Gepasi can now import and exportSBML
(the Systems Biology Markup Language). SBML is an XML format that allows
transfer of models between different software. SBML was developed
by the Caltech ERATO Kitano
group.
The MEG program is now included in the Gepasi
installation. MEG is a program to convert one Gepasi
model into a set of coupled similar models (some people call this an array
of models, but there are several topologies). The main use of
MEG is to create models of cell cultures and tissues.
3 new optimisation modules were added:
Simulated annealing
Nelder and Mead (Simplex)
Praxis
New option to set initial concentrations of metabolites to the end time concentrations
of a time course or the steady state values, in addition to leaving them unaltered
(default). This allows one to continue a simulation where it ended previously.
tan() is now allowed in mathematical expressions
rand(), and gauss() can now be used in kinetic equations (allowing for
the introduction of noise or other stochastic effects)
Adding optimization and fitting parameters is now easier through a Add/Close mechanism
(the dialog box does not have to be closed after adding one single paramater).
A count of optimization and fitting parameters is now displayed in the Fitting and
Optimization pages
Better help for multi-compartment models
Scan page now shows how many scan items have been selected
Standard deviations for estimated parameters are no longer calculated if the
product of data points by the number of fitting parameters exceeds 1,000,000.
This prevents allocation of very large memory blocks (over 100 Mbytes) and
hours of calculations. It turns out that calculation of standard deviations
for such systems is actually harder than the actual data fit.
BUGS FIXED
Several kinetic types were being miscalculated in models that had non-unitary volume
compartments. This is now corrected. The kinetic types were:
UDKtypes
Uni Uni
Iso Uni Uni
Ordered Uni Bi
Ordered Bi Uni
Ordered Bi Bi
Ping Pong Bi Bi
Reversible Allosteric Inhibition
Reversible Hill
Reversible Hill w/ 1 modifier
Reversible Hill w/ 2 modifiers
The calculation of the kinetic equation for the irreversible MWC with inhibitor
kinetic type was wrong, as well as the help file. This has been corrected in both
places.
Display of objective function value in Optimisation and Fitting pages is now set to
a fixed number of decimals
Context-sensitive help for optimisation and fitting pages is now properly displayed
A bug in the time course logic (loop controlling integrator) that could enter an infinite
loop has been fixed.
The Jacobian matrix displayed in report files was the transpose of the actual Jacobian,
this has been corrected.
The report file was displaying the units of fluxes erroneously as concentration/time. Gepasi
calculates fluxes in units of amount/time (concentration*volume/time). This has been
fixed and the correct units are now displayed. (In case you want fluxes in units of
concentration/time, you will have to divide the values displayed by the volume of
reference)
Error reports were not being displayed when running fitting or optimization