[RASMB] UltraScan 9.4 released

Borries Demeler demeler at biochem.uthscsa.edu
Sat Oct 20 08:01:41 PDT 2007


------------------------------- ANNOUNCEMENT -------------------------------

Dear Colleagues,

I am happy to announce the release of UltraScan ver. 9.4.  There are a
few new features and a number of changes. 

The USLIMS now supports fitting 2-dimensional spectrum analyses and
genetic algorithm analyses with molecular weight constraints, including
the Monte Carlo versions. The display and reporting routines in UltraScan
have been updated to accommodate the results from the new methods.

All compute intensive calculations are now multi-threaded for maximum
performance on multi-processor/multi-core architectures. This affects
global equilibrium fitting, finite element calculations and pseudo-3d
plot visualization routines. You need to set the number of threads to the
number of processors in the configuration section of UltraScan.

For windows users, we now include a VMWare image and the free vmware player,
allowing you to run a Linux version of UltraScan under Windows (NT, win2k, 
XP and Vista).

I have also added a program to support density calculations from the Anton
Paar densitometer, handling calibration and acquisition of density data.

A new utility for generating gradient color maps for use in 3D and 
pseudo-3D graphs is now included. 

Rendering of 3D plots in the finite element model viewer has been much
improved, providing more control over the image and improving resolution.

There have also been changes in the modules for storing vbar, density,
viscosity, extinction coefficient and refractive index information. The
LIMS now supports entries of partial specific volumes and extinction
coefficients that are not tied to the calculation of a peptide sequence
(for non-peptide polymers) as well as manually entered densities,
viscosities and refractive indices.

The new version can be downloaded from:

http://www.ultrascan.uthscsa.edu (select the "Download" tab)

Currently, we support the following versions natively:

	* AMD/Intel 32-bit: Linux, Mac OS-X, Windows (VMWare Image), FreeBSD,
	  NetBSD, and a CDROM Image of complete UltraScan Linux system

	* AMD/Intel 64-bit: Linux

	* Macintosh G3/G4/PPC: Linux, OS-X

	* VMWare Image of complete UltraScan Linux system (platform Independent)

Unix versions for Sun Solaris, AIX, HPUX, and Silicon Graphics Irix
are available upon request.

The USLIMS can be accessed from:

http://uslims.uthscsa.edu

(Let me know if you need an UltraScan LIMS portal account and 
remote supercomputing access)

******************************************************************************************

Upgrade notes:

For Linux Slackware users, users of the Linux UltraScan CDROM distro, and
for users of older versions of the VMWare image there is no need to download
the new version from our website. Instead, use swaret to upgrade your current version:

Include this line in /etc/swaret.conf:

ROOT=ftp://ftp.biochem.uthscsa.edu/pub/linux/slackware/slackware-$VERSION

then issue:
swaret --update
swaret --upgrade

Answer "Y" for the UltraScan 9.4 upgrade.

For Mac OS-X users, you need to have Fink and X11 installed, and then you
can update your version as follows:

If you have a Power PC based Mac add these two (2) lines to the bottom
of /sw/etc/apt/sources.list:

deb http://ultrascan.uthscsa.edu/fink-ppc stable main crypto
deb http://ultrascan.uthscsa.edu/fink-ppc local main

If you have an Intel based Macintosh add these three (3) lines to the bottom
of /sw/etc/apt/sources.list:

deb http://ultrascan.uthscsa.edu/fink-intel stable main crypto
deb http://ultrascan.uthscsa.edu/fink-intel unstable main crypto
deb http://ultrascan.uthscsa.edu/fink-intel local main

For first time installations

You will need to retrieve the UltraScan Fink packages (as well as the
related Fink packages that are required for UltraScan to work correctly)
from our server by issuing these commands:

sudo apt-get update
sudo apt-get install qt3
sudo apt-get install qwt
sudo apt-get install qwtplot3d
sudo apt-get install mysql14-shlibs
sudo apt-get install ultrascan
 
To upgrade to a newer version of Ultrascan, from a terminal issue only these
commands:

sudo apt-get update
sudo apt-get install ultrascan 

For all questions, please contact me directly.

Regards, -Borries
---
Borries Demeler, Ph.D.
Assistant Professor
The University of Texas Health Science Center at San Antonio
Dept. of Biochemistry, MC 7760
7703 Floyd Curl Drive, San Antonio, Texas 78229-3901
Voice: 210-567-6592, Fax: 210-567-1136, Email: demeler at biochem.uthscsa.edu



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