[BioC] Idea that needs feedback

[Rick Frausto]

Hello Radhouane,

As a new entrant into the world of R and Bioconductor I would welcome such
an initiative. I was a bit shell-shocked at the outset so I'd be interested
if your suggestion for an all encompassing "user-friendly" site is really
possible. As many other sites this may just require a few links to the other
established sites/sources.

Anyways, great suggestion!

-Rick


On 21/12/10 4:07 PM, "Radhouane Aniba" <aradwen at gmail.com> wrote:

> Hi all, Hi arne,
> 
> Well as I said in my first message, this is not intended to overlap any of
> Bioc services (website, forums, tutorials, workflows) that I found very well
> done and useful by the way.
> Well my point is that for new people getting involved in R/Bioc, the
> learning curve is different depending on each one capabilities. It could be
> very helpful for everyone, even for "guru" R/Bioc developpers to see what
> other already did that seems to be suitable for a part of a project. Just a
> word about tutorials, workflows and useful help in Bioc website; like every
> bio* project (Bioperl, Biojava, Biopython..) when a project is lunched and
> when people start to get involved in, there is always "how to do" sections
> and lot of tutorials that developers put in front so that people start to
> practice and to get more familiar with the langage syntax and tips. I
> remeber when I was developing using Biojava, with my respect to people
> behing that do a great job, there is only a wiki page which contains several
> helpful sections but this is only the top of the iceberg, such projects
> tends to evoluate exponentially and when a newbie start to get interested in
> using a package or langage X, it is already a mature field and people in the
> mailing lists and forum already speak a very hard t understand jargon, may
> be I am wrong, at least that was my case when I first started to learn
> biojava. Bioc is a relatively new, and more andmore used, and except the
> workflows and tutorials that exist in their website, this is for sure othe
> use cases and scenarios that some of us has already implemented in order to
> publish a paper or to develop a project, a lot of projects overlap in their
> biocomputational development parts, that's why I think personnaly that
> sharing knowledge on "how I did that" part or what workflow i developed used
> existing package in Bioc could be very helpful in the sens that it will lead
> automatically to save hours of developments and accelerate research, this is
> the basics of knowledge sharing let's say, and this is how I came to the
> point that sharing codes for R and BioC is a crucial and very helpful topic.
> Such platform that I have in mind has nothing to do with forums, actually
> people will be able to develop profile pages and write posts about their
> experience with R and Bioc, upload their presentations and posters so that
> all of us we can found directly the information we need instead of spending
> hours on the web looking for an information, it could be a very small
> portion of code, well commented and very clear, as it could be an entire
> workflow showing how to connect different bioc packages. I don't see if I am
> enough clear about the idea but with all respect that i have to all projects
> related to bio, non of them(us) is able to imagine in advance all possible
> scenarios using a specific tool. One example could be more speaking is what
> people behind Taverna package did developing myExperiment website, may be we
> can look at it and imagine features to a collaborative platform.
> 
> Any comment is welcome and thank you for answering.
> 
> Radhouane
> 
> 2010/12/21 <arne.mueller at novartis.com>
> 
>> Hi,
>> 
>> in principle this sounds good, but it seems there's much overlap with the
>> bioconductor web-site that already offers, packages, workflows,
>> documentation, tutorials and hands-on hints and discussion (mailing list)
>> ...
>> 
>> In my experience many packages are as abstract as possible (IRanges and
>> off-spring ...) whereas others are more tailored towards a specific need.
>> Most of the code that I write is just "glue" to stick packages together in a
>> workflow (or analysis), but it's not really re-usable workflow stuff, since
>> it's often project specific, etc ... . I think there's only limited
>> abstraction beyond the package level that's really useful - otherwise I'd
>> write a package ;-) .
>> 
>> Sorry, don't want to be negative, but maybe I didn't get your point. The
>> only thing I'd really find useful is a web-based subscription free forum (I
>> think this topic was briefly discussed at the last bioc developers
>> conference in Heidelberg, but I don't remember the outcome ;-).
>> 
>> Maybe instead of setting up a new web-site you could join the
>> bioc-developers and help improving their web-site (no offense, after getting
>> used to the new web-site I really started liking it ;-)
>> 
>>    best,
>> 
>>   arne
>> 
>> 
>> 
>>  *Radhouane Aniba <aradwen at gmail.com>*
>> Sent by: bioconductor-bounces at r-project.org
>> 
>> 12/21/2010 08:39 PM
>>   To
>> bioconductor at r-project.org
>> cc
>>   Subject
>> [BioC] Idea that needs feedback
>> 
>> 
>> 
>> 
>> Hi BioC users and contributors,
>> 
>> In order to improve collaboration between scientists, computer engineers,
>> bioinformaticians working with R and Bioconductor, I would like to see how
>> much among you here in the list, would be interested in developing or
>> making
>> part of a website that plays the role of collaborative platform for
>> R/Bioconductor codes, packages, workflows and contributions, so that we
>> develop the "re-use" and "don't reinvent the wheel" spirit in one hand, and
>> to put in practice a more collaborative work and interaction between people
>> working on R/Bioconductor related projects.
>> 
>> I already have experience in the development of such platforms and thought
>> it could be useful and interesting to propose such initiative to people
>> like
>> you and I working with R/BioC
>> 
>> This is in no way a competitive or alternative approach to Bioconductor
>> mailing list but a complementary platform for sharing codes / workflows /
>> analysis scenarios using R/BioC
>> 
>> Would you please take a few moment to answer to this topic so that I can
>> have an idea on your position in regards of such initiative.
>> 
>> Thank you
>> 
>> Radhouane
>> 
>> --
>> *Radhouane Aniba*
>> *Bioinformatics Research Associate*
>> *Institute for Advanced Computer Studies
>> Center for Bioinformatics and Computational Biology* *(CBCB)*
>> *University of Maryland, College Park
>> MD 20742*
>> 
>>                 [[alternative HTML version deleted]]
>> 
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>> 
> 

-- 
Rick Frausto
PhD Candidate
The University of Sydney
School of Molecular Bioscience G08
Camperdown, NSW 2006 AUSTRALIA
ricardo.frausto at sydney.edu.au
Phone: 61 2 9036 5354
Lab of Iain L. Campbell