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