[BioRuby] searching through large sets of features

[Jan Aerts]

That is a _really_ good resource. Unfortunately, R-Trees are not in there
(or I didn't look well enough). I was thinking of sending him an email to
ask if he could quickly add that to his library :-), but saw that he's
switching to python. (But that particular announcement was on the 1st of
April, so let's hope it's a joke)
j.

2009/4/10 Michael Barton <mail at michaelbarton.me.uk>

> There's also some ruby searching algorithms here
> http://algorithms.rubyforge.org/
>
> I'm happy to try and help if I can
>
> Cheers
>
> Mike
>
> 2009/4/10 Michael Barton <mail at michaelbarton.me.uk>
>
> > Would a bloom tree fit this problem?
> >
> http://www.igvita.com/2008/12/27/scalable-datasets-bloom-filters-in-ruby/
> >
> > 2009/4/10 Jan Aerts <jan.aerts at gmail.com>
> >
> > Hi all,
> >> I need to be able to handle millions of features for a visualization and
> >> therefore be able to search through them efficiently. I've been made
> aware
> >> of a so-called R-Tree (http://en.wikipedia.org/wiki/R-tree) data
> >> structure
> >> that could do just that. One of the issues that this approach would
> solve
> >> is
> >> that it doesn't need to load every single feature when the display
> >> resolution is not high enough (no use trying to plot 5 million points
> next
> >> to each other on a screen of 800 pixels wide; you can only plot 800
> >> points....)
> >>
> >> I'm now trying to write a ruby-implementation of an R-Tree that is more
> >> fit
> >> for loci (i.e. one less dimension than an R-Tree, and has to handle
> >> chromosome as well) at http://github.com/jandot/locustree. I'm trying
> to
> >> make it a module that can be mixed in, so anything which has a
> chromosome,
> >> start and stop can be indexed and searched using this R-Tree adaptation.
> >>
> >> Does anyone know a ruby-implementation of R-Tree? Or is anyone
> interested
> >> in
> >> helping me out?
> >>
> >> Thanks,
> >> jan.
> >> _______________________________________________
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >>
> >
> >
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>