[RASMB] daat analysis tools for sedimentation velocity experiments

Hayes, David HayesD at MedImmune.com
Mon Dec 21 08:15:14 PST 2009


Hi Kancha,

The choice of the best analysis software depends on what scientific
questions you are asking.

For quick quantitative analysis of aggregates, usually SEDFIT (written
by Peter Schuck) c(s) is used.  It is available at
http://www.analyticalultracentrifugation.com/default.htm.

John Philo has some analysis programs available that are very user
friendly and also seem to be used widely in industry.
http://www.jphilo.mailway.com 



For fitting interacting systems and more complicated analyses (usually
more in an academic setting, but becoming more and more important to
industry also) I prefer SEDANAL (written by Walter Stafford) which is
available on the RASMB software archive.
http://rasmb.bbri.org/software/windows/sedanal-stafford/

The program SEDPHAT (by Peter Schuck) also does more complicated
analyses for many interacting models and is available at 
http://www.analyticalultracentrifugation.com/sedphat/default.htm

Borries Demeler also has a comprehensive program suite called UltraScan.
I have not been a frequent user of ultrascan, but have seen
demonstrations that indicate is has some definite strengths for some
types of analysis and the integrated SOMO bead modeling program is
highly recommended if you would like to play with predicting
hydrodynamics from crystal structures.

http://www.cauma.uthscsa.edu/




AUC data analysis is a fairly sophisticated and mature branch of
practical mathematics.  An understanding of AUC instrument design and
use as well as careful experimental design are absolutely necessary for
successfully finding reliable hydrodynamic information from AUC
experiments.  I recommend reading the literature (search for papers by
Walter Stafford, John Philo, Peter Schuck, and Borries Demeler and don't
forget to drill down to the more classic papers by Yphantis and others:
you may have to actually go to a library for the classic thermodynamic
texts, many are not available online as yet). If possible, seek out some
training.  All of the software programmers mentioned show up for and/or
run training sessions.  Borries Demeler makes his sessions available by
a free internet teleconferencing system.

David Hayes
MedImmune, Gaithersburg MD



-----Original Message-----
From: rasmb-bounces at rasmb.bbri.org [mailto:rasmb-bounces at rasmb.bbri.org]
On Behalf Of Kanchan Gupta Phd Batch 2006 Cell Bio R.P.Roy
Sent: Monday, December 21, 2009 9:56 AM
To: rasmb at server1.bbri.org
Subject: [RASMB] daat analysis tools for sedimentation velocity
experiments

hi

i'm a beginner and wanted to know the software and data analysis tools 
available online to analyze the data for a sedimentation velocity
experiment 
from a XL-i system.

Kanchan Gupta
Research Scholar
Cell Biology Lab-II
National Institute of Immunology
Aruna asaf ali marg
New Delhi-110067

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