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@radhouane-aniba-4409
Last seen 8.5 years ago
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]]
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@susan-r-atlas-2659
Last seen 10.2 years ago
Hi, I think that this is a great idea. - Susan ---------------------------------------------------------------------- -- > 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 > > -- ------------------------------------------------------------------ Susan R. Atlas Research Associate Professor, Physics and Astronomy Director, Center for Advanced Research Computing Director, University of New Mexico Cancer Center Shared Resource for Bioinformatics and Computational Biology Department of Physics & Astronomy MSC07 4220 p: 505.277.1509 1 University of New Mexico e: susie@sapphire.phys.unm.edu Albuquerque, NM 87131-0001 n: www.phys.unm.edu/CompMaterials [[alternative HTML version deleted]]
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@arnemuellernovartiscom-2205
Last seen 9.1 years ago
Switzerland
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 [[alternative HTML version deleted]]
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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 > > -- *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-4409
Last seen 8.5 years ago
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@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@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 >> > >> > >> >> >> -- >> *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]]
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Hi Radhouane Aniba, What I understand from quick look of this discussion is ..you want to create a methods (R scripts) library with description in terms ..lets say.. R script 1.R input: ouptut: what is used for... how output looks like: modificaions: comments: and so, learners can easily grab the code and put it in their script or use the whole script to start learning R/BioC's capabilities? if that's the case..I like it..its good resource. Saurin ----- Original Message ---- From: Radhouane Aniba <aradwen@gmail.com> To: ttriche at usc.edu Cc: bioconductor at r-project.org Sent: Wed, December 22, 2010 10:04:50 AM 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]] _______________________________________________ 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
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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 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]] _______________________________________________ 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
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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@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@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 <tim.triche@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@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 > >> > > >> > > >> > >> > >> -- > >> *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]]
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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 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]] > > _______________________________________________ > 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
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Entering edit mode
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 <mcm@stowers.org> > 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 <emisshula@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@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 <tim.triche@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@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 > > >> > > > >> > > > >> > > >> > > >> -- > > >> *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]]
ADD REPLY •
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Entering edit mode
Thank you all for your feedback, I want more of course don't hesitate to reply to this thread. In order to get things more organized may be you can take a few moment filling this small form https://spreadsheets.google.com/viewform?formkey=dGpuSEk2ZlRRa2l2MWxXU GdIQzBjelE6MQ Thank you very much Radhouane 2010/12/22 Radhouane Aniba <aradwen@gmail.com> > 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 <mcm@stowers.org> > > 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 <emisshula@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@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 <tim.triche@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@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 >> > >> > >> > >> > >> > >> >> > >> >> > >> -- >> > >> *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* > > -- *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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Thanks guys for your positive and encouraging feedback Could you please (if you did not filled it already) fill this form http://bit.ly/eKwSxN<http: www.linkedin.com="" redirect?url="http%3A%2F%2" fbit%2ely%2fekwsxn&urlhash="An3v&amp;_t=tracking_disc">and send it to your collaborators friends and people you know working with R/Bioc. Hopefully a first version of the platform will be available in mid january. Kind regards Rad 2010/12/22 Radhouane Aniba <aradwen@gmail.com> > Thank you all for your feedback, I want more of course don't hesitate to > reply to this thread. > In order to get things more organized may be you can take a few moment > filling this small form > > > https://spreadsheets.google.com/viewform?formkey=dGpuSEk2ZlRRa2l2MWx XUGdIQzBjelE6MQ > > Thank you very much > > Radhouane > > 2010/12/22 Radhouane Aniba <aradwen@gmail.com> > > 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 <mcm@stowers.org> >> >> 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 <emisshula@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@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 <tim.triche@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@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 >>> > >> > >>> > >> > >>> > >> >>> > >> >>> > >> -- >>> > >> *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* >> >> > > > -- > *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]]
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