static printSensiMatrix(odeModel_t *odeModel, cvodeData_t *data)
{
int i, j;
const ASTNode_t *f = NULL;
char *formula;
/* first, get the number of equations of the ODE system */
int neq = ODEModel_getNeq(odeModel);
printf("i\\j ");
for ( j=0; j<ODEModel_getNsens(odeModel); j++ )
printf("%d ", j);
printf("\n");
for ( i=0; i<ODEModel_getNeq(odeModel); i++ ) {
printf("%d ", i);
for ( j=0; j<ODEModel_getNsens(odeModel); j++ ) {
f = ODEModel_getSensIJEntry(odeModel, i, j);
/* now let's see wether the entry is positive or negative at
this point */
if ( evaluateAST((ASTNode_t *)f, data) < 0 )
printf("- ");
if ( evaluateAST((ASTNode_t *)f, data) > 0 )
printf("+ ");
if ( evaluateAST((ASTNode_t *)f, data) == 0 )
printf("0 ");
}
printf("\n\n");
}
printf("\n");
}
static void printJacobian(odeModel_t *odeModel, cvodeData_t *data)
{
int i, j;
const ASTNode_t *f = NULL;
printf("i\\j ");
for ( j=0; j<ODEModel_getNeq(odeModel); j++ )
printf("%d ", j);
printf("\n");
for ( i=0; i<ODEModel_getNeq(odeModel); i++ ) {
printf("%d ", i);
for ( j=0; j<ODEModel_getNeq(odeModel); j++ ) {
f = ODEModel_getJacobianIJEntry(odeModel, i, j);
/* now let's see wether the entry is positive or negative at
this point */
if ( evaluateAST((ASTNode_t *)f, data) < 0 )
printf("- ");
if ( evaluateAST((ASTNode_t *)f, data) > 0 )
printf("+ ");
if ( evaluateAST((ASTNode_t *)f, data) == 0 )
printf("0 ");
}
printf("\n\n");
}
printf("\n");
}
void printOdes_fromFile(char* filename)
{
if (filename == NULL)
return;
int i;
char *formula;
variableIndex_t *vi = NULL;
odeModel_t *model =
ODEModel_createFromFile(filename);
if (model == NULL)
{
printf("create odemodel fails:\n");
return;
}
/* Get some information from constructed odeModel */
printf("\n\n");
printf("ODE Model Statistics:\n");
printf("Number of ODEs: %d\n",
ODEModel_getNeq(model));
printf("Number of Assignments: %d\n",
ODEModel_getNumAssignments(model));
printf("Number of Constants: %d\n",
ODEModel_getNumConstants(model));
printf(" ____\n");
printf("Total number of values: %d\n",
ODEModel_getNumValues(model));
printf("\n");
printf("ODEs:\n");
for ( i=0; i<ODEModel_getNeq(model); i++ ){
vi = ODEModel_getOdeVariableIndex(model, i);
formula = SBML_formulaToString(ODEModel_getOde(model, vi));
printf("d[%s]/dt = %s \n", ODEModel_getVariableName(model, vi), formula);
free(formula);
VariableIndex_free(vi);
}
// printf("Assigned Variables:\n");
// for ( i=0; i<ODEModel_getNumAssignments(model); i++ ){
// vi = ODEModel_getAssignedVariableIndex(model, i);
// formula = SBML_formulaToString(ODEModel_getOde(model, vi));
// printf("%s = %s \n", ODEModel_getVariableName(model, vi), formula);
// free(formula);
// VariableIndex_free(vi);
// }
printf("Constants:\n");
for ( i=0; i<ODEModel_getNumConstants(model); i++ ){
vi = ODEModel_getConstantIndex(model, i);
printf("%s\n", ODEModel_getVariableName(model, vi));
VariableIndex_free(vi);
}
printf("\n\n");
ODEModel_free(model);
}
int main(void)
{
int i;
char *formula;
variableIndex_t *vi = NULL;
odeModel_t *model =
ODEModel_createFromFile("basic-model1-forward-l2.xml");
/* Get some information from constructed odeModel */
printf("\n\n");
printf("ODE Model Statistics:\n");
printf("Number of ODEs: %d\n",
ODEModel_getNeq(model));
printf("Number of Assignments: %d\n",
ODEModel_getNumAssignments(model));
printf("Number of Constants: %d\n",
ODEModel_getNumConstants(model));
printf(" ____\n");
printf("Total number of values: %d\n",
ODEModel_getNumValues(model));
printf("\n");
printf("ODEs:\n");
for ( i=0; i<ODEModel_getNeq(model); i++ ){
vi = ODEModel_getOdeVariableIndex(model, i);
formula = SBML_formulaToString(ODEModel_getOde(model, vi));
printf("d[%s]/dt = %s \n", ODEModel_getVariableName(model, vi), formula);
free(formula);
VariableIndex_free(vi);
}
printf("Assigned Variables:\n");
for ( i=0; i<ODEModel_getNumAssignments(model); i++ ){
vi = ODEModel_getAssignedVariableIndex(model, i);
formula = SBML_formulaToString(ODEModel_getOde(model, vi));
printf("%s = %s \n", ODEModel_getVariableName(model, vi), formula);
free(formula);
VariableIndex_free(vi);
}
printf("Constants:\n");
for ( i=0; i<ODEModel_getNumConstants(model); i++ ){
vi = ODEModel_getConstantIndex(model, i);
printf("%s\n", ODEModel_getVariableName(model, vi));
VariableIndex_free(vi);
}
printf("\n\n");
ODEModel_free(model);
return 1;
}
int main(void)
{
int i, j, neq;
char *formula;
variableIndex_t *vi = NULL;
variableIndex_t *vj = NULL;
const ASTNode_t *f = NULL;
cvodeData_t *data = NULL;
cvodeSettings_t *set;
integratorInstance_t *iI;
/* first load an SBML model and directly construct the
internal odeModel from it */
odeModel_t *odeModel = ODEModel_createFromFile("MAPK.xml");
if ( ODEModel_constructSensitivity(odeModel) &&
ODEModel_getNeq(odeModel) ) {
printf("\n\nSuccessfully constructed the parametric matrix S ");
printf("as used for CVODES sensitivity analysis\n\n");
printf("We might be interested in the `sparsity' of S,\n");
printf("... we can just evaluate the parametric entries:\n\n");
/* we need cvodeData for evaluating formulas */
data = CvodeData_create(odeModel);
printf("... how many parametric entries: %d\n\n",
ODEModel_getNsens(odeModel));
/* now take a look at a all entries of S: */
for ( i=0; i<ODEModel_getNeq(odeModel); i++ ) {
vi = ODEModel_getOdeVariableIndex(odeModel, i);
printf("\nODE VARIABLE %d: %s\n", i+1,
ODEModel_getVariableName(odeModel, vi));
f = ODEModel_getOde(odeModel, vi);
formula = SBML_formulaToString(f);
printf("dY/dt = %s \n", formula);
free(formula);
for ( j=0; j<ODEModel_getNsens(odeModel); j++ ) {
vj = ODEModel_getSensParamIndexByNum(odeModel, j);
printf(" Parameter %d: %s ", j,
ODEModel_getVariableName(odeModel, vj));
f = ODEModel_getSensIJEntry(odeModel, i, j);
formula = SBML_formulaToString(f);
printf(" S[%d][%d] = %s \n", i, j, formula);
free(formula);
VariableIndex_free(vj);
}
VariableIndex_free(vi);
}
printf("\n\n");
printf("Sensitivity: parametric matrix with initial conditions:\n");
printSensiMatrix(odeModel, data);
/* we must free this cvodeData structure */
CvodeData_free(data);
printf("Thx and good bye!\n");
}
else {
SolverError_dumpAndClearErrors();
printf("Sorry, for this system we couldn't generate the Parametric.\n");
printf("Sensitivity can still be run with internal approximation.\n");
}
ODEModel_free(odeModel);
return 1;
}
int main(void)
{
char *formula;
variableIndex_t *vi = NULL;
variableIndex_t *vj = NULL;
const ASTNode_t *f = NULL;
cvodeData_t *data = NULL;
cvodeSettings_t *set;
integratorInstance_t *iI;
/* first load an SBML model and directly construct the
internal odeModel from it */
odeModel_t *odeModel = ODEModel_createFromFile("MAPK.xml");
if ( ODEModel_constructJacobian(odeModel) && ODEModel_getNeq(odeModel) ) {
printf("\n\nSuccessfully constructed the jacobian matrix J\n\n");
printf("We might be interested in the `sparsity' of J,\n");
printf("... we can just evaluate the jacobian entries:\n\n");
/* we need cvodeData for evaluating formulas */
data = CvodeData_create(odeModel);
/* ! IMPORTANT : initialize values */
CvodeData_initializeValues(data);
printf("Jacobian with initial conditions:\n");
printJacobian(odeModel, data);
/* we must free this cvodeData structure */
CvodeData_free(data);
printf("Does it change after integration?\n\n");
/* creating settings and integrate */
set = CvodeSettings_create();
CvodeSettings_setTime(set, 1000, 1);
iI = IntegratorInstance_create(odeModel, set);
IntegratorInstance_integrate(iI);
/* get cvodeData from integratorInstance, it contains
the values at the last time point,
and just do the same as above */
data = IntegratorInstance_getData(iI);
printf("Jacobian at time %g:\n", IntegratorInstance_getTime(iI));
printJacobian(odeModel, data);
printf("J[6,4] changed its sign. Let's take a look at the equations:\n\n");
vi = ODEModel_getOdeVariableIndex(odeModel, 6);
vj = ODEModel_getOdeVariableIndex(odeModel, 4);
f = ODEModel_getOde(odeModel, vi);
formula = SBML_formulaToString(f);
printf("The ODE d%s/dt = \n%s \n\n",
ODEModel_getVariableName(odeModel, vi),
formula);
free(formula);
f = ODEModel_getJacobianEntry(odeModel, vi, vj);
formula = SBML_formulaToString(f);
printf("The jacobian entry (d%s/dt)/d%s = \n%s \n\n",
ODEModel_getVariableName(odeModel, vi),
ODEModel_getVariableName(odeModel, vj),
formula);
free(formula);
VariableIndex_free(vi);
VariableIndex_free(vj);
printf("MAPK_P is both a substrate and a product of MKK_PP ");
printf("in different reactions.\nTherefor the corresponding ");
printf("entry in the jacobian can change its sign, depending ");
printf("on concentrations!\n");
/* finally draw a `species interaction graph' of the jacobian' */
drawJacoby(data, "jacobian", "gif");
printf("Take a look at jacobian interaction graph in");
printf("file jacobian_jm.gif that has just been constructed.\n");
printf("If you have compiled w/o graphviz, you just have a textfile");
printf(" jacobian.dot\n");
printf("Thx and good bye!\n");
/* note that this cvodeData MUST NOT be freed, it stays with and
will be freed together with integratorInstance */
IntegratorInstance_free(iI);
CvodeSettings_free(set);
}
else {
SolverError_dumpAndClearErrors();
printf("Sorry, for this system we couldn't generate the Jacobian.\n");
printf("Integration can still be run with internal approximation.\n");
}
ODEModel_free(odeModel);
return 1;
}
int
main (int argc, char *argv[])
{
int i, j, k;
int neq, nsens;
odeModel_t *om;
odeSense_t *os;
cvodeSettings_t *set;
integratorInstance_t *ii;
variableIndex_t *p1, *p2, *p3, *vi;
double *weights;
/* Setting SBML ODE Solver integration parameters */
set = CvodeSettings_create();
CvodeSettings_setTime(set, 30, 10);
CvodeSettings_setErrors(set, 1e-15, 1e-10, 1e9);
CvodeSettings_setMethod(set, 0, 5);
/* CvodeSettings_setStoreResults(set, 0); */
CvodeSettings_setJacobian(set, 1); /* for testing only */
CvodeSettings_setCompileFunctions(set, 0); /* for testing only */
/* CvodeSettings_dump(set); */
CvodeSettings_setFIM(set); /* ACTIVATE FIM */
/* creating the odeModel */
om = ODEModel_createFromFile("MAPK.xml");
ii = IntegratorInstance_create(om, set);
printf("\nFirst try a few integrations without sensitivity\n");
IntegratorInstance_dumpNames(ii);
printf("\n");
for ( i=0; i<2; i++ )
{
printf("Run #%d:\n", i);
IntegratorInstance_integrate(ii);
/* IntegratorInstance_dumpData(ii); */
IntegratorInstance_printResults(ii, stderr);
IntegratorInstance_reset(ii);
printf("finished\n\n");
}
/* ACTIVATE SENSITIVITY ANALYSIS */
CvodeSettings_setSensitivity(set, 1);
/* 0: simultaneous 1: staggered, 2: staggered1
see CVODES user guide for details */
CvodeSettings_setSensMethod(set, 0);
/* reset integrator to new settings */
IntegratorInstance_reset(ii);
printf("Now Activate Sensitivity\n\n");
os = IntegratorInstance_getSensitivityModel(ii);
nsens = ODESense_getNsens(os);
printf("nsens = %i\n\n", nsens);
for ( i=0; i<nsens; i++ ) {
vi = ODESense_getSensParamIndexByNum(os, i);
printf("%s\n", ODEModel_getVariableName(om, vi) );
VariableIndex_free(vi);
}
printf("\n");
printf("sensitivities calculated for all constants\n");
p1 = ODESense_getSensParamIndexByNum(os, 1);
p2 = ODESense_getSensParamIndexByNum(os, 2);
p3 = ODESense_getSensParamIndexByNum(os, 3);
printf("sensitivities printed for constants %s, %s, %s\n\n",
ODEModel_getVariableName(om, p1),
ODEModel_getVariableName(om, p2),
ODEModel_getVariableName(om, p3));
/* create non-default weights for computation of FIM */
/* weights should be extracted from objective function! */
neq = ODEModel_getNeq(om);
ASSIGN_NEW_MEMORY_BLOCK(weights, neq, double, 0);
for ( i=0; i<neq; i++ )
weights[i] = 1.;
/* set weights (to non-default values) */
IntegratorInstance_setFIMweights(ii, weights, neq);
/* *** *** *** *** *** *** discrete data *** *** *** *** *** *** *** */
CvodeSettings_setDiscreteObservation(set);
printf("DISCRETE DATA\n\n");
i = 0;
while ( i < 2 )
{
printf("Run #%d:\n", i);
while( !IntegratorInstance_timeCourseCompleted(ii) )
{
IntegratorInstance_dumpPSensitivities(ii, p1);
IntegratorInstance_dumpPSensitivities(ii, p2);
IntegratorInstance_dumpPSensitivities(ii, p3);
if ( !IntegratorInstance_integrateOneStep(ii) )
break;
}
IntegratorInstance_dumpPSensitivities(ii, p1);
IntegratorInstance_dumpPSensitivities(ii, p2);
IntegratorInstance_dumpPSensitivities(ii, p3);
fprintf(stderr, "FIM =\n");
for ( j=0; j<nsens; j++ )
{
for ( k=0; k<nsens; k++ )
fprintf(stderr, "%g ", IntegratorInstance_getFIM(ii,j,k));
fprintf(stderr, "\n");
}
fprintf(stderr, "\n");
IntegratorInstance_reset(ii);
i++;
}
/* *** *** *** *** *** *** continuous data *** *** *** *** *** *** *** */
CvodeSettings_unsetDiscreteObservation(set);
printf("CONTINUOUS DATA\n\n");
i = 0;
while ( i < 2 )
{
printf("Run #%d:\n", i);
while( !IntegratorInstance_timeCourseCompleted(ii) )
{
IntegratorInstance_dumpPSensitivities(ii, p1);
IntegratorInstance_dumpPSensitivities(ii, p2);
IntegratorInstance_dumpPSensitivities(ii, p3);
if ( !IntegratorInstance_integrateOneStep(ii) )
break;
}
IntegratorInstance_dumpPSensitivities(ii, p1);
IntegratorInstance_dumpPSensitivities(ii, p2);
IntegratorInstance_dumpPSensitivities(ii, p3);
/* calculate FIM */
IntegratorInstance_CVODEQuad(ii);
fprintf(stderr, "FIM =\n");
for ( j=0; j<nsens; j++ )
{
for ( k=0; k<nsens; k++ )
fprintf(stderr, "%g ", IntegratorInstance_getFIM(ii,j,k));
fprintf(stderr, "\n");
}
fprintf(stderr, "\n");
IntegratorInstance_reset(ii);
i++;
}
fprintf(stderr, "finished\n");
/* VariableIndex_free(y); */
VariableIndex_free(p1);
VariableIndex_free(p2);
VariableIndex_free(p3);
free(weights);
/* now we have the results and can free the inputs */
IntegratorInstance_free(ii);
CvodeSettings_free(set);
ODEModel_free(om);
return (EXIT_SUCCESS);
}
