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]]