Re: [SOSlib-devel] todo for next release

[W E. W. <wew...@gm...>]

Hi Rainer , all...


Add 1

Currently I went further and have introduced two "classes"
CB_SimulatorInterface and CB_Solver which encapsulate
the integrator instance - allow for an easy update of parameters and return
a structure CB_SimulatorOutput and CB_SimulatoroutputSet ...  which are part
of an CaliBayes API which we are developing here in Newcastle in the
programming language C.
Both those classes CB_SimulatorInterface and CB_Solver depend on a patched
version of the SBML ode Solver API .. it would be a huge help if this patch
could be integrated into the standard development tree of the SBML ode
Solver API  ...

The changes I would be going to make are going to include:
editing src/Makefile.am
adding src/varySettings.c
adding src/sbmlsolver/varySettings.h

editing Makefile.am <http://makefile.am/> in directory example.
and adding
examples/Sensitivitytest.c
examples/DesignPointExample.c


I kept all the functions which I would like to have added to SBML_Solver in
varySettings.c and varySettings.h. However, I do patch many of the existing
structures in the lib e.g.

SBML_ODESOLVER_API Variable_t * OdeModel_getVariable( odeModel_t * odemodel
, double value, char * parameterStr , char *   reactionStr );
SBML_ODESOLVER_API Variable_t * VariableIndex_getVariable( variableIndex_t *
vi, double value, char *parameterStr , char *reactionStr);
SBML_ODESOLVER_API void Variable_free( Variable_t *variable );
SBML_ODESOLVER_API int
IntegratorInstance_setDesignPoint(integratorInstance_t * integratorInstance,
DesignPoint_t * designpoint);
SBML_ODESOLVER_API Variable_t * Variable_create(  double value, char
*parameterStr , char *reactionStr);
SBML_ODESOLVER_API int Model_change(Model_t *model, /*SBML level 2! See
example*/
                                    DesignPoint_t *dp);
SBML_ODESOLVER_API cvodeResults_t * Model_solve(Model_t * model ,
cvodeSettings_t *settings);

the only new struct I introduced is DesignPoint (ParameterSet migth be a
better name).


I remember adding varySettings.h and varySettings.c 2006 only to find this
files deleted a few weeks later...  it might be better if a few people
review the code first so that a more persistent change if wished can be
made.
I attach the files...


cheers
Eryk



On 11/23/06, Rainer Machne <ra...@tb...> wrote:
>
> Hi Friends,
>
> here a rough todo list for the next release ... at least some of the
> stuff below should be done before the next release. If you have
> preferences/opions or want to add things feel free:
>
> Functionality:
> General:
> * odeSolverBatch (use Eryk's code)
> * assignment rule ordering (also consider DAE systems/IDA solver
> extension)
> * variable compartments, ODEs in amounts
> * online compilation
> * exact event detection
> -> Rainer and Xtof
>
> Text-based input files for:
> ** reaction network: Vienna Reaction library
> ** ODE system: xppaut format
> -> Xtof
>
> Sens. Analysis output:
> * Direct Lyapunov Exponent analysis
> * Fisher Information Matrix
> -> James and Stefan :-) ???
>
> Dependencies:
> * libSBML 3
> * Sundials 2.3.0
> -> Rainer and Xtof
>
> Pending:
> * Test suite ??
> ** Functionality
> ** Performance
>
> Configure:
> * malloc.h
> * -R/-rpath switch
> * general refactoring!!
> -> Rainer and Xtof
>
>
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