Changelog File for UltraScan 5.0 -> 6.0
Please mail demeler@biochem.uthscsa.edu if you know of any bugs or
if you are missing a feature which isn't listed here.
Bug Fix:
us_velocreport.cpp: Module fails to compile on certain platforms, moved
code segment from constructor to separate function - seems to fix it.
Bug Fix:
us_minimize.cpp: Changed filename for help file to nls.html (same
as fit_ctrl.html)
New Feature:
finite1.cpp: Eliminated positive constraint for S to allow for
fitting of floating material.
Bug Fix:
us_rundetails.cpp: fields for wavelengths/scans positions 2 and 3 were
not automatically blanked and reset, this is now fixed.
New Feature:
us_eqmodelctrl.cpp: Added loading of pre-fitted extinction profiles
without the need to regenerate profile each time.
New Feature:
us_extinction.cpp: Added feature to delete already loaded scans from
project before fitting is enabled
New Feature:
simwin.cpp: Added a dc/dt monitor to the finite element simulation
program to allow user to determine more easily when equilibrium is
reached.
New Feature:
simwin.cpp: Added feature to change speed during finite element
simulation for single component, equilibrating and isomerizing models.
Bug Fix:
usglobalequil.cpp: Added check to make sure initialization isn't
performed when no scans are available
New Feature:
usglobalequil.cpp: Scans can now be selected before initialization
Bug Fix:
usglobalequil.cpp: Changes in the active scanlist now automatically
requires a new initialization of the fitting variables. This will
prevent crashes.
New Feature:
usglobalequil.cpp: Reworked initialization routine to provide a
much improved initialization of fitting parameters by using a
one dimensional line search over the monomer molecular weight
and using general linear least squares for amplitude and baseline.
New Feature:
us_eqfitter.cpp: First stage fitting in multi-component self-
associating models is not required for monomer-dimer association
and has been eliminated because of improved monomer MW estimation
during initialization.
New Feature:
us_minimize.cpp: Added Quasi-Newton nonlinear least squares fitting
algorithm with BFGS updating and custom line search
New Feature:
usglobalequil.cpp: Initialization provides option to use MW in the
model control window as base for the initialization or to calculate
new estimate
New Feature:
us_config.cpp: Added width and hight dimensions of 6-channel centerpiece
sector dimensions. This will be used in the total mass integral
calculations in the global equilibrium fitting module.
Bug Fix:
usglobalequil.cpp: Modified the button logic to assure proper
updating of arrays and vectors if changes are made to selected
scans.
Bug Fix:
usglobalequil.cpp: Modified the initialization of scans so that
scans can be selected even before the arrays are initialized.
Adjusted the button logic accordingly.
Bug Fix:
usglobalequil.cpp, us_eqfitter.cpp: if scan range is changed after
fitting has completed, the fitting window will close to force an
update of array bounds for applicable vectors and arrays
Bug Fix:
finite1.cpp: Fixed an initialization bug that could cause crashes
after the program had received a new model control configuration
New Feature:
UltraScan: Upgraded namespace to be consistent with us_ prefix to
each module.
New Feature:
UltraScan: Upgraded UltraScan to be compatible with the QT-3.x
library
New Feature:
UltraScan: Changed UltraScan into a dynamically loadable library
and wrote wrapper programs for various functions.
New Feature:
us_win.cpp: converted function calls into QProcess() calls to
allow parallel and multi-threaded processing of individual
modules in UltraScan.
New Feature:
us_font.cpp: Added font selection support for UltraScan
New Feature:
UltraScan: added centerpiece database support to
UltraScan to allow definition and run-time selection of
centerpiece properties. Those properties include: number
of channels, material, bottom of channel(s), geometry of
channel (circular, rectangular, sector shaped, synthetic),
radius/width/angle of channel, pathlength and a unique serial
number for each make and model ever to be used in the XLx
New Feature:
UltraScan: added rotor database support to allow run-time calculation
of rotor stretching and meniscus/bottom of cell displacement.
New Feature:
UltraScan: added translation classes to all of UltraScan to allow
for generation of translation tables for internationalization of
UltraScan
Bug Fix:
us_win.cpp, us_util.cpp, us_config.cpp: Fixed initialization bug for
loading .usrc from old versions.
Bug Fix:
us_globalequil.cpp: Forced re-initialization if scan has been deleted
or added to fit
Bug Fix:
us_eqfitter.cpp: Fixed runs and runs statistics not being calculated
or calculated incorrectly
New Feature:
added feature to allow inversion of sign for improperly loaded samples
New Feature:
allow for loading of intensity scans under estinction modelling program
Bug Fix:
us_selectmodel10.cpp: Fixed bug that caused model selection to crash
program for user-defined monomer-N-mer system.
Bug Fix:
us_globalequil.cpp: Fixed bug that caused crash when speeds where checked
from run detail window
New Feature:
us_combine.cpp: X limits can now be manually defined, and arbitrary
distributions can be removed from the list.
New Feature:
us_simwin.cpp: Added capability of exporting scans in XLA format
New Feature:
us_merge.cpp: Added new utility that allows re-ordering and merging of
scanfiles from different directories.
New Feature:
us_vhwdat.cpp: Added calculation of initial concentration from
extrapolation to t=0 and using plateau absorbance. Only stable
plateau scans can be included
New Feature:
us_vhwdat.cpp: Added function to automatically generate an input
model for finite element fits from vHW data when groups are defined.
partial concentrations and S-values are estimated, Diffusion coefficients
and v-bar values need to be double-checked before fitting. Other parameters
are assumed.
Bug Fix:
us_edit.cpp: when accidentally clicking on excluding range program used
to crash.
Bug Fix:
reorder.cpp: program didn't use to reset memory between loading of different
directories, this is fixed now.
New Feature:
us_config.cpp, us_edit.cpp, us_reorder.cpp: upper/lower case of input
file data doesn't need to be specified any longer, the program can now
figure this out automatically.
New Feature:
us_config.cpp: includes version, if the version doesn't match, a new
configuration file is automatically produced.
New Feature:
us_velocdudmc_t.cpp: added terminal-based beowulf driver for DUD-based
Monte Carlo analysis.
New Feature:
us_dtctrl.cpp/us_win.cpp: Added function to allow copying of edited data to
a new run so multiple distributions can be generated.
Bug Fix:
us_dtactrl.cpp: allowed baseline subtraction from plateau only for
run_type == 1 to prevent plateau value to change between copying, cell-ID changes,
export and printing of edited data
Bug Fix:
us_extinction.cpp: made fitting_widget a global variable which prevents
crashes when closing the fitter.
New Feature:
us_globalequil.cpp: Added a feature which allows the user to choose
between plotting the optical density histogram or the
enxtinction-corrected molar concentration for an absorbance spectrum.
Bug Fix:
us_rundetails.cpp: now correctly sets the caption to velocity for
veloc interference data.
New Feature:
us_edit.cpp: includes the cell description in the plot title for editing
Update:
QWT version 0.4.1 upgrade
New Feature:
us_finite_ad.cpp/us_fitfinite.cpp: Added automatic differentiation-based finite
element fitter
New Feature:
added SQL database support to UltraScan (big one!). Data can now be served and searched
from an online SQL database (Oracle or MySQL) and provide investigator, contents,
description, buffer, protein/DNA information, cell data, wavelength data, diffusion
data, equilibrium and velocity scans, as well as centerpiece and rotor data. Data
can be retrieved based on multiple criteria, incl. investigator, time/date, data type and
experiment type/name/serial number. Ancillary data such as rotor, centerpiece, density,
viscosity, vbar, extinction etc. are automatically updated in velocity and equilibrium
experiments.
New Feature:
us_equil_db.cpp Technician DB upload module: The data acquisition personnel can now
enter the data into the database and provide all ancillary data and prepare it ready
for the investigator's analysis
New Feature:
Windows Win32 Port available (Win 9x/ME/NT/2000/XP) incl. MySQL support
New Feature:
us_win.cpp: user license module provides license keys
New Feature:
us_config.cpp: database login information entry module added
New Feature:
us_equilsim.cpp: new Equilibrium Simulation module allows the simulation of various
models of equilibrium systems for different speeds, concentrations and cell dimensions.
Bug Fix:
us_dtactrl.cpp and us_globalequil.cpp: data loading is not crashing anymore
due to uninitialized rotor database entry.
New Feature:
us_buffer.cpp: All buffer handling instances changed to use the Database version
New Feature:
us_vbar.cpp: All protein/vbar handling instances changed to use the Database version
Bug Fix:
us_buffer_db_tbl.cpp: uninitialized classes in resizeEvent() corrected - no more
crashes.
Update:
All QtMultiLineEdit instances replaced by QTextEdit, QtMultiLineEdit removed from tree
Update:
QtTable support removed from tree since it isn't necessary in QWT anymore.
New Feature:
us_vhwdat.cpp: Added vertical bar to indicate the scan position about to be excluded
in the vhw extrapolation plot
Bug Fix:
us_db_tbl_vbar.cpp, us_vbar.cpp: Fixed bugs in vbar calculation routine:
Now program can handle files that don't have a blank line at the end
and also can handle non-peptide characters in the sequence (i.e.,
numbers and characters not in the peptide alphabet are ignored)
Bug Fix:
us_lncr2.cpp: fixed the molecular weight calculation - only the first speed was used
to calculate a MW for all scans, even if multiple speeds were used.
Bug Fix:
us_dtactrl.cpp: Channel selection listbox is now disabled for experiments that have
less than 2 channels.
Bug Fix:
us_eqfitter.cpp: model calculation for monomer-nmer-mmer updated to correctly
parse the second equilibrium constant
Bug Fix:
us_equilmodelctrl.cpp: when generating new extinction profile, all data are
correctly imported and apply to all available scans.
Bug Fix:
us_reports: All reports now permit canceling out without creating extraneous
files in the root directory
Update:
major update in the UltraScan documentation and manual -> 6.0 compatible
Bug Fix:
us_selectmodel.cpp: Corrected typo in message window showing incorrect formulas
(bracket missing)
New Feature:
QWT library links now provide capability to edit the appearance of each scan
on a plot window, either in group or individually. The entire plot window
and contents can now be customized.
Update:
Webpage update for pending UltraScan 6.0 release
www contact: Borries Demeler
This document is part of the UltraScan Software
Documentation distribution.
Copyright © notice
The latest version of this document can always be found at:
http://www.ultrascan.uthscsa.edu
Last modified on January 12, 2003.