[Bioc-devel] Invitation to the bioC developers Meeting in Seattle Mon 15 Aug

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Thu Aug 4 18:38:19 CEST 2005

> I think Gordon raises here an important issue:
> As a *once-a-while* developer (but also heavily  user) of Bioconductor,
> I would like to  point out that bioconductor so far has offered us (*not
> belonging-to-the-core-developers) the opportunity
> to present own software to a wider audience -- which one does appreciate  especially
> in the case that you don't come from a big and famous bioinformatics lab and wouldn't get
> an larger audience otherwise!
> Of course, I see the Bioconductor project does need some structure, since I myself keep

Did you see the "Task views" entry under "Download"?  That is a very
provisional approach to 1) establishing a vocabulary for tasks addressed
by bioc software and 2) mapping the packages to the vocabulary.  The
devel package biocViews helps to do this.

This has been known to the core for some time, and perhaps even to the
devel list.  Not much constructive input has come forth on the hard problems
of building a vocabulary and associating packages to the terms.
We need input on both.

> frequently loosing track of which packages have been newly contributed or might helpful for
> my research. Furthermore, even if I would know, I am frequently puzzled
> how poorly documented the packages are. A minimum standard would be nice here.

Did you disclose your appraisal of the documentation to the package author(s)?
Without constructive inputs from users and reviewers authors may not
know where to put their documentation energies.

> And equally importantly: An agreement on a small number of data formats which should
> then be used  in newly contributed packages. If new data formats are included
> a package, a set of conversion tools from and to the standard Bioconductor data formats
> should be included.

Please be more specific on what deficits need to be addressed.
exprSet has a reasonable role as a target format for the combination of
experiment metadata (MIAME object in description slot), sample level data
(phenoData slot), and assay quantitations (exprs slot).  Various software
tools and a convert package make use of this container structure.

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