[BioC] Idea that needs feedback

Wed Dec 22 16:58:09 CET 2010

I think a site that makes it easy and fun to post and access R/Bioconductor code snippets would get used. If it was done well.

Maybe something kind of like shell-fu.org, but with longer code snippets?

Some people are already posting bioconductor related questions and code on biostar, just in case you weren't aware of it:
http://biostar.stackexchange.com/questions/961/r-bioconductor-combining-probesets-in-an-expressionset

Madelaine Gogol
Programmer Analyst
Stowers Institute

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Radhouane Aniba
Sent: Wednesday, December 22, 2010 9:32 AM
To: Evan Misshula
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Idea that needs feedback

Hi again,

To Evan : it is for sure more than a discussion forum.
To Saurin : What you described is a possible (very possible ) scenario, this is the shape that could have some pages dedicated to contributors codes. When submitting a source code or a scirpt people will possibly have to fill a 3 steps form so that everything is uniformly classified and the search in the website could be very simple and effective. so yes : absolutely yes.

Rad

2010/12/22 Evan Misshula <emisshula at jjay.cuny.edu>

> Hi Rad,
> For what it worth, git is really hardcore.  It was originally written
> to host linux.  You checkout, fork and merge code, clone repositories,
> etc.  The discussion forum you were talking,  an open exchange so that
> we are not always reinventing the wheel, I would be interested in
> participating in was more of a discussion forum.  Git is more
> application rather than research centric.
>
> Best,
>
> Evan
> ________________________________________
> From: bioconductor-bounces at r-project.org [
> bioconductor-bounces at r-project.org] On Behalf Of Radhouane Aniba [
> aradwen at gmail.com]
> Sent: Wednesday, December 22, 2010 10:04 AM
> To: ttriche at usc.edu
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] Idea that needs feedback
>
> Tim,
>
> Thank you for your message.
> GitHub is for managing projects as far as I know, I personnaly never
> been there, but browsing a little bit their homepage R is not in their
> top 10 popular langages ! May be I am wrong. My proposal is not to
> create another project management website platform, other equivalent
> to GitHub are doing a great job. A collaborative platform for sharing
> code sources could work either as a platform for a scripts/code "show
> case" or a mean by which people get in touch with each other so that
> they speed up their development using what others already did (using
> is also modifying and enriching the scripts database).
>
> I need more feedback on that issue, would you please (some of you who
> did not participated in this thread already) take two minutes of your
> time to tell if you find this idea useful or interesting or not.
>
>
> Regards
>
> Rad
>
> 2010/12/21 Tim Triche <tim.triche at gmail.com>
>
> > it sounds like you're proposing something along the lines of GitHub
> > gists and/or StackOverflow for Bioconductor users.
> >
> > While I'm not against this idea, I wonder how much traction it would
> > get, since the Internet is practically a testament to wheel
> > reinvention.  (Reinventing wheels is not all bad -- if you're
> > learning how to build
> and
> > balance wheels, it's kind of mandatory)
> >
> > In any event, good luck.  The community could stand to have a more
> > rough-and-tumble hub than the BioC website, if only for hashing out
> > good
> vs.
> > bad ideas.  Personally I put my code up on GitHub, communicate with
> > the relevant people, and see what happens...
> >
> >
> > On Tue, Dec 21, 2010 at 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]]
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor at r-project.org
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >> >
> >>
> >>
> >> --
> >> *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]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >
> >
> > --
> > If people do not believe that mathematics is simple, it is only
> > because they do not realize how complicated life is. John von
> > Neumann<
> http://www-groups.dcs.st-and.ac.uk/%7Ehistory/Biographies/Von_Neumann.
> html
> >
> >
> >
>
>
> --
> *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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>

--
*Radhouane Aniba*
*Bioinformatics Research Associate*
*Institute for Advanced Computer Studies
Center for Bioinformatics and Computational Biology* *(CBCB)* *University of Maryland, College Park MD 20742*

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