[Bioclusters] RE: Bioclusters digest, Vol 1 #305 - 7 msgs

WILSON GREGORY bioclusters@bioinformatics.org
Tue, 15 Jul 2003 13:42:29 -0400


Thank you, it was timely

-----Original Message-----
From: bioclusters-request@bioinformatics.org
[mailto:bioclusters-request@bioinformatics.org] 
Sent: Tuesday, July 15, 2003 12:02 PM
To: bioclusters@bioinformatics.org
Subject: Bioclusters digest, Vol 1 #305 - 7 msgs

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Today's Topics:

   1. Re: looking into workstations for bioinformatics: visualization
       software for Linux (Cliff Miller)
   2. Re: hello we are also looking into workstations for
       bioinformatics (Doug Shubert)
   3. Re: Re: looking into workstations for bioinformatics:
       visualization software for Linux (Andrew Shewmaker)
   4. visualization software for Linux (Joseph Landman)

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Message: 1
Date: Tue, 15 Jul 2003 09:52:04 +0900
From: Cliff Miller <cliff@mountainviewdata.com>
To: <bioclusters@bioinformatics.org>
Subject: [Bioclusters] Re: looking into workstations for bioinformatics:
visualization
 software for Linux
Reply-To: bioclusters@bioinformatics.org

On 030715 1:01, "bioclusters-request@bioinformatics.org"
<bioclusters-request@bioinformatics.org> wrote:

> From: WILSON GREGORY <GREGORY.WILSON@hamptonu.edu>
> To: "'bioclusters@bioinformatics.org'" <bioclusters@bioinformatics.org>
> Date: Mon, 14 Jul 2003 10:48:05 -0400
> Subject: [Bioclusters] hello we are also looking into workstations for
> bioinformatics
> Reply-To: bioclusters@bioinformatics.org
> 

...

> I am also trying to get good but cheap visualization software to work with
> Linux,most is quite expensive. Could you tell what your university is
using?

You might take a look at Sci-run, available for download at the Scientific
Computing and Imaging Institute:

  http://www.sci.utah.edu/
  http://software.sci.utah.edu/scirun-biopse_1_10.html

Cliff Miller
Mountain View Data
www.mountainviewdata.com


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Message: 2
Date: Tue, 15 Jul 2003 08:23:39 -0400
From: Doug Shubert <doug@accessgate.net>
To: bioclusters@bioinformatics.org
Subject: Re: [Bioclusters] hello we are also looking into workstations for 
 bioinformatics
Reply-To: bioclusters@bioinformatics.org


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WILSON GREGORY wrote:

> I saw your entry and wondering if ever decided on what workstation(s)
> for end users of your cluster(s). I noticed Dell mentioned but I
> thought Sun systems would be better. I am also considering Apple Mac
> OSx workstations. If you have any ideas on this could you please send
> some information? Thank you.
>
> I am also trying to get good but cheap visualization software to work
> with Linux,most is quite expensive. Could you tell what your
> university is using?
>

if you are visulising MD, VMD works great on Linux.

--------------
What is VMD?  See also http://www.ks.uiuc.edu/Research/vmd/

VMD is designed for the visualization and analysis of biological
systems such as proteins, nucleic acids, lipid bilayer assemblies,
etc.  It may be used to view more general molecules, as
VMD can read standard Protein Data Bank (PDB) files and display the
contained structure.  VMD provides a wide variety of methods for
rendering and coloring molecule.  VMD can be used to animate and analyze

the trajectory of molecular dynamics (MD) simulations, and can
interactively manipulate molecules being simulated on remote computers
(Interactive
MD).
--------------

-Doug



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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
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&nbsp;
<p>WILSON GREGORY wrote:
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<div class=Section1>
<div class="MsoNormal"><span style='font-size:10.0pt;
font-family:Arial'><font face="Arial"><font size=-1>I
saw your entry and wondering if ever decided on what workstation(s) for
end users of your cluster(s). I noticed Dell mentioned but I thought Sun
systems would be better. I am also considering Apple Mac OSx workstations.
If you have any ideas on this could you please send some information? Thank
you.</font></font></span></div>


<p class="MsoNormal"><span style='font-size:10.0pt;
font-family:Arial'></span>

<p class="MsoNormal"><span style='font-size:10.0pt;
font-family:Arial'><font face="Arial"><font size=-1>
I am also trying to get good but cheap visualization software to work with
Linux,most is quite expensive. Could you tell what your university is
using?</font></font></span></div>
</blockquote>

<p><br>if you are visulising MD, VMD works great on Linux.
<p>--------------
<br>What is VMD?&nbsp; See also <A
HREF="http://www.ks.uiuc.edu/Research/vmd/">http://www.ks.uiuc.edu/Research/
vmd/</A>
<p>VMD is designed for the visualization and analysis of biological
<br>systems such as proteins, nucleic acids, lipid bilayer assemblies,
<br>etc.&nbsp; It may be used to view more general molecules, as
<br>VMD can read standard Protein Data Bank (PDB) files and display the
<br>contained structure.&nbsp; VMD provides a wide variety of methods for
<br>rendering and coloring molecule.&nbsp; VMD can be used to animate and
analyze
<br>the trajectory of molecular dynamics (MD) simulations, and can
<br>interactively manipulate molecules being simulated on remote computers
(Interactive
<br>MD).
<br>--------------
<p>-Doug
<br>&nbsp;
<br>&nbsp;
</body>
</html>

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--__--__--

Message: 3
Date: Tue, 15 Jul 2003 07:39:30 -0600
From: Andrew Shewmaker <shewa@inel.gov>
To: bioclusters@bioinformatics.org
Subject: Re: [Bioclusters] Re: looking into workstations for bioinformatics:
 visualization software for Linux
Reply-To: bioclusters@bioinformatics.org

I don't know if anyone has ever used it for biology datasets,
but from what I have seen ViSit is very capable.

http://www.llnl.gov/VisIt/home.html

Andrew

-- 
Andrew Shewmaker, Associate Engineer
Phone: 1-208-526-1276
Idaho National Eng. and Environmental Lab.
P.0. Box 1625, M.S. 3605
Idaho Falls, Idaho 83415-3605


--__--__--

Message: 4
From: Joseph Landman <landman@scalableinformatics.com>
To: biocluster <bioclusters@bioinformatics.org>
Date: 15 Jul 2003 10:16:34 -0400
Subject: [Bioclusters] visualization software for Linux
Reply-To: bioclusters@bioinformatics.org

For full blown visualization, have a look at

	OpenDX:   http://www.opendx.org
	Khoros:	  http://www.khoral.com/khoros/
	AVS:	  http://www.avs.com/

for basic visualization/plotting have a look at

	Matlab,
	Octave		http://www.octave.org	
	gnuplot,XMGR,etc...
	MayaVI		http://mayavi.sourceforge.net/
	


for molecular/genomic visualization have a look at

	Artemis:	http://www.sanger.ac.uk/Software/Artemis/
	VMD:		http://www.ks.uiuc.edu
	Dino3d:		http://cobra.mih.unibas.ch/dino/
	Ghemical:	http://www.uku.fi/~thassine/ghemical/
	PyMood:		http://allometra.com/	
	ViewMol:	http://viewmol.sourceforge.net/
	
for API's...

	VTK:		http://public.kitware.com/VTK/

and then the symbolic math environments which can usually link to nice
visual packages

	Mathematica	http://www.wolfram.com
	Maxima		http://maxima.sourceforge.net/
	Maple		http://www.maplesoft.com/

...


On Tue, 2003-07-15 at 09:39, Andrew Shewmaker wrote:
> I don't know if anyone has ever used it for biology datasets,
> but from what I have seen ViSit is very capable.
> 
> http://www.llnl.gov/VisIt/home.html
> 
> Andrew
-- 
Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman@scalableinformatics.com
  web: http://scalableinformatics.com
phone: +1 734 612 4615




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