[Biopython] Genome browser for BioPython annotations

[Peter Cock]

This sounds a bit like the GSoC 2014 GenomeDiagram project idea:

http://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas#Interactive_GenomeDiagram_Module

> Interactive GenomeDiagram Module
>
> Rationale:
> The GenomeDiagram genome/comparative genomics visualisation module currently
> produces static images (bitmap format), or images with relatively limited interactive
> capability such as click-throughs (.pdf, .svg). This is fine for its original intent of producing
> publication-quality graphics, but interactivity such as dynamic formatting, data selection,
> and box-outs would greatly enhance the value of the existing visualisations, and enable
> new uses.
>
>  Approach & Goals:
> The [http://bokeh.pydata.org/ Bokeh] interactive visualisation library uses the standalone
> [http://bokeh.pydata.org/dev_guide.html BokehJS] backend for in-browser visualisation.
> Targeting BokehJS with GenomeDiagram ought to be possible.
>
>  Difficulty and needed skills:
>  Looks tricky to me. Introduction of BokehJS brings dependencies that may not be
> desirable for Biopython. BokehJS is in Coffeescript - the Python interface is not well
> documented. Familiarity with Javascript would be very useful.
>
>  Possible Mentors:
>  Leighton Pritchard though I'd be learning as much as the student, so others very welcome.


Peter

On Wed, Apr 26, 2017 at 3:01 PM, Spencer Bliven
<spencer.bliven at gmail.com> wrote:
> I'm trying to compare sequence annotations from a few sources. I'm currently
> displaying the annotations as different tracks in a GenomeDiagram. However,
> I occasionally need single-base resolution, and I'm not aware of any options
> in GenomeDiagram for displaying the sequence. It would also be nice to have
> some user interaction (zooming, toggling tracks, etc), e.g. as a jupyter
> widget.
>
> My ideal would be a html/javascript genome browser that had been wrapped up
> as a jupyter widget and would accept SeqRecord objects as the datasource and
> display any SeqFeatures. There appears to be a project based off BioJulia to
> display the Dalliance browser
> (https://github.com/BioJulia/Dalliance.jl/blob/master/src/Dalliance.jl), but
> dalliance isn't really suited for light-weight visualization. Is anyone
> aware of similar projects for BioPython? Are there other tools that might be
> useful in visualizing the positions of SeqFeatures at a detailed level?
>
> BTW, I was a bit surprised at how much code it took to add BioPython objects
> to a GenomeDiagram. No doubt this is due to the package history. Would there
> be interest in tighter integration of GenomeDiagram into BioPython?
>
> -Spencer
>
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