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

A.J. Rossini blindglobe at gmail.com
Thu Aug 4 06:42:29 CEST 2005

Top posting, to avoid cite style clash.

Good agenda topic.  I'd like to twist and refine it in one way, though
I'm sure other ways are acceptable as well.

One could imagine that the current situation, which has a number of
small (perhaps too small) development groups, ought to be doing both
-- i.e. experimenting with methodological as well as technological
innovation (what is the right way for an integrated application to
look like, anyway?  For a single audience, it might look like A, but
for another audience, B, but there isn't a UI equivalent of A+B).
We've got one variant of this UI work, i.e. the "package" and
"package"GUI versions, but it leaves one walking away feeling that
something might be missing.

So should there be additional focus?


On 8/4/05, Gordon Smyth <smyth at wehi.edu.au> wrote:
> I wish to propose an agenda topic:
> - Is Bioconductor's primary aim to provide a focused repository of
> packages, aiming to attract software implementing cutting edge
> bioinformatics research from as many quality labs around the world as
> possible. Or is to produce a set of packages implementing more or less a
> single integrated application?
> - If the primary aim is that of a repository, would it be worthwhile to
> spin off a much smaller set of packages with a smaller developer team to
> try to develop towards an integrated application?
> Background. Although Bioconductor might have some characteristics of both a
> repository and an integrated application, one of these two paradyms needs
> to take precedence I think. To make an analogy, is it the aim of
> Bioconductor to be the software analog of a research journal, or is it to
> be the software analog of a monograph?
> Under the first model, the development of different packages providing
> different approaches to the same problem, i.e., competing with one another,
> is to be expected and even encouraged. The aim is to promote a stimulating
> environment for the development and dissemination of new techniques. The
> obvious down-side is that a research journal however provides a very steep
> learning curve for non-statistical users. A research journal can provide
> occasional review articles for a wider audience.
> Under the second model, it is not reasonable to expect every lab in the
> world to participate. Instead, one needs to select a smaller team of close
> collaborators. Co-authors on research monographs are normally collaborators
> who are also co-authors on associated research papers. Also, it is not
> realistic to expect a monograph to keep up with the pace of a research
> journal in terms of development of new techniques. So this model with move
> more slowly and be less inclusive, but will be easier to present as an
> integrated solution to a non-specialist audience.
> I think that one could view R itself, meaning the set of packages in the
> default distribution, as being an example of the second model. This seems
> to me that this is appropriate considering that the statistical methodology
> implemented by the standard distribution of R is reasonably
> well-established, mostly part of the canonical core of the statistical
> discipline. On the other hand, the research problems being addressed by
> Bioconductor, almost without exception, do not yet have generally accepted
> solutions. On the contrary, the race is very much on to explore what is
> possible and what is best. This situation makes the contrast between a
> research journal and a monograph unusually marked, with the latter at risk
> of being dated unusually quickly.
> Best regards
> Gordon
> At 03:44 AM 4/08/2005, Wolfgang Huber wrote:
> >Hi bioC developers,
> >
> >this is an invitation to the bioconductor developers meeting in
> >Seattle on Mon 15 Aug.
> >
> >It will be 13.00-17.00h at the FHCRC (http://www.fhcrc.org/about/maps)
> >in room M2-A823. Visitors will need to present to the reception and
> >someone will come down and greet them.
> >
> >Agenda topics are (you are encouraged to raise additional ones!) :
> >
> >- Overview of downloads, contributors ("annual report") - Seth, 15 min.
> >
> >- Overview over Task views - Vince
> >
> >- Whom do we want as our audience? Lab biologists? Practical
> >Bioinformaticians?  Statistics consultants/academics? All of them? What
> >are the implications for how design our projects.
> >
> >- How can we identify duplication or 'synergies' and how can encourage
> >integration of efforts (packages) that are currently duplicating (or
> >competing with) each other.
> >
> >- Are we happy with the way the project moves? Which people have we
> >lost, which ones do we want to welcome more?
> >
> >- Do we need a 3-day bioC developers retreat to go into more depth? If
> >yes, settle on when, where, and who's organizing it.
> >
> >- Short- and medium term goals for bioC?
> >
> >
> >
> >         *   *   *
> >
> >For those who are interested, I propose we can also have an informal
> >follow up over drinks and perhaps food afterwards.
> >
> >Best regards
> >    Wolfgang
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


"Commit early,commit often, and commit in a repository from which we can easily
roll-back your mistakes" (AJR, 4Jan05).

A.J. Rossini
blindglobe at gmail.com

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