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

Matthias Futschik m.futschik at biologie.hu-berlin.de
Thu Aug 4 09:58:34 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
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.

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.

best wishes,

Gordon Smyth 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
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Matthias E. Futschik
Institute for Theoretical Biology
Charite - Medical Devision
Humboldt-University zu Berlin
Invalidenstrasse 43
10115 Berlin

email: m.futschik at biologie.hu-berlin.de
phone: + 49-30-2093 9106
fax:   + 49-30-2093 8801
URL:   http://itb.biologie.hu-berlin.de/~futschik

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