verify (model, variant)

Validate and verify SimBiology model

Syntax

verify(modelObj)

verify(modelObj,csObj)

verify(modelObj,dvObj)

verify(modelObj,csObj,dvObj)

verify(modelObj,csObj,variantObj,doseObj)

Description

verify(modelObj) performs checks on a Model modelObj to verify that you can simulate the model. This function generates stacked errors and warnings if it finds any problems. To see the entire list of errors and warnings, use sbiolasterror and sbiolastwarning. The function uses the active configuration set, any active doses and active variants for verification.

verify(modelObj,csObj) verifies a model modelObj using the specified configset object csObj and any active variants and active doses. Any other configsets are ignored. If you set csObj to empty [], the function uses the active configset.

verify(modelObj,dvObj) verifies a model modelObj using doses or variants specified by dvObj and the active configset. dvObj can be one of the following:

• Variant object

• ScheduleDose object

• RepeatDose object

• Array of doses or variants

If you set dvObj to empty [], the function uses the active configset, active variants, and active doses.

If you specify dvObj as variants, the function uses the specified variants and active doses. Any other variants are ignored.

If you specify dvObj as doses, the function uses the specified doses and active variants. Any other doses are ignored.

verify(modelObj,csObj,dvObj) verifies a model modelObj using a configset object csObj and doses or variants specified by dvObj.

If you set csObj to [], then the function uses the active configset object.

If you set dvObj to [], then the function uses no variants, but uses active doses.

If you specify dvObj as variants, the function uses the specified variants and active doses. Any other variants are ignored.

If you specify dvObj as doses, the function uses the specified doses and active variants. Any other doses are ignored.

verify(modelObj,csObj,variantObj,doseObj) verifies a model modelObj using a configset object csObj, variants (variantObj) and doses (doseObj). Any other configset, doses, and variants are ignored.

If you set csObj to [], then the function uses the active configset object.

If you set variantObj to [], then the function uses no variants.

If you set doseObj to [], then the function uses no doses.

Input Arguments

modelObj — SimBiology^® model

SimBiology model object

SimBiology model, specified as a SimBiology model object.

csObj — Configuration set object

configset object

Configuration set object, specified as a Configset object that stores simulation-specific information.

dvObj — Dose or variant object

dose object or array of dose objects | variant object or array of variant objects

Dose or variant object, specified as a ScheduleDose object , RepeatDose object , an array of dose objects, Variant object , or an array of variant objects.

• When dvObj is a dose object, verify uses the specified dose object as well as any active variant objects if available.

• When dvObj is a variant object, verify uses the specified variant object as well as any active dose objects if available.

variantObj — Variant object

variant object or array of variant objects

Variant object, specified as a Variant object or an array of variant objects.

doseObj — Dose object

dose object or array of dose objects

Dose object, specified as a ScheduleDose object , RepeatDose object , or an array of dose objects. A dose object defines additions that are made to species amounts or parameter values.

Examples

Verify a SimBiology Model While Using a User-Defined Configset Object

Load a sample SimBiology model.

sbioloadproject radiodecay.sbproj

Add a new configuration set using a different stop time of 15 seconds.

csObj = addconfigset(m1,'newStopTimeConfigSet');
csObj.StopTime = 15;

Verify the model while using the configset object.

verify(m1,csObj);

After verification, check the latest errors and warnings if there is any.

sbiolasterror

ans = 

  0x1 empty struct array with fields:

    Type
    MessageID
    Message

sbiolastwarning

ans = 

  0x1 empty struct array with fields:

    Type
    MessageID
    Message

Simulate the model.

sim = sbiosimulate(m1,csObj);
sbioplot(sim);

Verify a SimBiology Model While Using Configset and Dose Objects

Load a sample SimBiology model.

sbioloadproject radiodecay.sbproj

Get the default configuration set from the model.

defaultConfigSet = getconfigset(m1,'default');

Add a scheduled dose of 100 molecules at 2 seconds for species x.

dObj = adddose(m1,'d1','schedule');
dObj.Amount = 100;
dObj.AmountUnits = 'molecule';
dObj.TimeUnits = 'second';
dObj.Time = 2;
dObj.TargetName = 'unnamed.x';

Verify the model while using the default configset object and added dose object.

verify(m1,defaultConfigSet,dObj);

After verification, check the latest errors and warnings if there is any.

sbiolasterror

ans = 

  0x1 empty struct array with fields:

    Type
    MessageID
    Message

sbiolastwarning

ans = 

  0x1 empty struct array with fields:

    Type
    MessageID
    Message

Simulate the model using the same configset and dose objects.

sim = sbiosimulate(m1,defaultConfigSet,dObj);

Plot the result.

sbioplot(sim);

Verify SimBiology Model While Using Configset, Dose, and Variant Objects

Load a sample SimBiology model.

sbioloadproject radiodecay.sbproj

Add a new configuration set using a different stop time of 15 seconds.

csObj = m1.addconfigset('newStopTimeConfigSet');
csObj.StopTime = 15;

Add a scheduled dose of 100 molecules at 2 seconds for species x.

dObj = adddose(m1,'d1','schedule');
dObj.Amount = 100;
dObj.AmountUnits = 'molecule';
dObj.TimeUnits = 'second';
dObj.Time = 2;
dObj.TargetName = 'unnamed.x';

Add a variant of species x using a different initial amount of 500 molecules.

vObj = addvariant(m1,'v1');
addcontent(vObj,{'species','x','InitialAmount',500});

Verify the model while using the configset, dose, and variant objects. Note that the order of arguments should be as described.

verify(m1,csObj,vObj,dObj);

After verification, check the latest errors and warnings if there is any.

sbiolasterror

ans = 

  0x1 empty struct array with fields:

    Type
    MessageID
    Message

sbiolastwarning

ans = 

  0x1 empty struct array with fields:

    Type
    MessageID
    Message

Simulate the model using the same configset, variant, and dose objects.

sim = sbiosimulate(m1,csObj,vObj,dObj);

Plot the result.

sbioplot(sim);