[RASMB] SedAnal: Sedimentation Velocity Analysis package called SedAnal

Thu Oct 17 15:09:01 PDT 2002

Walter,
      Thank you very much for this information.   I consider myself a novice to
average user of the XL-A and have had the instrument for about 8 years.  What I
find most difficult to understand about this technique is the large variety of
software available for data analysis.  It is all very confusing.  At the present
time I am using Peter Schuck's Sedfit but I have also used John Philo's and
Borries Demeler's software.  I have learned the ins and outs of these analysis
packages and what they can do for me and what they can't but it took a lot of
time.
      Why should I try out SedAnal?  Let me put it a different way, why was
SedAnal written?  The implication is that there are failings in the other
software that this new software will address.  What are these failings and are
they relevant to someone like me?  Should I spend a considerable amount of time
I don't really have to try SedAnal out?
      Please do not misinterpret my email...I am not being critical of anyone
and in fact think it is wonderful to have such variety.  I have found to my
pleasure that the members of the AUC community are truly 'salt of the earth
people'.  The problem perhaps I am trying to articulate is the lack of say a
'Consumer's Reports' in which software is 'peer reviewed' and the plus and
minuses of each described.   This report or publication would recommend software
for the typical user with the typical applications.  Such a comparison would be
a tremendous boon to the community!
      Thanks!
      Jim Bloom

                      Walter Stafford                                                                          
                      <stafford at bbri.org>          To:       rasmb at rasmb-email.bbri.org                        
                      Sent by:                     cc:                                                         
                      rasmb-admin at rasmb-ema        Subject:  [RASMB] SedAnal: Sedimentation Velocity Analysis  
                      il.bbri.org                   package called SedAnal                                     

                      10/17/2002 10:17 AM                                                                      

Dear RASMBers;
        A new software package called SedAnal has been developed at BBRI and has
been made available on the RASMB FTP archive site.

SedAnal will perform curve fits to sedimentation velocity data obtained from
interacting (and non-interacting) systems. It can fit for sedimentation
coefficients, molecular weight. loading concentrations and equilibrium
constants. It is capable of  fitting up to 3 thermodynamic components, and up to
7 species  related by up to 6 chemical reactions. It can fit globally data from
up to 5 cells, simultaneously.  It runs under Windows98 and has an easy to use
graphical user interface. It is accompanied by a User's Manual.

It fits to time difference data to eliminate time-independent,
radially-dependent systematic noise completely. It has a preprocessor section
that allows choice of the meniscus and base positions as well as the radial
range of data to use for fitting. The preprocessor allows essentially complete
removal of radially-independent, time-dependent optical "jitter" and correction
for  integral fringe shifts associated with interference data.

The package contains a Model Editor that allows the user to develop a database
of reaction schemes which can be used to fit the data.

The fitting section ( Control Screen) allows the user to choose one of the
models, select and enter initial values for the parameters to be fit (or held)
and select the cells to be combined for global fitting.

The model editor allows one to create various reaction schemes ranging from a
single-component, single-species system (i.e. no interactions) to a
single-component, 2 species system (e.g.. simple monomer, n-mer
self-association, 2A=A2), to a 3 component, 3 species system (i.e. simple
complex formation of the type A + B = C), a 2 component, 4 species system (i.e.
simple complex formation with self association of one of the reactants or the
complex (e.g. A+B=C; 2A=A2), a 2 component, 4 species system like an
antigen-antibody reaction (e.g. A+B=C;C+B=D) and so on.
The current version of SedAnal can handle up to 3 components, 7 species and 6
chemical reactions  in any combination consistent with the constraint that
Number_of_components = number_of_species - number_of_chemical_reactions, of
course. (This is probably more than one should ever dare to use without some
prior knowledge). Isodesmic self-association will be handled in a future
version.

The Control Screen also allows the user to generate synthetic data using any of
the models.
The internal routine uses numerical solutions to the Lamm equation solved using
Claverie's finite-element method. Mass action is accounted for by various
kinetic schemes and is solved internally by the Bulirsch-Stoer differential
equation solver routine. Least squares minimization is done by the Simplex
method of Nelder and Mead.

There is an user's manual in PDF format. The manual is fairly extensive and
still evolving.

The software/documentation package can be downloaded from the RASMB FTP archives
at

ftp://rasmb.bbri.org/rasmb/spin/ms_dos/sedanal-stafford/
The zip archive contains the user manual, the model editor, an example Model
database file, Sedanal.exe, which is the interface to the Preprocessor and the
Fitter Control Screen. Please read the README file and the user's manual first.
AND take note of the mandatory directory structure. The unzipping process should
put everything into the correct directory tree structure.

There is a separate email discussion group at
http://www.rasmb.bbri.org/mailman/listinfo/sedanal
for those who want to discuss the more arcane aspects of using SedAnal without
cluttering up the RASMB email list.

--
-------------------------------------------------------------------------------------------------------
Walter Stafford
mailto:stafford at bbri.org
direct dial:    617-658-7808
receptionist: 617-926-8040