A shiny version of visnab would be insanely great. Might be possible to farm out at least some of the heavy lifting for eg Circos style plots to d3, which is also insanely great. Off topic, but have you played with Scribl at all? It seemed fairly usable for some of the tasks I find IGV handles. I can't say I will miss IGV if something better (webbier) comes along, but it is extensible in some important respects. The extending does take some work, though, and Java would not be my first choice for writing extensions if R and/or JS alternatives are available. --t On Jan 4, 2013, at 3:58 PM, Michael Lawrence <lawrence.michael@gene.com> wrote: > The visnab package has different goals from IGV. It aims to provide an extensible, R-based platform for interactive genomic visualization. Currently, IGV isn't very extensible at all, i.e., no plugin support, some nice scripting capabilities via its HTTP interface but no callback handling. We decided to focus our energy on ggbio for a while, but Tengfei is still very much interested in pushing visnab forward. It is currently implemented on top of the R/Qt interface. One idea that has been floated is a port to the web browser, while retaining R callback support, via something like shiny. Over the holidays, I started porting the qtpaint API to javascript and the HTML5 canvas. So the foundations are forming. > > Michael > > > > On Fri, Jan 4, 2013 at 3:17 PM, Tim Triche, Jr. <tim.triche@gmail.com> wrote: >> IGV would seem to have obsoleted some aspects of visnab. >> >> ggbio, on the other hand, is awesome, as is Gviz. Perhaps those may meet >> your needs? Tengfei has certainly been pouring effort into ggbio, and Gviz >> is also released. the two are complementary IMHO >> >> >> >> >> On Fri, Jan 4, 2013 at 2:41 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: >> >> > Hi Abhishek, >> > >> > On Fri, Jan 4, 2013 at 2:32 PM, Abhishek Pratap <apratap@lbl.gov> wrote: >> > > I saw an old note to myself that I wrote a while ago to check on >> > > visnab...and I dont see it as part of bioC as of now. Can anyone who is >> > > aware of the developments give me an update on the status of the >> > package. I >> > > am interested in playing with it. >> > >> > According to this github page: >> > >> > https://github.com/tengfei/visnab/wiki/Installation-Instruction >> > >> > visnab is not released to BioC yet. >> > >> > Perhaps Tengfei can give us a further status update. >> > >> > Dan >> > >> > >> > >> > >> > > >> > > Thanks! >> > > -Abhi >> > > >> > > [[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 >> > >> >> >> >> -- >> *A model is a lie that helps you see the truth.* >> * >> * >> Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> >> >> [[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]]

Hi Thanks a lot for all the clarification, suggestions and reference above and sorry for the late reply. Frankly speaking, I haven't been working on visnab for a while... and have been working on ggbio and some other projects at school recently, but does plan to get visnab on bioconductor eventually. It's experimenting and prototyping on some new packages and ideas, e.g. Michael's MutableRanges package, qt interface and the idea on the web, we had lots discussion on infrastructure too, it does involve lots of work on it. I cannot promise anything yet, but I will definitely devote more time this year on it and work closely with Michael, try to get the prototyped package out in bioconductor for you to try . For installation, you probably cannot get it run normally for now even you install all the dependencies manually, due to some upgrade in bioc, there are some known issues in visnab and related package waiting to be fixed. Anyway, thanks again for your interests in visnab, we will keep the list updated on this. Tengfei On Fri, Jan 4, 2013 at 5:58 PM, Michael Lawrence <lawrence.michael@gene.com>wrote: > The visnab package has different goals from IGV. It aims to provide an > extensible, R-based platform for interactive genomic visualization. > Currently, IGV isn't very extensible at all, i.e., no plugin support, some > nice scripting capabilities via its HTTP interface but no callback > handling. We decided to focus our energy on ggbio for a while, but Tengfei > is still very much interested in pushing visnab forward. It is currently > implemented on top of the R/Qt interface. One idea that has been floated is > a port to the web browser, while retaining R callback support, via > something like shiny. Over the holidays, I started porting the qtpaint API > to javascript and the HTML5 canvas. So the foundations are forming. > > Michael > > > > On Fri, Jan 4, 2013 at 3:17 PM, Tim Triche, Jr. <tim.triche@gmail.com> >wrote: > > > IGV would seem to have obsoleted some aspects of visnab. > > > > ggbio, on the other hand, is awesome, as is Gviz. Perhaps those may meet > > your needs? Tengfei has certainly been pouring effort into ggbio, and > Gviz > > is also released. the two are complementary IMHO > > > > > > > > > > On Fri, Jan 4, 2013 at 2:41 PM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > > > > > Hi Abhishek, > > > > > > On Fri, Jan 4, 2013 at 2:32 PM, Abhishek Pratap <apratap@lbl.gov> > wrote: > > > > I saw an old note to myself that I wrote a while ago to check on > > > > visnab...and I dont see it as part of bioC as of now. Can anyone who > is > > > > aware of the developments give me an update on the status of the > > > package. I > > > > am interested in playing with it. > > > > > > According to this github page: > > > > > > https://github.com/tengfei/visnab/wiki/Installation-Instruction > > > > > > visnab is not released to BioC yet. > > > > > > Perhaps Tengfei can give us a further status update. > > > > > > Dan > > > > > > > > > > > > > > > > > > > > Thanks! > > > > -Abhi > > > > > > > > [[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 > > > > > > > > > > > -- > > *A model is a lie that helps you see the truth.* > > * > > * > > Howard Skipper< > > http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> > > > > [[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]] > > _______________________________________________ > 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 > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 [[alternative HTML version deleted]]