High Level Interfaces

Collaboration diagram for High Level Interfaces:

This module contains high level interfaces to SOSlib, which take an SBML model and integratorSettings as input and return results mapped back to SBML structures. More...

Modules
	Parameter Variation Settings
	Create the varySettings structure with a series of parameter values used for the batch functions.
	SBML Results Interface
	This module contains interfaces to the results structures returned by the high level interfaces to SOSlib.
Functions
SBML_ODESOLVER_API SBMLResults_t *	SBML_odeSolver (SBMLDocument_t *d, cvodeSettings_t *set)
	Solves the timeCourses for a SBML model, passed via a libSBML SBMLDocument structure and according to passed integration settings and returns the SBMLResults structure.
SBML_ODESOLVER_API SBMLResultsMatrix_t *	SBML_odeSolverBatch (SBMLDocument_t *d, cvodeSettings_t *set, varySettings_t *vs)
	Solves the timeCourses for a SBML model, passed via a libSBML SBMLDocument structure and according to passed integration and parameter variation settings and returns the SBMLResultsMatrix containing SBMLResults for each varied parameter (columns) and each of its values (rows).
SBML_ODESOLVER_API SBMLResults_t *	Model_odeSolver (Model_t *m, cvodeSettings_t *set)
	Solves the timeCourses for a SBML model, passed via a libSBML Model_t (must be level 2 SBML!!) and according to passed integration settings and returns the SBMLResults structure.
SBML_ODESOLVER_API SBMLResultsMatrix_t *	Model_odeSolverBatch (Model_t *m, cvodeSettings_t *set, varySettings_t *vs)
	Solves the timeCourses for a SBML model, passed via a libSBML Model_t (must be level 2 SBML!!) structure and according to passed integration and parameter variation settings and returns the SBMLResultsMatrix containing SBMLResults for each varied parameter (columns) and each of its values (rows).

---

Detailed Description

This module contains high level interfaces to SOSlib, which take an SBML model and integratorSettings as input and return results mapped back to SBML structures.

Please see sbmlResults for interfaces to the returned result structures.

---

Function Documentation

SBML_ODESOLVER_API SBMLResults_t* SBML_odeSolver (  SBMLDocument_t *  d, cvodeSettings_t *  set )

Solves the timeCourses for a SBML model, passed via a libSBML SBMLDocument structure and according to passed integration settings and returns the SBMLResults structure. Convert SBML Document level 1 to level 2, and get the contained model Call Model_odeSolver free temporary level 2 version of the document

SBML_ODESOLVER_API SBMLResultsMatrix_t* SBML_odeSolverBatch (  SBMLDocument_t *  d, cvodeSettings_t *  set, varySettings_t *  vs )

Solves the timeCourses for a SBML model, passed via a libSBML SBMLDocument structure and according to passed integration and parameter variation settings and returns the SBMLResultsMatrix containing SBMLResults for each varied parameter (columns) and each of its values (rows). Convert SBML Document level 1 to level 2, and get the contained model Call Model_odeSolverBatch free temporary level 2 version of the document

SBML_ODESOLVER_API SBMLResults_t* Model_odeSolver (  Model_t *  m, cvodeSettings_t *  set )

Solves the timeCourses for a SBML model, passed via a libSBML Model_t (must be level 2 SBML!!) and according to passed integration settings and returns the SBMLResults structure. At first, ODEModel_create, attempts to construct a simplified SBML model with reactions replaced by ODEs. SBML RateRules, AssignmentRules,AlgebraicRules and Events are copied to the simplified model. AlgebraicRules or missing mathematical expressions produce fatal errors and appropriate messages. All function definitions are replaced by their values or expressions respectively in all remaining formulas (ie. rules and events). If that conversion was successful, an internal model structure (odeModel) is created, that contains indexed versions of all formulae (AFM's AST_INDEX) where the index of a former AST_NAME corresponds to its position in a value array (double *), that is used to store current values and to evaluate AST formulae during integration. Second, an integratorInstance is created from the odeModel and the passed cvodeSettings. If that worked out ... .... the integrator loop can be started, that invoking CVODE to move one time step and store. The function will also handle events and check for steady states. finally, map cvode results back to SBML compartments, species and parameters

SBML_ODESOLVER_API SBMLResultsMatrix_t* Model_odeSolverBatch (  Model_t *  m, cvodeSettings_t *  set, varySettings_t *  vs )

Solves the timeCourses for a SBML model, passed via a libSBML Model_t (must be level 2 SBML!!) structure and according to passed integration and parameter variation settings and returns the SBMLResultsMatrix containing SBMLResults for each varied parameter (columns) and each of its values (rows). At first, globalize all local (kineticLaw) parameters to be varied Then create internal odeModel: attempts to construct a simplified SBML model with reactions replaced by ODEs. See comments in Model_odeSolver for details. an integratorInstance is created from the odeModel and the passed cvodeSettings. If that worked out ... now, work through the passed parameters in varySettings .... the integrator loop can be started, that invokes CVODE to move one time step and store results. These functions will also handle events and check for steady states. map cvode results back to SBML compartments, species and parameters localize parameters again, unfortunately the new globalized parameter cannot be freed currently

---