Included in the package is now a command line version of Gepasi
(bgepasi.exe). This program is invoked from the command line with a
series of simulation filenames that it then executes. The files must
have been written with the "normal" version of Gepasi. The command
line version is useful to set up batches of simulations to run at
scheduled times.
New metabolites can now be added to the model directly in the
metabolites dialog box. This is useful for adding external
metabolites that do not take part in any reactions.
In the kinetics dialog box, the "Help on kinetics" button now shows
the function and other details of the kinetic type even when it is
a user-defined one. Previously users would have to edit the kinetic
type in order to check the equation or other details.
In the report file, flux-control coefficients are now listed before
the concentration-control coefficients.
New predefined kinetic types were added for the reversible Hill
kinetics (thanks to Jannie Hofmeyr and Athel Cornish-Bowden for
providing a manuscript with these equations prior to its
publication).
Gepasi now attempts to automatically find the "branch structure" of
the pathway.
The time course and steady state data files now have default names.
When a steady state is not found, Gepasi still prints the set of
values that it was attempting as steady-state candidates. Note that
many times these values might not even be valid concentrations (if
the Newton method was being used).
BUGS FIXED
The Intel version now catches floating point overflow and divisions
by zero.
The hmm.gps example had one error in the definition of the "Km"
function that would cause a division by zero.
The program is now properly scaling the elasticities of fixed
concentration (external) metabolites when the "scaled MCA" option
is selected. The variable (internal) metabolites were not affected
by this error.
If the report or data files were opened and locked by other programs
when the simulation was running, Gepasi would crash. Currently Gepasi
fails to carry out the simulation but does not crash. Those files
must be available for writing when Gepasi runs! Beware of programs
that keep files opend all the time, rather than just when they need
to read/write (Excel is one example).
When other methods failed to find a steady state, backwards
integration was always used even when the user had not selected this
option. Currently this is only attempted if the option is set (but
note that this option is on by default).
A floating point "invalid operation" was sometimes generated when the
simulation engine started on the DEC alpha version. This seems to
have been due to the code optimiser. It has been solved with a small
(10 ms) waiting interval. If you find that this error is still
persistent, please report it to the author
(optimiser errors are very hard to diagnose so this may not yet have been properly fixed).