Hello everyone, Thank you again for your useful comments and ideas. Finally the website is up and running, would you please join me there and send me your comments and suggestions. Please feel free to ask any question you have. The website URL is http://biocoders.net Thank you again and hope you find the website intuitive and useful. Regards Radhouane > Radhouane > > 2011/1/3 Radhouane Aniba <aradwen@gmail.com> > > Hello Rick, >> >> Thank you for your email. I totally agree with you. >> Could you please fill in this form in order to announce the website. >> Here is the link *http://tinyurl.com/23aod4n >> >> Thank you for the feedback >> >> Radhouane >> * >> 2011/1/3 Rick Frausto <ricardo.frausto@sydney.edu.au> >> >> 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@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@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@gmail.com>* >>> >> 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 >>> >> >>> >> >>> > >>> >>> -- >>> Rick Frausto >>> PhD Candidate >>> The University of Sydney >>> School of Molecular Bioscience G08 >>> Camperdown, NSW 2006 AUSTRALIA >>> ricardo.frausto@sydney.edu.au >>> Phone: 61 2 9036 5354 >>> Lab of Iain L. Campbell >>> >>> >>> >>> >>> >>> >>> >> >> >> -- >> *Radhouane Aniba* >> *Bioinformatics Research Associate* >> *Institute for Advanced Computer Studies >> Center for Bioinformatics and Computational Biology* *(CBCB)* >> *University of Maryland, College Park >> MD 20742* >> >> > > > -- > *Radhouane Aniba* > *Bioinformatics Research Associate* > *Institute for Advanced Computer Studies > Center for Bioinformatics and Computational Biology* *(CBCB)* > *University of Maryland, College Park > MD 20742* > > -- *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]]