[BiO BB] doing clustering based on similarity matrix

[Mike Marchywka]

I was going to post this earlier, essentially suggesting the same source
but also pointing out that the source code is available ( as a programmer,
that is my answer to everything, see comments below).

>From time to time, I end up reinventing a wheel ( for instance, after I
started moving clustalw to c++ the authors released their own c++ version 
and
I just wrote another xml parser... ). If you can post links to the existing 
art and an
input format, I may be able to adapt something I have and you can 
simultaneously
make your request more informative for everyone and avoid responses
regarding things you've already examined.

While I haven't looked lately, I was doing document clustering earlier and 
found many
packages available with source code ( you can adapt it as you like). Oddly 
enough,
I ended up using gene expression software to cluster documents as you
can make document properties look like expression amounts.

As I illustrated earlier, you can do proof of concept of novel clustering 
ideas in perl/bash scripts
with limited "real" code.

I think I used the treeview software related to this, as one example:

http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv

"People that want to make use of the clustering algorithms in their own C, 
C++, or Fortran programs can download the source code of the C Clustering 
Library. "



Mike Marchywka
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here. Thanks.





>From: "Tomer Handelman" <tomer.handelman at gmail.com>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: Re: [BiO BB] doing clustering based on similarity matrix
>Date: Mon, 3 Sep 2007 11:12:32 +0300
>
>I checked it out,
>it recieves only raw data and creates the matrix by itself .
>thanks anyway,
>Tomer
>
>
>
>2007/9/3, Iddo Friedberg <idoerg at gmail.com>:
>
> > Have you tried Michiel de Hoon's OS Cluster package?
> >
> > http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/index.html
> >
> > Iddo
> >
> > On 9/2/07, Tomer Handelman <tomer.handelman at gmail.com> wrote:
> > >
> > > hello all,
> > > I'm looking for a piece of software that will allow me to do 
>clustering
> > > based on a given similarity matrix and not on raw data from Micro
> > arrays.
> > > everything I found so far works only on raw data...
> > >
> > > thanks in advance,
> > > Tomer
> > > _______________________________________________
> > > General Forum at Bioinformatics.Org -
> > > BiO_Bulletin_Board at bioinformatics.org
> > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> > >
> >
> >
> >
> > --
> >
> > I. Friedberg
> >
> > "The only problem with troubleshooting is that
> > sometimes trouble shoots back."
> > _______________________________________________
> > General Forum at Bioinformatics.Org -
> > BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
>_______________________________________________
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