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]] >> >> _______________________________________________ >> 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 >> >> > -- 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

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* [[alternative HTML version deleted]]