Mathworks SIMBIOLOGY RELEASE NOTES

SimBiology
®
Release Notes
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SimBiology
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Release Notes
Summary by Version ............................... 1
Contents
Version 3.2 (R2010a) SimBiology Software
Version 3.1 (R2009b) SimBiology Software
Version 3.0 (R2009a) SimBiology Software
Version 2.4 (R2008b) SimBiology Software
Version 2.3 (R2008a) SimBiology Software
Version 2.2 (R2007b+) SimBiology Software
Version 2.1.2 (R2007b) SimBiology Software
Version 2.1.1 (R2007a) SimBiology Software
Version 2.1 (R2006b+) SimBiology Software
Version 2.0.1 (R2006b) SimBiology Software
........... 5
........... 10
........... 13
........... 17
........... 28
.......... 31
.......... 44
.......... 45
.......... 46
.......... 49
Version 2.0 (R2006a+) SimBiology Software
Version 1.0.1 (R2006a) SimBiology Software
Version 1.0 (R14SP3+) SimBiology Software
Compatibility Sum mary for SimBiology Software
.......... 50
.......... 55
.......... 56
.... 62
iii
iv Contents
SummarybyVersion
This table provides quick access to what’s new in each version. For clarification, see “Using Release Notes” on page 2 .
SimBiology®Release Notes
Version (Release)
Latest Versi V3.2 (R2010a
V3.1 (R2009b)
V3.0 (R2009a)
V2.4 (R2
V2.3 (R2008a)
V2.2 (R2007b+)
2 (R2007b)
V2.1.
.1 (R2007a)
V2.1
1 (R2006b+)
V2.
on
008b)
New Features and Changes
Yes
)
Details
Yes Details
Yes Details
Yes Details
Yes Details
Yes
ls
Detai
No No Bug Reports No
No No Bug Reports No
Yes Details
Version Compatibilit Consideratio
Yes Summary
Yes Summary
No Bug R epor
Yes Summary
Yes Summary
Yes Summa
Yes Summary
ry
Fixed Bugs
y
and Known
ns
Problems
Bug Reports Includes fix
Bug Reports Includes fixes
Includes
Bug Reports Includes fixes
Bug Reports Includes fixes
Bug Rep Inclu
Bug Reports Includes fixes
des fixes
ts
fixes
orts
Related Documentation at Web Site
Printable Release
es
Notes: PDF
Current product documentation
No
No
No
No
No
No
V2.0.1 (R2006b)
V2.0 (R2006a+)
No No Bug Reports
Includes fixes
Ye De
s
tails
s
Ye
mmary
Su
g Reports
Bu
cludes fixes
In
No
No
1
SimBiology®Release Notes
Version (Release)
V1.0.1 (R2006a)
V1.0 (R14SP3+)
New Features and Changes
Yes Details
Yes Details
Version Compatibility Considerations
No Bug Reports No
No Bug Reports No
Fixed Bugs and Known Problems
Related Documentation at Web Site
Using Release Notes
Use release notes when upgrading to a newer version to learn about:
New features
Changes
Potential impact on your existing files and practices
Review the release notes for other MathWorks™ products required for this product (for example, MATLAB bugs, or compatibility considerations in other products impact you.
If you are upgrading from a software version other than the m ost recent one, review the current release notes and all interim versions. For example, when you upg rade from V1.0 to V1.2, review the release notes for V1.1 and V1.2.
®
or Simulink®). Determine if enhancements,
What Is in the Release Notes
New Features and Changes
New functionality
Changes to existing functionality
Version Compatibility Con si derations
When a new feature or change introduces a reported incompatibility between versions, the Compatibility Considerations subsection explains the impact.
2
SummarybyVersion
Compatibility issues reported after the product release appear under Bug Reports at The MathWorks™ Web site. Bug fixes can sometimes result in incompatibilities, so review the fixed bugs in Bug Reports for any compatibility impact.
Fixed Bugs and Known Problems
The MathWorks offers a user-searchable Bug Reports database so you can view Bug Reports. The development team updates this database at release time and as more information becomes available. Bug Reports include provisions for any known workarounds or file replacem ents. Information is available for bugs existing in or fixed in Release 14SP2 or later. Information is not avail able for all bugs in earlier releases.
Access Bug Reports using y our MathWorks Account.
About Functions Being Removed
This section lists functions removed or in the process of being removed. Functions typically go through several stages across multiple releases before being co mplete ly removed. This provides time for you to make adjustments to your code.
Announcement – The release notes announce the planned removal, but
there are no functional changes; the function runs as it did before.
Warning – When you run the function, it displays a warning message
indicating it will be removed in a future release; otherwise the function runs as it did before.
Error – When you run the function, it produces an error. The error message
indicates the function was removed and suggests a replacement function, if one is available.
Removal – When you run the function, it fails. The error message is the
standard message when MATLAB does not recognize an entry.
Functions might be in a stage for one or more releases before moving to another stage. Functions are listed in the Functions Being Removed sectio n only when they enter a new stage and their behavior changes. For example, if a function displayed a warning in the previous release and errors in this
3
SimBiology®Release Notes
release, it appears on the list. If it continues to display a warn i ng , it does n ot appear on the list because there was no change between the releases.
Not all functions go through all stages. For example, a function’s impending removal might not be announced, but instead the first notification might be that the function displays a warning.
The release notes include actions you can take to mitigate the effects of a function’s removal, such as adapting your code to use a replacement function.
4
Version 3.2 (R2010a) SimBiology®Software
Version 3.2 (R2010a) SimBiology Software
This table summarizes what’s new in Version 3.2 (R2010a):
New Features and Changes
Yes Details below
Ver sion Compatibility Considerations
Yes—Details labeled as Compatibility Considerations, below. See also Summary.
New features and changes introduced in this version are:
“Stochastic Approximation Expectation-Maximization (SAEM) Algorithm
for Fitting Population Data” on page 5
“Enhanced Support for Importing NONMEM Formatted Files” on page 6
“New Mode for Accelerating Simulations” on page 6
“Enhanced Support for Applying Dosing to a Model and Dosing Multiple
Compartments” on page 6
“Support for Parameter Transformations” on page 8
“Support for Error Models ” on page 8
“Functions and Propertie s Being Removed” on page 9
Fixed Bugs and Known Problems
Bug Reports Includes fixes
Related Documentation at Web Site
Printable Release Notes: PDF
Current product documentation
Stochastic Approximation Expectation-Maximization (SAEM) Algorithm for Fitting Population Data
Now you can choose the SAEM algorithm when fitting population data. This functionality requires Statistics Toolbox™ (Version 7.3 or later).
The new stochastic algorithm for fitting NLME models is more robust with respect to starting values, enables parameter transformations, and relaxes assumption of constant error variance.
For more information, see:
5
SimBiology®Release Notes
sbionlmefitsa in the SimBiology®documentation
nlmefitsa in the Statistics Toolbox documentation
“Pharmacokinetic Modeling Functionality” in the SimBiology
documentation
Enhanced Support for Importing NONMEM Formatted Files
Import data files with NONMEM®interpretation of column headers. SimBiology interprets the data file d uring import and creates the data set to use during fitting. For more information see “Importing Data — Supported Files and Data Types”. After import you can also create dose s chedules using the information in the imported data.
New Mode for Accelerating Simulations
SimBiology enables you to prepare your mo de ls for accelerated simulations. Use this functionality to run many simulations with different initial conditions, or to run very long simulations (for example, simulations that take a minute or longer to run). Before you can use this feature you must install a Ccompiler,andrun information see “Accelerating Simulations” in the SimBiology documentation.
mex -setup before you can use this feature. For more
Enhanced Support for Applying Dosing to a Model and Dosing M ultiple Compartments
Create and apply dosing using RepeatDose Object, ScheduleDose Object and the adddose method at the command line or the Doses pane in the desktop.
6
Version 3.2 (R2010a) SimBiology®Software
Compatibility Considerations
Previously, sim u la tin g mode ls with dosing informatio n required the
sbiosetdosingprofile function. Using sbiosetdosingprofile now
7
SimBiology®Release Notes
errors and you must change how you apply dosing. For related information on dosing in pharmacokinetic models see “About Dosing Types” in the SimBiology documentation.
Previously, you could specify that a parameter is dosed. No w only species
can accept a dose.
Previously, the PK models you created using the New Project Wizard or
the
construct method varied depending on the dose chosen. Now you get
the same model, w hich allows you to change between dosing types.
Support for Parameter Transformations
During parameter fitting, you now can specify parameter transformations. The following parameter transformations are now supported:
none
log
probit
logit
You can specify parameter transformations in individual (sbionlinfit) and population fitting ( “Specifying Parameter Transformations” in the SimBiolog y documentation.
sbionlmefit or sbionlmefitsa) functions . See
Compatibility Considerations
Previously, sbionlinfit and sbionlmefit returned the log-transformed estimates for the fixed effects. Now
sbionlmefitsa) return untransformed and transformed estimates for the
fixed effects.
sbionlinfit, sbionlmefit (and
Support for Error Models
Parameter fitting functionality now supports the following error models:
constant
proportional
combined
8
Version 3.2 (R2010a) SimBiology®Software
exponential
Youcanspecifyanerrorterminconjunction with a population fitting (
sbionlmefitsa) function.
For more information see, “Specifying an Error Model” in the SimBiolo gy documentation.
Functions and Properties Being Removed
For more information about the process of removing functions, see “About Functions Being Removed” in “What Is in the Release Notes” on page 2.
Function or Property Name
sbiosetdosingprofile
What Happens When You Us e Function or Property?
Errors
Use This Instead Compatibility
Considerations
RepeatDose Object, ScheduleDose Object, adddose
See th e Compat ibility Considerations subheading in“Enhanced Support for Applying Dosing to a Model and Dosing Multiple Compartments” on page 6.
9
SimBiology®Release Notes
Version 3.1 (R2009b) SimBiology Software
This table summarizes what’s new in Version 3.1 (R2009b):
New Features and Changes
Yes Details below
Ver sion Compatibility Considerations
Yes—Details labeled as Compatibility Considerations, below. See also Summary.
New features and changes introduced in this version are:
“Increased Performance When RepeatedlySimulatingaModel”onpage10
“Enhanced Desktop Support for Scanning Using Monte Carlo Methods”
on page 11
“Desktop Support for Copy and Paste ” on page 11
“View Status of Parameter Fitting Task During Run” on page 11
“Improved Usability for Model Building and Debugging” on page 11
“Unit Conversion C ompatibility Considerations” on page 12
“Functions and Properties Being Removed” on page 12
Fixed Bugs and Known Problems
Bug Reports Includes fixes
Related Documentation at Web Site
No
Increased Performance When Repeatedly Simulating aModel
Many analysis tasks that involve repeatedly simulating a model now run faster. These tasks include parameter fits and scans, as well as repeatedly simulating the same model using different variants or setting different values for the and the the model generates any applicable warnings only the first time. To display warnings again, use the verification methods described in “Verifying that a Model H as No W a rnings or Errors” in the SimBiology User’s Guide.
InitialAmount of species, the Capacity of compartments,
Value of parameters. Under these conditions, repeatedly simulating
10
Version 3.1 (R2009b) SimBiology®Software
Enhanced Desktop Support for Scanning Using Monte Carlo Methods
Scanning analysis now includes additional support for Monte Carlo methods. You can specify sampling using the options
distribution
The Statistics Toolbox is required for this functionality. For more information, see “Scanning Analysis” in the SimBiology User’s Guide documentation.
or lat in hypercube sample with a normal distribution.
multivariate normal
Desktop Support for Copy and Paste
The SimBiology desktop now supports copying and pasting. Use the typical keyboard shortcuts or the context menus to execute these commands.
View Status of Parameter Fitting Task During Run
You can track the status of a parameter fit when using nonlinear mixed effects with the selecting an option in the SimBiology desktop. For more information, see “Obtaining the Status of Fitting” (command line) or “Obtaining the Status of Fitting” (desktop).
sbiofitstatusplot function at the command line or by
Improved Usability for Model Building and Debugging
The SimBiology des kto p now supports:
Dynamically updated error indicators for variants, configuring plots,
and defining scans — Shows correctly defined, incorrectly defined, and warning indicators (green, red, and yellow) for additional help with model debugging.
M-Lint indicators — Wherever code appears in the desktop, the indicators
used by M-lint also appear.
Help for us er-identified MATLAB code—Selectandusethecontextmenu
to find help on functions where code appears in the desktop.
11
SimBiology®Release Notes
Unit Conversion
Previously a mod off. Now, a model an error. Set
Functions and
For more infor Functions Be
Function or Property Name
-flat as an option for
getstoichmatrix and getadjacencymatrix
Compatibility Considerations
el with no units specified could have unit conversion on or
with no units specified that has
itConversion
Un
off for models without units.
UnitConversion on shows
Properties Being Removed
mation about the process of removing functions, see “About
ing Rem ove d” in “What Is in the Release Notes” on page 2.
What Happens When You Us e Function or Property?
Errors
Use This Instead Compatibility
Considerations
Not appli
cable
Since support for submodels has been removed, this option no longer applies.
12
Version 3.0 (R2009a) SimBiology®Software
Version 3.0 (R2009a) SimBiology Software
This table summarizes what’s new in Version 3.0 (R2009a):
New Features and Changes
Yes Details below
Ver sion Compatibility Considerations
No Bug Reports
New features and changes introduced in this version are:
“New Feature to Import, Visualize, and Statistically Analyze Clinical and
Experimental Data” on page 13
“New Functionality to Create Pharmacokinetic Models” on page 14
“New Functionality to Fit Data and Estimate Parameters Using Nonlinear
Mixed Effects” on page 14
“New Diagnostic Plots for Individual and Population Fitting Results” on
page 15
“New Project Wizard to Add Data, Create Models, and Specify Tasks” on
page 15
“New simbiology Command to Open the SimBiology Desktop” on page 16
“Enhanced Usability Features in the SimBiology Desktop” on page 16
“New Demo for Pharmacokinetic Modeling” on page 16
Fixed Bugs and Known Problems
Includes fixes
Related Documentation at Web Site
No
New Feature to Import, Visualize, and Statistically Analyze C linical and Experimental Data
You can import tabular data into the SimBiology desktop or the MATLAB Workspace. The supported file types are
At the command line, you can process and visualize the data using command-line functions. In the SimBiology desktop, you can filter the raw data to suppress outliers, visualize data using MATLAB plots, and calculate
.xls, .csv,and.txt.
13
SimBiology®Release Notes
statistics to analyze the data. You can further choose to plot the imported data with any analysis task.
See “Importing Data — Supported Files and Data Types” in the SimBiology User’s Guide for more information.
New Functionality to Create Pharmacokinetic Models
You can automatically generate pharmacokinetic (PK) models by specifying number of compartments, dosing type, and method of elimination. If you plan to use the MATLAB command line, see “Creating PK Models at the Command Line” in the SimBiology User’s Guid e for more information.
If you plan to use the SimBiology desktop, the new Add Model wizard lets you automatically generate PK models in the desktop. See “Creating PK Models in the SimBiology Desktop Using a Wizard” in th e SimBiology User’s Guide for more information.
In addi tion, in the Sim B iology desktop you can start by creating a new project using the new Project Wizard which also lets you add data, create models, and add analysis tasks in a SimBiology project. See “New Project W izard to Add Data, Create Models, and Specify Tasks” on page 15 for additional information.
14
New Functionality to Fit Data and Estimate Parameters Using Nonlinear Mixed Effects
You can perform both individual and population fits to grouped longitudinal data.
Individual fit — Fit data using nonlinear least squares method, estimate
parameters, and calculate residuals and the estimated coefficient covariance matrix.
Population fit — Estimate the fixed effects and the random sources of
variation on parameters, using nonlinear mixed-effects models.
You can use the following methods to estimate the fixed effects:
- LME — Linear mixed-effects approximation
- RELME — Restricted LME appr ox imation
Version 3.0 (R2009a) SimBiology®Software
- FO — First-order estimate
- FOCE — First-order conditional estimate
For more information, see “Pharmacokinetic Modeling Functionality” in the SimBiology User’s Guide.
New Diagnostic Plots for Individual and Population Fitting Results
In the SimBiology desktop, after fitting the data, the analysis generates diagnostic plots that show:
The predicted time courses and observations for an individual or the
population
Observed versus predicted values
Residuals versus time, group, or predictions
Distribution of the residuals
A box-plot for random effects or parameter estimates from individual
fitting.
For more information, see “Visualizing Parameter Fitting Results and Generating Diagnostic Plots” in the SimBiology User’s Guide.
New Project Wizard to Add Data, Create Models, and Specify Tasks
The newly added P roject Wizard in the SimB iology desktop lets you:
Add data from text files, spreadsheets, or the MATLAB Workspace.
Create models, including autom ati cal ly generate pharmacokinetic models
by specifying number of compartments, dosing type, and me thod of elimination.
Specify analysis tasks to add to the project.
15
SimBiology®Release Notes
For an example of how to use the Project Wizard, see “Modeling U sing the SimBiology Graphical User Interface” in the SimBiology Getting Started Guide.
New simbiology Command to Open the SimBiology Desktop
A new function, simbiology , has been added for enhanced usability in opening the SimBiology desktop. function, which is also supported.
simbiology is equivalent to the sbiodesktop
Enhanced Usability Features in the SimBiology Desktop
The following enhancements to the SimBiology desktop are included in this release:
Back and Forward buttons to help with navigation between desktop panes
16
In Preferences, the ability to choose default model tasks to add to a
model when loading an SBML file or importing a model from the MATLAB Workspace
New Demo for Pharmacokinetic Modeling
There is a new demo showing pharmacokinetic modeling functionality (Modeling the Population Pharmacokinetics of Phenobarbital in Neonates). To see all demos, click SimBiology demos or type
'SimBiology')
at the command prompt.
demo('MATLAB',
Version 2.4 (R2008b) SimBiology®Software
Version 2.4 (R2008b) SimBiology Software
This table summarizes what’s new in Version 2.4 (R2008b):
New Features and Changes
Yes Details below
Ver sion Compatibility Considerations
Yes—Details labeled as Compatibility Considerations, below. See also Summary.
New features and changes introduced in this version are:
“Enhanced Usability with the Redesigned Reaction Pane” on pag e 17
“Additional Support for Showing Usages and Generating Reports in the
SimBiology Desktop” on page 18
“Support for Specifying Additional Inputs in Custom Plot Types” on page 19
“Edit Graphical Models Using the New Block Property Editor” on page 20
“Manage and Share Libraries Using the New Library Explorer” on page 21
“Additional Options for Renaming Compartments, Species, and
Parameters” on page 23
“Change in the Random Number Generator Used During Stochastic
Simulations” on page 24
Fixed Bugs and Known Problems
Bug Reports Includes fixes
Related Documentation at Web Site
No
“Functions and Properties Being Removed” on page 25
Enhanced Usability with the Redesigned Reaction Pane
In the SimBiology desktop, the redesigned reaction pane consolidates the procedure to configure kinetic law, rate parameters, rate species, and reaction rates on one screen.
17
SimBiology®Release Notes
18
Additional Support for Showing Usages and Generating Reports in the SimBiology Desktop
Additional Support for Showing Usages
The Compartments and Species panes now have added support for showing usages of compartments and species in a model. To show usages of a component, right-click (Windows
®
), or Ctrl+click (Macintosh®)the
Version 2.4 (R2008b) SimBiology®Software
compartment or species table, and select Show Usages. Support has also been added for showing usages from the Diagram View.
Additional Sup port for Generating Reports
You can now automatically populate report contents with one click in the Report pane. In the Project Explorer, right-click (Windows), or Ctrl+click (Macintosh) Project Tasks and select Add Task > Generate report to create a report. Select Help > SimBiology Desktop Help to see the context-sensitive help for information on how to generate reports. Click AutoBuild to populate the contents of your report automatically.
port for Specifying Additional Inputs in Custom
Sup
tTypes
Plo
can now specify additional inputs for plot types and define their types,
You
fault values, and ranges where applicable. For example, you can use this
de
aturetoextendthe
fe
Time plot with an additional input to specify markers.
19
SimBiology®Release Notes
Compatibility Considerations
This consideration applies when you previously created custom plot types. Before, you could define the number of species or parameters that could be specified for should modify your plot code to enforce this constraint. For an example of enforcing the constraint, see the code for the built-in plot type
To access this code:
1 In the SimBiology desktop, select Desktop > Library Explorer.The
Library Explorer opens.
2 Select Plot Types.
3 In the plot types table, select XY. The code section updates to show XY plot
type code.
x or y arguments. This functionality has been removed. You
XY.
Edit Graphical Models Using the New Block Property Editor
The Block Property Editor is a tool that facilitates model building using the Diagram View pane by docking next to the diagram and allowing you to change properties of the selected block in the diagram. If you select multiple blocks, you can edit the properties that are common between each block. To open the Block Property Editor, select a block in the Diagram View pane, and then select Diagram > Tools > Block Property Editor.
20
Version 2.4 (R2008b) SimBiology®Software
Manage and Share Libraries Using the New Library Explorer
The Library Explorer adds the ability to add, modify, and share the contents of kinetic law, plot type, unit, unit prefix, and blo ck libraries. To open the
Library Explorer, in the SimBiology desktop, select Desktop > Show Library Explorer.
21
SimBiology®Release Notes
The Library Explorer shows all built-in and user-defined components, namely kinetic laws, units, unit prefixes, plot types, and blocks.
22
Kinetic Laws — C ontains kinetic laws that you can use as templates
while creating a reaction rate expression.
Units — Contains units that you can specify for compartment capacity,
species amounts and parameter values, to do dimensional analysis and unit conversion during simulation.
Unit Prefixes — Contains all unit prefixes that you can specify in
combination with a valid unit for compartment capacity, species amounts and parameter values, to do dimensional analysis and unit conversion during simulation.
Plot Types — Contains different types of plots that you can use with
Model Tasks to visualize your results.
Blocks — Contains blocks that you can use in the Diagram View.
For help, open the Library Explorer and select Help > SimBiology
Desktop Help to see the context-sensitive help. Select a library in the Library Explorer to view information specific to the library.
Version 2.4 (R2008b) SimBiology®Software
Additional Options for Renaming Compartments, Species, and Parameters
New Method for Renaming at the Command Line
The newly added rename method allows you to change the name of a compartment, species, or parameter, and update the name in expressions that refer to the component. Use the enable the name change and expression update.
New Options for Renaming in the SimBiology Desktop
You can specify how compartments, species, and parameter names should be updated in expressions. When you rename a compartment, species, or parameter, by default the names are settobeupdatedinallexpressionsthat refer to the component being renamed. During renaming, if the component is used in one or more expressions, you will see a dialog box that tells you which expressions will be updated. For example, the following dialog box appears when you try to rename species
rename method instead of the set method to
G to Gnew.
You can choose not to see this dialog box for every instance of renaming. You can also set your preferences on whether ex pre ssio n s should be updated. To select preferences for renaming:
1 Select File > Preferences. The Preferences dialog box opens.
23
SimBiology®Release Notes
2 Click Rename to view and select default renaming options.
You can also specify whether to update expressions while renaming a component in the Compartment, Species,orParameter panes. Right-click (Windows or Linux compartment table and select Rename. Thisallowsyoutoselectwhetherto use the new name in all expressions referring to the component.
®
)orCtrl+click (Macintosh) the species, parameters, or
Compatibility Considerations
Previously, if you changed the name in a table or the diagram, expressions that used the components were not updated unless you selected Rename in Expressions from the context menu. Now the default is to change the name in expressions. But, you will see a dialog box that allows you to cancel the action if necessary, and you can specify the default as shown in “Additional Options for Renaming Compartments, Species, and Parameters” on page 23.
Change in the Random Number Generator Used During Stochastic Simulations
The default random number generator used during stochastic simulation has changed. The stochastic solver now uses the random numbers from the MATLAB default stream. When you run a model using a stochastic solver, and have set the different simulation results relative to previous releases because the random numbers used may be different.
RandomState property in the configuration set, you may se e
24
For more information about the change to the random number generator, see Upgrade to Random Number Generator in the MATLAB release notes.
Compatibility Considerations
If you never set the RandomState property, there should be no compatibility considerations. If however, you have previously set model and want to reproduce your previous results, type at the command line before running the simulation. This sets the random number generator to the one used in previous releases.
RandomState for your
rand('state',0);
Version 2.4 (R2008b) SimBiology®Software
Functions and Pr
For more informa Functions Being
Function or Property Name
sbioevent
sbiopara
sbioreaction
Mode
argu
iorule
sb
meter
l name
ment for
as an input
sbioroot
operties Being Removed
tion about the process of removing functions, see “About
Removed” in “What Is in the Release Notes” on page 2.
What Happens When You Us e Function or Property?
Errors
Errors
Errors
Errors
Errors
Use This Instead Compatibility
Considerations
addevent
Events must model. Rep instances with ad dev
addparam
eter
Parameters must belong to a model or a kinetic law. Replace all existing instances of with addparame ter.
addreaction
Reactions must belong to a model. Replace all existing instances of with addreac tion .
sbioselect
drule
ad
root
sbio
el name as an input
amod
ment. Use
argu
uery models by name.
to q
Rules must belong to a model. Replace all existing instances of
addrule.
belong to a
lace all existing
of
sbioevent
ent
.
sbioparameter
sbioreaction
does not accept
sbioselect
sbiorule with
25
SimBiology®Release Notes
Function or Property Name
sbiospecies
sbioregisterunit
sbiounregisterunit
sbioregisterunitprefix
sbiounregisterunitprefix
BuiltInKineticLaws
BuiltInUnitPrefixes
BuiltInUnits
What Happens When You Us e Function or Property?
Errors
Errors
Errors
Errors
Errors
Errors
Errors
Errors
Use This Instead Compatibility
Considerations
addspecies
Species must belong to a compartment. Replace all existing instances of
sbiospecies with
addspecies.
Unit object and sbioaddtolibrary
See “New Way to Add Units and Unit Prefixes” on p a ge
40.
sbioremovefromlibrary
See “New Way to Add Units and Unit Prefixes” on p a ge
40.
Unit object and sbioaddtolibrary
See “New Way to Add Units and Unit Prefixes” on p a ge
40.
sbioremovefromlibrary
See “New Way to Add Units and Unit Prefixes” on p a ge
40.
BuiltInLibrary
See “Changes to the Library Structure in the Root” on page 37.
BuiltInLibrary
See “Changes to the Library Structure in the Root” on page 37.
BuiltInLibrary
See “Changes to the Library Structure in the Root” on page 37.
26
Version 2.4 (R2008b) SimBiology®Software
Function or Property Name
UserDefinedKineticLaws
UserDefinedUnits
UserDefinedUnitPrefixes
What Happens When You Us e Function or Property?
Errors
Errors
Errors
Use This Instead Compatibility
Considerations
UserDefinedLibrary
See “Changes to the Library Structure in the Root” on page 37.
UserDefinedLibrary
See “Changes to the Library Structure in the Root” on page 37.
UserDefinedLibrary
See “Changes to the Library Structure in the Root” on page 37.
27
SimBiology®Release Notes
Version 2.3 (R2008a) SimBiology Software
This table summarizes what’s new in Version 2.3 (R2008a):
New Features and Changes
Yes Details below
New features and changes introduced in this version are:
“Support for 64-Bit Microsoft Windows” on page 28
“Functions and Properties Being Removed” on page 28
Support for 64-Bit Microsoft Windows
SimBiology software now has added support for 64-bit Windows (Win64).
Functions and Properties Being Removed
For more information about the process of removing functions, see “About Functions Being Removed” in “What Is in the Release Notes” on page 2.
Function or Property Name
sbioevent
sbioparameter
Ver sion Compatibility Considerations
Yes Summary
What Happens When You Us e Function or Property?
Warns
Warns
Fixed Bugs and Known Problems
Bug Reports Includes fixes
Use This Instead Compatibility
addevent
addparameter
Related Documentation at Web Site
No
Considerations
Events must belong to a model. Replace all existing instances of with ad deve nt.
Parameters must belong to a model or a kinetic law. Replace all existing
sbioevent
28
Version 2.3 (R2008a) SimBiology®Software
Function or Property Name
sbioreaction
Model name as an input
argument for
sbiorule
sbiospecies
sbioregisterunit
sbiounregisterunit
sbioregisterunitprefix
sbioroot
What Happens When You Us e Function or Property?
Warns
Errors
Warns
Warns
Errors
Errors
Errors
Use This Instead Compatibility
Considerations
instances of sbiopa rameter with addparame ter.
addreaction
Reactions must belong to a model. Replace all existing instances of
sbioreaction
with addreac tion .
sbioselect
sbioroot
does not accept a model name as an input argument. Use to query models by name.
addrule
Rules must belong to a model. Replace all existing
addspecies
instances of
addrule.
Species must belong to
sbiorule with
a compartment. Replace all existing instances of
sbiospecies with
addspecies.
Unit object and sbioaddtolibrary
See “New Way to Add Units and Unit Prefixes” on p a ge
40.
sbioremovefromlibrary
See “New Way to Add Units and Unit Prefixes” on p a ge
40.
Unit object and sbioaddtolibrary
See “New Way to Add Units and Unit Prefixes” on p a ge
40.
sbioselect
29
SimBiology®Release Notes
Function or Property Name
sbiounregisterunitprefix
BuiltInKineticLaws
BuiltInUnitPrefixes
BuiltInUnits
UserDefinedKineticLaws
UserDefinedUnits
UserDefinedUnitPrefixes
What Happens When You Us e Function or Property?
Errors
Errors
Errors
Errors
Errors
Errors
Errors
Use This Instead Compatibility
Considerations
sbioremovefromlibrary
See “New Way to Add Units and Unit Prefixes” on p a ge
40.
BuiltInLibrary
See “Changes to the Library Structure in the Root” on page 37.
BuiltInLibrary
See “Changes to the Library Structure in the Root” on page 37.
BuiltInLibrary
See “Changes to the Library Structure in the Root” on page 37.
UserDefinedLibrary
See “Changes to the Library Structure in the Root” on page 37.
UserDefinedLibrary
See “Changes to the Library Structure in the Root” on page 37.
UserDefinedLibrary
See “Changes to the Library Structure in the Root” on page 37.
30
Version 2.2 (R2007b+) SimBiology®Software
Version 2.2 (R2007b+) SimBiology Software
This table summarizes what’s new in Version 2.2 (R2007b+):
New Features and Changes
Yes Details below
Ver sion Compatibility Considerations
Yes—Details labeled as Compatibility Considerations, below. See also Summary.
New features and changes introduced in this version are:
“Changes to the Model Structure” on page 31
“Events” on page 33
“Variants” on page 33
“Support for Analysis Tasks in the Desktop” on page 34
“Changes to the Library Structure in the Root” on page 37
“New Features for Solvers and Simulation Settings” on page 38
“New Plot Functions” on page 40
“New Sensitivity Analysis PropertyforSpeciesOutputs”onpage40
“New Way to Add Units and Unit Prefixes” on page 40
Fixed Bugs and Known Problems
Bug Reports Includes fixes
Related Documentation at Web Site
No
“Functions and Properties Being Removed” on page 41
Changes to the Model Structure
The following new features and changes apply to a model’s structure:
“Compartments Now Supported” on page 32
“Submodel Support Will Be Removed” on page 32
31
SimBiology®Release Notes
Compartments Now Supported
SimBiology models now let you add compartments to a model, specify compartment size, simulate, and do analysis with multiple compartments. Any model co ntaining species must have a compartment, and the species must belong to a compartment. You can also perform dimensional analysis and unit conversion accounting for the specified compartment size. For more information on compartments, refer to the following sources in the documentation:
“Compartment” — Introduction to compartments in the SimBiology Getting
Started Guide.
Compartment object — Reference for compartment objects.
Submodel Support Will Be Removed
Support for submodels will be removed in a future release. You can still open models containing submodels and create submodels, but you cannot simulate or perform any analysis tasks on the model. Therefore, you should transition to using compartments where applicable.
32
Compatibility Cons id er ati ons . If you have submodels in your previously created model, you can still open your model, but you must convert the submodels into top-level SimBiology models to be able to perform any tasks.
To convert submodels, use
sbioupdate.
If you open a model that contains submodels in the SimBiologydesktop, the submodels are automatically converted to models and placed in separate model sessions. See
As a result o f removing submodels, the of the model object are no longer relevant. You can still access the
sbioupdate for more information.
addmodel method and Models property
addmodel
method and the Models property for this version of the software, though it may be removed in a future release.
Version 2.2 (R2007b+) SimBiology®Software
Events
You can now add events to SimBiology models. Use events to describe sudden changes in a model system. Events are supported only by the and the stochastic solver
For more information on events, refer to the following:
“Events” — Introduction to events in the SimBiology Getting Started Guide.
“Changing Model Component Values Using Events” — Discussion about
events including how events are evaluated in the SimBiology User’s Guide.
Event object — Reference for event objects.
“Sundials Solvers” — Deterministic solver for simulating models with
events in the SimBiology User’s Guide.
Models containing events do not s upport sensitivity analysis.
ssa.
sundials so lver
Variants
Variants let you store the names and values of model components and use the values stored in a variant as the alternate value to apply during a simulation. You can store values for species compartment
Capacity in a variant.
InitialAmount,parameterValue,and
For more information on variants, refer to the following:
“Variants” — Introduction to variants in the SimBiology Getting Started
Guide.
Variant object — Reference for variant objects in the SimBiology
Reference.
“Desktop Example — Applying Changes to Parameter Value Using a
Variant” — Example in a tutorial in the SimBiology Model Reference.
In the SimBiology desktop, expand Model Variable Settings and double-click Variants to open the Variants pane. The SimBiology Desktop Help updates with more information on adding and setting variants. If the help is not open in the desktop, select Help > SimBiology Desktop Help.
33
SimBiology®Release Notes
Support for Analysis Tasks in the Desktop
The SimBiologydesktop now supports adding and managing analysis tasks through the following features:
34
“Task Manager” on page 34
“Sensitivity Analysis in the Desktop” on page 35
“Scanning and Scanning with Sensitivities in the Desktop” on page 36
“Ensemble Simulation Runs in the Desktop” on page 36
“Conserved Cycle Calculations in the Desktop” on page 36
“Create Custom Analysis Tasks” on page 37
“Generate Reports for Projects” on page 37
Task Manager
The Task Manager lets you add and manage simulation and analysis tasks. In the Project Explorer, double-click Model Session.TheModel Session pane opens with the Task Manager listed on the right.
Version 2.2 (R2007b+) SimBiology®Software
Click a task to add it to your model. The desktop adds the task to the Project Explorer and op ens the task pane. For more information on setting up and running a task in the desktop, open the task pane and select Help > SimBiology Desktop Help to see the context-sensitive help.
Sensitivity Analysis in the Desktop
Sensitivity analysis is now supported in the desktop. Sensitivity analysis was previously available only through command line. Sensitivity analysis lets you calculate the time-dependent sensitivities of a species specified in SpeciesOutputs with respect to species initial conditions and parameter values.
35
SimBiology®Release Notes
See “Performing Sensitivity AnalysisUsingtheDesktop”intheSimBiology User’s Guide for more information. You must have a model in the desktop for this feature to be enabled.
For more information on sensitivity a nalysis, see “Sensitivity Analysis” in the SimBiology User’s Guide.
Scanning and Scanning with Sensitivities in the Desktop
You can perform species and parameter scanning analysis alone or in combination with sensitivity analysis in the d esk t op . Scan a parameter value or a species initial amount to determine the effect of a range of values of the parameterorspecies.
Combine the scan with sensitivity analysis to explore the sensitivity of a species with respect to a range of values of a paramet er or a species.
Forinformationonhowtoaddthetasktoamodel,see“TaskManager”on page 34. For more information on setting up and running the task in the desktop, open the task pane and select Help > SimBiology Desktop Help to see the context-sensitive help. Youneedamodelinthedesktopforthis featuretobeenabled.
36
Ensemble Simulation Runs in the Desktop
The SimBiologydesktop now supports ensemble simulations. You can perform ensemble simulations using the stochastic solvers to gather data from multiple stochastic runs of the model.
See “Running Ensemble Simulations in the Desktop” in the SimBiology User’s Guide for more information. You need a mode l in the desktop for this feature to be enabled.
Conserved Cycle Calculations in the Desktop
The SimBiologydesktop now supports conserved cycle calculations. This feature l ets you calculate a complete set of linear conservation relations for the species in a SimBiology model object. For an introduction, see “Moiety Conservation” in the SimBiology User’s Guide .
Version 2.2 (R2007b+) SimBiology®Software
Forinformationonhowtoaddthetasktoamodel,see“TaskManager”on page 34. For more information on setting up and running the task in the desktop, open the task pane and select Help > SimBiology Desktop Help to see the context-sensitive help. Youneedamodelinthedesktopforthis featuretobeenabled.
Create Custom Analysis Tasks
The SimBiologydesktop lets you create custom tasks that are associated with a project. You can either write new code or copy and modify task code from built-in tasks in the desktop. For more information about creating custo m tasks, see “Desktop Example — Creating Custom Analysis” in the SimBiology User’s Guide.
Forinformationonhowtoaddthetasktoamodel,see“TaskManager”on page 34. For more information on setting up and running the task in the desktop, open the task pane and select Help > SimBiology Desktop Help to see the context-sensitive help. Youneedamodelinthedesktopforthis featuretobeenabled.
Generate Reports for Projects
You can now generate reports for your projects. Report templates let you generate a report with specified information about a model. To generate a template, in the Project E xplorer,clickReport Templates to open the Report Templates pane. Select Help > SimBiology Desktop Help to see the context-se ns itive help for information on how to generate reports.
Changes to the Library Structure in the Root
Built-in and user-defined libraries for units, unit prefixes, and abstract kinetic laws are now organized under two root object properties,
UserDefinedLibrary, with subcategories for units, unit prefixes, and abstract
kinetic laws. See in SimBiology Reference for more information.
Root object, BuiltInLibrary,andUserDefinedLibrary
Compatibility Considerations
In previous versions, the libraries were organized under six properties:
UserDefinedKineticLaws
BuiltInLibrary and
37
SimBiology®Release Notes
BuiltInKineticLaws
UserDefinedUnits
BuiltInUnits
UserDefinedUnitPrefixes
BuiltInUnitPrefixes
The changes to the library structure improve the organization of root object properties.
To illustrate the change using an example, previously you would access a user-defined kinetic law using the following syntax:
rootObj = sbioroot; get(rootObj, 'UserDefinedKineticLaws')
You must now use the following syntax:
rootObj = sbioroot; get(rootObj.UserDefinedLibrary, 'KineticLaws')
38
New Features for Solvers and Simulation Settings
The following new features and changes apply to solvers and simulation settings:
“Support for Sundials Solvers” on page 38
“New Property in Configuration Sets to Specify Species Dimensions” on
page 39
“SimData Object Holds All Si mulation Data” on page 39
Support for Sundials Solvers
The Sundials package of solvers has been added in this release. The Sundials solvers are part of a freely available third-party package developed at Lawrence Livermore National Laboratory. Models that contain events are supported by the Sundials solver s and by the stochastic solver information, see “Sundials Solvers” in the SimBiology U ser’s Guide.
ssa.Formore
Version 2.2 (R2007b+) SimBiology®Software
New Property in Configuration Sets to Specify Species Dimensions
The new property DefaultSpeciesDimension lets you specify whether the default species dimensions should be
concentration (default) or substa nce.
This property thus lets you specify whether the solver should account for compartment capacity. If however, you specify the species units in the
InitialAmountUnits property, these units define the species dimension
regardless of the value in
DefaultSpeciesDimension.
SimData Object Holds All Simulation Data
The SimBiology SimData object now stores the data returned from any simulation. For example, the output from the now stored in a
SimData object which holds time and state data as well
as metadata, such as the types and names for the logged states or the configuration set used during simulation.
You can also store data from multiple simulation runs as an array of SimData objects. Thus, the output of objects. See
SimData object for more information and a list of methods and
sbioensemblerun is an array of SimData
properties.
sbiosimulate function is
Compatibility Considerations. The SimData object is now the preferred container for simulation and analysis task data. Previously, simulation and analysis data w ere stored as time series objects. Functions that used to return time series objects now return SimData objects. If you have time series objects in your projects, you can convert them using
sbioupdate. Functions
that used to take a time series object as an input argument now take SimData object. You can use time series objects in an input argument, but you see a warning. Support for time series objects in SimBiology functions may be removed in a future version.
The
sbiogetsensmatrix and sbiogetnamedstate functions are being
replaced by the SimData object methods
getsensmatrix and selectbyname
respectively.
39
SimBiology®Release Notes
New Plot Functio
Therearetwonew functions let yo Object Holds Al
sbioplot plot
objects from a the object. Th tree, where y
sbiosubplot
objects int object. You subset of th
New Sensit
u plot data directly from the SimData object (see “SimData
l Simulation Data” on page 39).
s each simulation run for a SimData object or array of SimData
model in the same figure. The plot is a time plot of each state in
e figure also shows a hierarchical display of all the runs in a
ou can choose which trajectories to show.
plotseachsimulationrunforaSimDataobjectorarrayof
o its own subplot. The subplot is a time plot of each state in the
can navigate through the plots in the figure window and select a e plots to view.
ivity Analysis Property fo r Species
ns
plot functions —
sbioplot and sbiosubplot.Both
Outputs
To set up s called you want
Compatibility Considerations
Previo the spe improv
ensitivity analysis, you must now specify an additional property
eciesOutputs
Sp
to compute sensitivities.
usly, sensitivity analy s is used the species specified in
cies for which sensitivities should be calculated.
es the functionality by separating the use of the properties.
.InSpeciesOutputs, specify the species for which
StatesToLog as
SpeciesOutputs
40
have models from a previous version configured for sensitivity analysis,
If you you mu
Speci
give to us this
Spec
New
Un an
st specify species for which you want to compute sensitivities in the
esOutputs
sawarningthatthe
e the species specified in
context may not be available in a future version, so you should set the
iesOutputs
property. Until this property is specified, sensitivity analysis
SpeciesOutputs property is not set, and continue s
StatesToLog. The use of StatesToLog in
property for your models, if applicable.
Way to Add Units and Unit Prefixes
its and unit prefixes are now represented by objects. You can create units
d prefixes and add them to the user-defined library using the function
Version 2.2 (R2007b+) SimBiology®Software
sbioaddtolibrary.SeeUnit object and UnitPrefix object for more
information.
Compatibility Considerations
Previously, sbioregisterunit and sbiounregisterunit created and removed units respectively. These functions now produce warnings and will be removed in a future version. Use unit objects and instead.
sbioremovefromlibrary
Similarly, created and removed unit prefixes respectively. These functions now produce warnings and will be removed in a future version. Use unit prefix objects and
sbioremovefromlibrary instead.
Functions and Properties Being Removed
For more information about the process of removing functions, see “About Functions Being Removed” in “What Is in the Release Notes” on page 2.
Function or Property Name
addmodel
Models
sbioregisterunitprefix and sbiounregisterunitprefix
What Happens
Use This Instead Compatibility
Considerations When You Us e Function or Property?
Warns
addcompartment,where
applicable
See “Submodel
Support Will Be
Removed” on page
32.
Still runs
Compartments,where
applicable
See “Submodel
Support Will Be
Removed” on page
32.
41
SimBiology®Release Notes
Function or Property Name
Model name as an input
argument for
sbioregisterunit
sbiounregisterunit
sbioregisterunitprefix
sbiounregisterunitprefix
sbiogetsensmatrix
sbioroot
What Happens When You Us e Function or Property?
Warns
Warns
Warns
Warns
Warns
Warns
Use This Instead Compatibility
Considerations
sbioselect
sbioroot
does not accept a model name as an input argument. Use
sbioselect to
query models by name.
Unit object and sbioaddtolibrary
See “New Way to Add Units and Unit Prefixes” on page 40.
sbioremovefromlibrary
See “New Way to Add Units and Unit Prefixes” on page 40.
Unit object and sbioaddtolibrary
See “New Way to Add Units and Unit Prefixes” on page 40.
sbioremovefromlibrary
See “New Way to Add Units and Unit Prefixes” on page 40.
getsensmatrix
See “SimData Object Holds All Simulation Data” on page 39.
42
Version 2.2 (R2007b+) SimBiology®Software
Function or Property Name
sbiogetnamedstate
BuiltInKineticLaws
BuiltInUnits
BuiltInUnitPrefixes
UserDefinedKineticLaws
UserDefinedUnits
UserDefinedUnitPrefixes
What Happens When You Us e Function or Property?
Warns
Warns
Warns
Warns
Warns
Warns
Warns
Use This Instead Compatibility
Considerations
selectbyname
See “SimData Object Holds All Simulation Data” on page 39.
BuiltInLibrary
See “Changes to the Library Structure in the Root” on page 37.
BuiltInLibrary
See “Changes to the Library Structure in the Root” on page 37.
BuiltInLibrary
See “Changes to the Library Structure in the Root” on page 37.
UserDefinedLibrary
See “Changes to the Library Structure in the Root” on page 37.
UserDefinedLibrary
See “Changes to the Library Structure in the Root” on page 37.
UserDefinedLibrary
See “Changes to the Library Structure in the Root” on page 37.
43
SimBiology®Release Notes
Version 2.1.2 (R2007b) SimBiology Software
This table summarizes what’s new in Version 2.1.2 (R2007b):
New Features and Changes
No No Bug Reports No
Ver sion Compatibility Considerations
Fixed Bugs and Known Problems
Related Documentation at Web Site
44
Version 2.1.1 (R2007a) SimBiology®Software
Version 2.1.1 (R2007a) SimBiology Software
This table summarizes what’s new in Version 2.1.1 (R2007a):
New Features and Changes
No No Bug Reports No
Ver sion Compatibility Considerations
Fixed Bugs and Known Problems
Related Documentation at Web Site
45
SimBiology®Release Notes
Version 2.1 (R2006b+) SimBiology Software
This table summarizes what’s new in Version 2.1 (R2006b+):
New Features and Changes
Yes Details below
Ver sion Compatibility Considerations
Yes—Details labeled as Compatibility Considerations, below. See also Summary.
New features and changes introduced in this version are:
“Printing and Exporting the Diagram” on page 46
“Diagram Menu” on page 46
“Block Overview Tool” on page 47
“Miscellaneous Desktop Enhancements” on page 47
Fixed Bugs and Known Problems
Bug Reports Includes fixes
Related Documentation at Web Site
No
Printing and Exporting the Diagram
You can annotate and print your pathway’s block diagram in SimBiology, or export the diagram using can annotate the diagram with the name of the author, the date, notes, and name of the organization. You can choose to place this content as a header or footer on the diagram page.
.svg, . jpeg,or.pdf file formats. For example, you
46
Diagram Menu
The SimBiology desktop supports multiple diagra m features and actions through the Diagram menu. Use the menu options to do the following:
Copy, paste, and delete blocks.
Select model or diagram components by category (for example, select all
lines or all S pecies blocks).
Version 2.1 (R2006b+) SimBiology®Software
Filter selected portions of a model diagram to include only model or
diagram components b y category.
Edit multiple blocks or lines.
Add selected blocks to a Block Library.
Annotate and print, or export your model diagram.
Perform layout tasks, for example, hide and show blocks, move blocks to the
front or back of a diagram, rotate a block, and pin or unpin selected blocks.
Copy the style of a block and apply the style to a group of selected blocks.
Reload a graphic used for a block in the Block Properties dialog box.
Access diagram tools such as the Diagram Table View, Block L ibrary
Browser, Diagram Overview, and Block Overview.
Compatibility Considerations
There is a compatibility consideration regarding the s upport for editing multiple blocks or lines. In SimBiology Versions 2.0 and 2.0.1, if you selected multiple blocks and/or lines and applied an editing action such as Hide, Pin, or Hide Name, the action applied only to the block on w hich you selected the right-click (context) menu. Starting in Version 2.1, applicable editing actions arepropagatedtoallselectedblocks.
Block Overview Tool
The Block Overview tool provide s a summary of key information about a particular block. Hover the mouse over a block to find information in the Block Overview pane. Each block includes information pertinent to that type of block, for example, a species block overview shows Name, InitialAmount, InitialAmountUnits, the number and list of reactions the species is involved in, and a descriptionofanyindicatorsshowninthe diagram.
Miscellaneous Desktop Enhancements
The enhancements for the SimBiologydesktop let you do the following:
47
SimBiology®Release Notes
Set your preference to open a SimBiology pane with a single-click in the
Project Explorer. Select File > Preferences to open the Preferences dialog box.
Interrupt and stop m odel verification by clicking Stop when Verify is
running.
Sorttheavailableplot arguments in the Simulation and Data panes. The
XandYargumentlistsarenowtabulated.
View a species and any of its cloned blocks from the search results for the
species.
Select and view multiple results for Find and Bookmarks in either the
diagram or the table form.
48
Version 2.0.1 (R2006b) SimBiology®Software
Version 2.0.1 (R2006b) SimBiology Software
This table summarizes what’s new in Version 2.0.1 (R2006b):
New Features and Changes
No No Bug Reports
Ver sion Compatibility Considerations
Fixed Bugs and Known Problems
Includes fixes
Related Documentation at Web Site
No
49
SimBiology®Release Notes
Version 2.0 (R2006a+) SimBiology Software
This table summarizes what’s new in Version 2.0 (R2006a+):
New Features and Changes
Yes Details below
Ver sion Compatibility Considerations
Yes—Details labeled as Compatibility Considerations, below. See also Summary.
New features and changes introduced in this version are:
“Diagram Interface” on page 50
“Find and Bookmarks in Projects” on page 51
“Sensitivity Analysis” on page 51
“Parameter Estimation” on page 52
“Ensemble Simulation Runs” on page 52
“Moiety Conservation” on page 52
“Model Verification and Validation” on page 53
“Simulation and Solvers” on page 53
“New Demos for SimBiology Version 2.0” on page 54
Fixed Bugs and Known Problems
Bug Reports Includes fixes
Related Documentation at Web Site
No
50
Diagram Interface
The Diagram is a graphical user interface you can use to enter model pathways using block representations for species, reactions, and submodels. Use the Plot block to visualize simulation data during a simulation. For a tutorial, see “Modeling U sing the SimBiology Diagram” in the SimBiology Getting Started Guide. You can also access video demos from a list of SimB iology demos.
Version 2.0 (R2006a+) SimBiology®Software
Find and Bookmar
Find —Typeastri
components in t
Bookmarks —Us
create a custo
he project and in abstract kinetic laws.
m a nd persistent set of desktop and project objects.
ks in Projects
ng in the Find box to quickly find matching model
ecomplexrulestoidentifyobjectsfromtheproject,and
Compatibility Considerations
In Versions 1 the project s search into is saved and search, you than a sear
All functi bookmark search ro and or,wh
all or an
Sensiti
You can
.0 and 1.0.1, SimBiology projects saved searches. In Version 2.0,
aves bookmarks. The software converts a previous version’s saved
a b ookmark. After you save a project in Version 2.0, a bookmark
the old search is no longer available. If a project contains a
see a warning that the project file will contain a bookmark rather
ch after saving.
onality available in Version 1.0 searches are present in Version 2.0
s except for the ability to mix and match
ws. If you have a multiple-row search saved with a mixture of
en you load this project into Version 2.0, it is converted to either
y
based on whether the software first encounters and or or.
vity Analysis
perform sensitivity analysis using the following properties:
and and or between t h e
and
Sensit
the ti
State
param
Sens
anal
Sens
- Spec
- Par
ivityAnalysis
me-dependent sensitivities of all the species states defined by the
sToLog
eter values.
itivityAnalysisOptions
ysis options in the configuration set object. Properties of
itivityAnalysisOptions
t to compute the sensitivities of the species states in your model.
wan
ameterInputFactors
ch you want to compute the sensitivities of the species states in your
whi
del.
mo
property with respect to species initial conditions and
iesInputFactors
— Configuration set property that lets you calculate
— An object that holds the sensitivity
are summarized below:
— Specify the species with respect to which you
— Specify the parameters with respect to
51
SimBiology®Release Notes
- Normalizatio n — Specify the normalization for the calculated
sensitivities.
For an introduction and an example, see “Sensitivity Analysis” in the SimBiology User’s Guide.
Parameter Estimation
The sbioparamestim function lets you estimate any or all parameters in your model using the experimental data you provide. The software uses the optimization functions in the MATLAB, Optimization Toolbox™, and Global Optimization Toolbox software to enable parameter estimation.
Optimization Toolbox and Global Optimization Toolbox software are not required for you to use installed,
For an introduction and an example, see “Parameter Estimation” in the SimBiology User’s Guide.
sbioparamestim uses the MATLAB function fminsearch by default.
sbioparamestim. If you do not have these products
52
Ensemble Simulation Runs
You can perform ensemble simulations using the stochastic solvers to gather data from multiple stochastic runs of the model. The following functions let you perform ensemble runs:
sbioensemblerun — P erforms multiple stochastic ensemble runs of the
SimBiology model object.
sbioensembleplot — Shows a 2-D distribution plot or a 3-D shaded plot
ofthetimevaryingdistributionofone or more specified species in the ensemble data generated by
sbioensemblestats — Gets mean and variance as a function of time for all
the species in the ensemble data generated by
sbioensemblerun.
sbioensemblerun.
Moiety Conservation
The sbioconsmoiety function lets you calculate a com plete set of linear conservation relations for the species in a SimBiology model object.
Version 2.0 (R2006a+) SimBiology®Software
For an introduction and an example, see “Moiety Conservation” in the SimBiology User’s Guide.
Model Verification and Validation
SimBiology software performs model verification and validation eith er during simulation, or whe n you explicitly execute the commands for verification before simulation.
Verification at the Command Line
The following new functions let you verify and validate, at the command line, that your model is ready for simulation:
verify — Performs checks on a model to verify that you can simulate the
model. You see stacked errors and warnings if any problems are found. To see the entire list of errors and warnings, use
sbiolastwarning.
sbiolasterror — Returns a SimBiology diagnostic structure array
containing the last errors that are generated.
sbiolasterror and
sbiolastwarning — Returns a SimBiology diagnostic structure array
containing the last warnings that are generated.
Verification on the SimBiology Desktop
Click the Verify button on the SimBiology desktop toolbar to perform verification and validation of your model. The Output pane opens to show the errors and warnings. You can double-click a result row to go to the location of theerrororwarning.
Simulation and Solvers
The following new features and changes apply to simulation settings and solvers:
MaxStep — Lets you specify the upper bound on solver step size for a
deterministic solver.
Implicit Tau solver settings —For
holds the value for convergence tolerance fo r the nonlinear solver that
MaxStep is a property of the SolverOptions object.
impltau, AbsoluteTolerance
53
SimBiology®Release Notes
is used internally by the Implicit Tau solver. You can now specify
AbsoluteTolerance for impltau. Previously, if you selected the Implicit
Tau solver, the software ignored any changes to the
AbsoluteTolerance
and RelativeTolerance options within a configuration set and used the default values set internally.
UnitConversion — Supported by both deterministic solvers and stochastic
solvers. Previously
UnitConversion was supported only by the stochastic
solvers.
Implicit Tau Solver Settings Compatibility Considerations
The RelativeTolerance property is no longer valid for the Implicit Tau (
impltau)solver.
When you load a file created in a previous version, the project loads the
RelativeTolerance property. But when you save the file, the software
updates the change.
Unit Conversio n Compatibility Considerations
The UnitConversion property default is now 'false'.Ifyouloada SimBiology project created in a previous version into the SimBiology desktop, the
UnitConversion setting in each model in the project remains as the s aved
setting. If however, you are running a script, you must now remember to set the
UnitConversion property to true if you want the software to perform
unit conversions
54
New Demos for SimBiology Version 2.0
There are 14 new demos for SimBiology Version 2.0. Click SimBiology demos or type
demo('MATLAB', 'SimBiology') at the command prompt.
Version 1.0.1 (R2006a) SimBiology®Software
Version 1.0.1 (R2006a) SimBiology Software
This table summarizes what’s new in Version 1.0.1 (R2006a):
New Features and Changes
Yes Details below
Ver sion Compatibility Considerations
No Bug Reports No
The changes introduced in this version are:
The characters
supported in rules.
Rules are now supported in submodels.
\, ^,and* in species and parameter names are now
Fixed Bugs and Known Problems
Related Documentation at Web Site
55
SimBiology®Release Notes
Version 1.0 (R14SP3+) SimBiology Software
This table summarizes what’s new in Version 1.0 (R14SP3+):
New Features and Changes
Yes Details below
Version Compatibility Considerations
No Bug Reports No
The features introduced in this version are:
“Introduction” on page 56
“Features” on page 57
“Known Software Problems” on page 57
“Upgrading from a Beta Release” on page 61
Fixed Bugs an d Known Problems
Related Documentation at Web Site
Introduction
SimBiology Version 1.0 (Release 14SP3+) is an integrated environment for modeling biological proce sses, simulating the dynamic behavior of these processes, and analyzing simulation and experimental data. Biological processes include metabolic, genetic, and signaling pathways with transform, binding, and transport reactions. You can use SimBiology software as a tool in three major areas:
Model — Design and build m odels by entering model components with a
graphical desktop interface, or use the MATLAB Command Window.
56
Simulate — Select deterministic or stochastic solvers and observe the
changes in species amounts and variable parameter values over time.
Analyze — Log data from a simulation and export the data to the MATLAB
workspace. Compare simulation with experimental data for parameter estimation and model validation.
Version 1.0 (R14SP3+) SimBiology®Software
Features
The features in SimBiology Version 1.0 are the following:
Graphical user interface — Provides access to the command-line
functionality through a g raphical user interface (GUI).
Command-line interface — All the features are accessible and executable
from the MATLAB Command Window.
Data formats and projects — Organize and save related models,
simulation data, and analysis results in project files. Save user-defined kinetic laws and units. Share models by exporting SBML Level 2 files.
Modeling — Create biological models by adding components that include
reactions, species, parameters, kinetic laws, rules, and submodels.
Simulation — Select either deterministic or stochastic solvers with
dimensional analysis and unit conversion.
Analysis — SimBiology so ftware is fully integrated with MATLAB. Record
data during a simulation and analyze results in MATLAB.
Known Software Problems
To vie w important open bugs for SimBiology Version 1.0, use the Bug Rep orts interface on the MathWorks Web site.
Note If you are not already logged in to your MathWorks Account, when you link to the Bug Reports interface (see below), you will be prompted to log in or create an account.
Afteryouareloggedin,usethisBug Reports link. You will see the bug report for SimBiology. The report is sorted with fixed bugs listed first, and then open bugs. You can select the Status column to list the open bugs first.
If you are viewing these release notes in PDF form on the MathWorks Web site, you can refer to the HTML form of the release notes on the MathWorks Web site and use the link provided.
Software problems include unsupported SBML features and current feature and function limitations.
57
SimBiology®Release Notes
Unsupported SBML Level 2 Version 1 Features
SimBiology software supports a subset of the SBML Level 2 Version 1 specification. Unsupported features include:
Compartments — Model compartments are not supported. If an imported
SBML model has a sin gle compartment, the model is loaded as a top-level model. If the model has multiple compartments, you see a warning and the software does not load the SBML file.
Volume — Volume is not supported and cannot be specified.
Events—EventsinanSBMLfileareignored when you are importing
into a project.
Piecewise kinetics — Models with piecewise kinetics are loaded in, but the
software ignores the definitions for piecewise kinetics.
Function definitions — Models containing functional definitions are loaded,
but you see a warning and the software ignores the function definitions.
MATLAB incompatible variable names in
have variable names incompatible with MATLAB in
UnitDefinition — Models that
UnitDefinition are
not loaded and you see an error message.
Functional Limitations
Simulation and Solvers
Stochastic solvers support only mass action kinetics, while ODE solvers
support all built-in and user-defined kinetic laws.
If you use a stochastic solver to simulateamodel,thesoftwareignoresany
rate, assignment, or algebraic rules if present in the model.
If you have
stochastic solvers, note that the software assumes that volume is unity during simulation. The stochastic solvers perform calculations using species units in molecules. Therefore, if you specify the species units in molecules per unit volume or moles per unit volum e, the software assumes volume to be unity and converts species amounts to molecules for simulation. The results are finally plotted in the units you specified for the species.
DimensionalAnalysis and UnitConversion on for the
58
Version 1.0 (R14SP3+) SimBiology®Software
In addition, if you have reactions with stoichiometric coefficients greater than or equal to stochastic rate constants. For example,
v=k[R]^2.IfR is moles/liter, the deterministic rate constant k has units of liter/mole-second. If the unit of species concentration is molecule,then
the stochastic rate constant
2k/NV
where N is Avogadro’s Number, 6.022e23 molecules/mole,andV
2, you need to convert the deterministic rate constants to
2R->Phas a reaction rate of
c has units of 1/molec ule- second,andc=
isthevolumeofthemodelinliters.
When you select the Implicit Tau solver, the software ignores any
changes to
AbsoluteTolerance and RelativeTolerance options within a
configuration set and uses the default values that are set internally.
By default,
logged. Variable parameters are those that have or
false. If you choose the species to log, however, you cannot log the
StatesToLog is set to 'all ' and all variable parameters are
ConstantValue cleared
variable parameters.
The characters
\, ^,and* in species and parameter names are not
supported in rules.
Units
Stochastic solvers support dimensional analysis and unit conversion. ODE
solvers support dimensional analysis but not unit conversion.
You can delete a unit that is being used in a model; however, you will see
an error when you try to simulate the model or export to SBML.
Submodels
The context menus (right-click options) for the Species, Reaction,
Parameter and Rule nodes that appear beneath a submodel node all act
on the corresponding parent model node, and not on the submodel node. For example, if you select Delete All Species in the submodel Species node, this selection deletes the species in the parent model.
Rules are not supported in submodels.
59
SimBiology®Release Notes
SBML Export Limitations
There are features in SimBiology software that are not supported in SBML. When you export a model to an SBML file, you might lose some of these features.
Submodels are not supported by SBML export.
The abstract kinetic law name and corresponding expression are not
supported by SBML, but the associated reaction rate equation is exported to SBML.
The properties
export.
Tag, UserData,andActive are not supported by SBML
Tips
Naming SimBiology Variables
If you are using a species or parameter name that is not a valid MATLAB
variable name, do the following:
- Enclose the name in square brackets when writing a reaction rate
equation or a rule.
- Enter the name without brackets when you are creating the species or
parameter, or when you add a reaction.
For example, enclose within brackets in reaction rates and rules, but, enter DNA polymerase+ or K_DNA polymerase+ when creating a species, adding a reaction, or creating a parameter.
The names
in abstract kinetic laws, reaction rates, and rules are considered to be MATLAB code, the software evaluates not as the value of species interpreted to have three names, to protect such variables.
i and j are reserved MATL AB characters. Because expressions
[DNA polymerase+] and [K_DNA polymerase+]
i or j as an imaginary number and
i or j. For example, an expression V*S*i/K is
V, S,andK, instead of four. Use brackets
60
If a variable in a reaction rate equation or rule has the same name as a MATLABfunction,thesoftwareevaluatestheexpressionasacalltothe MATLAB function. In general, when creating variable names, you should
Version 1.0 (R14SP3+) SimBiology®Software
avoid using MATLAB function names or variable names that are invalid in MATLAB.
Changing SimBiology Variable Names
If you change the
Name of a parameter you must configure all applicable
elements, such as rules that use the parameter, any user-specified
ReactionRate, or the kinetic law object property ParameterVariableNames.
Use the method
setparameter to configure ParameterVariableNames.
To update parameter names in the SimBiology graphical user interface, access each appropriate pane through the Project Explorer.
If you change the
Name of a spe cie s you must configure all applicable
elements, such as rules that use the parameter, any user-specified
ReactionRate, or the kinetic law object property SpeciesVariableNames.
Use the method
setspecies to configure SpeciesVariableNames.
To update species names in the SimBiology graphical user interface, access each appropriate pane through the Project Explorer.Thesoftware automatically updates species names for reactions that use
MassAction
kinetic law.
Upgrading from a Beta Release
Any projects that you created and saved with the SimBiology beta release version will not load in Version 1.0.
As a workaround, before upgrading to Version 1.0, save your models to SBML, upgrade to Version 1.0, and then import the SBML models into Version 1.0 projects. Alternatively, contact the MathWorks for help with your conversion.
61
SimBiology®Release Notes
Compatibility Summary for SimBiology Software
This table summarizes new features and changes that might cause incompatibilities when you upgrade from an earlier version, or wh en you use files on multiple versions. Details are provided in the description of the new feature or change.
Version (Rel ea se) New Features and Chang e s with Version Compatibility
Impact
Latest Version V3.2 (R2010a)
V3.1 (R2009b) See the following:
V3.0 (R2009a)
V2.4 (R2008b) See the Compatibility Considerations subheadings for:
See the Compatibility Considerations subheadings for:
“Enhanced Support for Applying Dosing to a Model and Dosing
Multiple Compartments” on page 6
“Support for Parameter Transformations” on page 8
See “Functions and Properties Being Removed” on page 9.
“Unit Conversion Compatibility Considerations” on page 12
“Functions and Properties Being Removed” on page 12
None
“Support for Specifying Additional Inputs in Custom Plot Types”
on page 19
“Additional Options for Renaming Compartments, Species, and
Parameters” on page 23
“Change in the Random Number Generator Used During
Stochastic Simulations” on page 24
See “Functions and Properties Being Removed” on page 25.
V2.3 (R2008a) See “Functions and Properties Being Removed” on page 28.
62
Compatibility Summary for SimBiology®Software
Version (Rel ea se) New Features and Chang e s with Version Compatibility
Impact
V2.2 (R2007b+) See the Compatibility Considerations subheadings for:
“Submodel Support Will Be Removed” on page 32
“Changes to the Library Structure in the Root” on page 37
“SimData Object Holds All Simulation Data” on page 39
“New Sensitivity Analysis Property for Species Outputs” on
page 40
“New Way to Add Units and Unit Prefixes” on page 40
See “Functions and Properties Being Removed” on page 41.
V2.1.2 (R2007b)
V2.1.1 (R2007a)
None
None
V2.1 (R2006b+) See the Compatibility Considerations subheading for “Diagram
Menu” on page 46.
V2.0.1 (R2006b)
None
V2.0 (R2006a+) See the Compatibility Considerations subheading for “Find and
Bookmarks in Projects” on page 51 and the following:
“Implicit Tau Solver Settings C om patibility Considerations” on
page 54
“Unit Conversion Compatibility Considerations” on page 54
V1.0.1 (R2006a)
V1.0 (R14SP3+)
None
None
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