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Frederic Y. Bois | 3 Apr 08:56
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fixed incompatibility in PRINTREC defined in sim.h and use in simi.c

The following bug has been fixed in mcsim/sim: sim.h defines
struct tagPRINTREC with member cTimes is an "int", while cTimes is
conditionally assigned "LONG_MAX" in GetPrintStep (in simi.c).

cTimes is now defined as a long.

The corrected sim.h file(in mcsim/sim) is available in the official 
CVS repository at http://savannah.gnu.org/projects/mcsim

Frederic
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Frederic Bois | 1 Apr 23:31
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The two bugs of Feb 16 2009 (reading SBML models) are fixed

The previously found bugs have been fixed. The corrected code (in
mod/modiSBML.c) is available in the official CVS repository at
http://savannah.gnu.org/projects/mcsim

The new code correctly reads in multiple parameter declaration sections
and assign stoichiometry of 1 by default to species references in reaction
sections.
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Frederic Y. Bois | 24 Feb 13:11
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OptimalDesign bugs of Feb 22 2009 fixed

The previously found bugs have been fixed. The corrected code (in optdesign.c 
and optdesign.h) is available in the official CVS repository at
http://savannah.gnu.org/projects/mcsim
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Frédéric BOIS | 22 Feb 22:48
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OptimalDesign fails to properly initialize state variables

Initial assignments of State variables having an initial value different
from zero are not properly taken into account 
if the assignment is made outside of a Simulation {} section. This is a
bug, since global assignments should be possible.

F. Bois
who just found that one.
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Frederic Y. Bois | 16 Feb 08:55
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Two problems reading SBML

An error occurs when reading an SBML model in which parameter declarations are 
dispatched in the reactions definitions. While wainting for a code fix, it is
best to group parameter declarations in one section at the beginning. 

Next, GNU MCSim requires stoichiometries to be defined, and an error occurs if 
they are not. The code will be fixed (assuming value one when the stoichiometry 
is not given).
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Frédéric BOIS | 27 Dec 21:51
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Boundary conditions and stoichiometry bugs fixed

The previously signaled bugs have been fixed. The corrected code is
available in the CVS repository at
http://savannah.gnu.org/projects/mcsim
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Frédéric BOIS | 27 Dec 09:31
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Two bugs in SBML translation by GNU MCSim "mod"

Boundary conditions and stoichiometry are sometimes improperly accounted
for by mod when reading an
SBML model. No boundary conditions should be set and stoichiometric
coefficients should be 1. This should be
fixed quickly.
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Frederic Y. Bois | 3 Oct 13:43
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On the integration problem (addition)

Compiling the files in mcsim/sim/ in gcc with the -O - ffloat-store options 
will fix the problem and is strongly recommended (implies rebuilding the 
libmcsim.so shared library).
But it multiplies computation time by a factor 1.5 (less efficient optimization).
The solution is to compile only modelu.c with the -O - ffloat-store options 
(the problem only stems from one routine in modelu.c). All the other files can
be compiled as before with the -O option. The loss in speed is minimal in that 
case.

F. Bois
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Frederic Y. Bois | 25 Mar 15:00
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possible integration problem with v5.1 and v5.2

You may encounter problems when integrating a set of differential equations: 
with a very dense scheduling of output or input function discontinuities, 
the integrator may get stuck at a stopping point and does not advance past it. 
This seems to happen only when the code is compiled with the optimization option
on (at least with gcc), which is by default when you use the Makefiles provided. 
You can try running an non-optimized executable.
The simplest way to get at that is, for example:
cd ~/mcsim/sim
mod mymodel.model
gcc -o mymodel.exe *.c -lgsl -lgslcblas -lm

for optimized code you would do 
gcc -O -o mymodel.exe *.c -lgsl -lgslcblas -lm

This assumes that "mod", the model translation software is on you command path.

In any case, I am trying to understand and fix the problem. It is not a sneaky 
bug that would produce wrong results silently. The failure is reported and the 
program aborts immediately, the problem does not go unnoticed.

F. Bois
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Karl Berry | 10 Mar 20:23
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mailing list moderation

Greetings,

It appears that this mailing list, bug-mcsim <at> gnu.org, (among many others),
has no known owner/moderator, and accepts mail from non-subscribers.
The result is passing through of lots of spam.

So we need to do something.  I'm writing to get input on the best thing
to do.  Please reply to me if you have any thoughts on the following:

(1) If this list is obsolete and should be deleted.  We'd keep the
    archives, just make the address inactive, so any future mail to it
    would bounce.

(2) If the list is *not* obsolete, and should remain as a live address.
    In many cases there is so much junk in the archives that it is hard
    to tell, hence my query.  In other cases, I could guess, but I felt
    it would be best to just inquire about everything.

In case (2), if you can volunteer to help moderate the list (and/or
others!), that would be most appreciated.  But even if not, I'd still
like to know if the list is still live; I'm recruiting volunteer
moderators to help with the job.

Any other information or suggestions is welcome too.  For example, if
someone is already administering the list but just isn't listed in the
mailman interface.

Thanks much,
Karl
(Continue reading)

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Wells Fargo | 30 Oct 15:38
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Gmane