Frederic Bois | 22 Jan 15:21
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fixed an SBML model processing bug in modiSBML2.c

Inline statements in templates were ill processed (e.g. blank spaces 
were removed) when coupled to an SBML model.
That is now fixed. Inline () statements are transcribed "as is".
The latest version of the file is available on
http://cvs.savannah.gnu.org/viewvc/mcsim/mod/?root=mcsim

F. Bois

Frederic Bois | 22 Jan 11:12
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fixed a printing bug in mh.c

When printing a fit check after MCMC simulations, the model prediction 
and data values were printed wrong
and mismatched if the Print and Data statements did follow the same 
order in the simulation input file. That did not affect
the results of MCMC simulations at all, but would eventually mess up the 
fit check.
That is now fixed (the latest version of the file is available on

http://cvs.savannah.gnu.org/viewvc/mcsim/sim/?root=mcsim)

F. Bois

Frederic Bois | 11 Nov 13:27
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fixed a small bug in mh.c

A stray line code at the end of mh.c caused a systematic crash when  
exiting MCMC simulations. That is now fixed (the latest version of the  
file is available on
http://cvs.savannah.gnu.org/viewvc/mcsim/sim/?root=mcsim)

F. Bois

Frederic Bois | 18 Jan 23:25
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GNU MCSim version 5.4.0 is available

Check the http://www.gnu.org/software/mcsim/ to access it.
It is now under FSF GPL v3

Frederic Bois

Frederic Bois | 15 Jan 18:05
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MCSim mod improvements

The latest "mod" code on 
http://cvs.savannah.gnu.org/viewvc/mcsim/mcsim/mod/ fixes a bug in SBML 
processing. You can also specify the name of the default (external) 
compartment in SBML files.
If you want to read in SBML files, we strongly recommend that you 
install libSBML prior to compiling mod (compilation with _HAS_SBML_LIB 
defined). SBML parsing without libSBML will not be maintained.
A new distribution should come out soon.

Frederic Bois

Frederic Bois | 15 Jan 17:59
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SBML parsing with PK template: Bug fixed

A bug preventing the proper merging of SBML files with a transport 
equations template has been fixed.
It occurred when using libSBML code. The native code, used if libSBML 
was not installed, did not suffer from it.

Frederic Bois.

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

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.

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

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.

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).


Gmane