Tengfei Yin | 5 Jan 01:26 2013
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Re: status of visnab

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@...>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@...
> >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@...>
> wrote:
> >
> > > Hi Abhishek,
> > >
> > > On Fri, Jan 4, 2013 at 2:32 PM, Abhishek Pratap <apratap@...>
> 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]]
> > > >
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> >
> >
> > --
> > *A model is a lie that helps you see the truth.*
> > *
> > *
> > Howard Skipper<
> > http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
> >
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--

-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274

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