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 Send Bioclusters mailing list submissions to bioclusters@bioinformatics.org To subscribe or unsubscribe via the World Wide Web, visit https://bioinformatics.org/mailman/listinfo/bioclusters or, via email, send a message with subject or body 'help' to bioclusters-request@bioinformatics.org You can reach the person managing the list at bioclusters-admin@bioinformatics.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioclusters digest..." 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) --__--__-- 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 --__--__-- 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 --------------BD0CB8C9532F000EB3FD7BBB Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 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 --------------BD0CB8C9532F000EB3FD7BBB Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit <!doctype html public "-//w3c//dtd html 4.0 transitional//en"> <html> <body link="#0000FF" vlink="#800080" lang="EN-US"> <p>WILSON GREGORY wrote: <blockquote TYPE=CITE><style> <!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; margin-bottom:.0001pt; font-size:12.0pt; font-family:"Times New Roman";} a:link, span.MsoHyperlink {color:blue; text-decoration:underline;} a:visited, span.MsoHyperlinkFollowed {color:purple; text-decoration:underline;} span.EmailStyle17 {font-family:Arial; color:windowtext;} @page Section1 {size:8.5in 11.0in; margin:1.0in 1.25in 1.0in 1.25in;} div.Section1 {page:Section1;} --> </style> <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? 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. 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. VMD provides a wide variety of methods for <br>rendering and coloring molecule. 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> <br> </body> </html> --------------BD0CB8C9532F000EB3FD7BBB-- --__--__-- 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 --__--__-- _______________________________________________ Bioclusters maillist - Bioclusters@bioinformatics.org https://bioinformatics.org/mailman/listinfo/bioclusters End of Bioclusters Digest