[Bioc-devel] Invitation to the bioC developers Meeting in Seattle Mon 15 Aug
smyth at wehi.edu.au
Thu Aug 4 06:24:15 CEST 2005
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.
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.
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