share the code with you if you are interested.

Hope that helps.

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/

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