Thank you Madelaine, Yes I am aware of Biostar, personnaly I am thinking it is a modified version of a forum, it is a specialized version of a model called question/answer website, which is great but not what I am willing to do. Thanks for your feedback. Rad 2010/12/22 Gogol, Madelaine > 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@r-project.org [mailto: > bioconductor-bounces@r-project.org] On Behalf Of Radhouane Aniba > Sent: Wednesday, December 22, 2010 9:32 AM > To: Evan Misshula > Cc: bioconductor@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 > > > 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@r-project.org [ > > bioconductor-bounces@r-project.org] On Behalf Of Radhouane Aniba [ > > aradwen@gmail.com] > > Sent: Wednesday, December 22, 2010 10:04 AM > > To: ttriche@usc.edu > > Cc: bioconductor@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 > > > > > 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 > >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 > > >> > > >> > 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 * > > >> > Sent by: bioconductor-bounces@r-project.org > > >> > > > >> > 12/21/2010 08:39 PM > > >> > To > > >> > bioconductor@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@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@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]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@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@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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]]