Version 1.0 (R14SP3+) SimBiology Software

This table summarizes what's new in Version 1.0 (R14SP3+):

New Features and Changes	Version Compatibility Considerations	Fixed Bugs and Known Problems
Yes Details below	No	Bug Reports

The features introduced in this version are:

• Introduction

• Features

• Known Software Problems

• Upgrading from a Beta Release

Introduction

SimBiology Version 1.0 (Release 14SP3+) is an integrated environment for modeling biological processes, 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 models by entering model components with a graphical desktop interface, or use the MATLAB Command Window.

• 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.

Features

The features in SimBiology Version 1.0 are the following:

• Graphical user interface — Provides access to the command-line functionality through a graphical 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 software is fully integrated with MATLAB. Record data during a simulation and analyze results in MATLAB.

Known Software Problems

To view important open bugs for SimBiology Version 1.0, use the Bug Reports 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.

After you are logged in, use this Bug 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.

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 single 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 — Events in an SBML file are ignored 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 UnitDefinition — Models that have variable names incompatible with MATLAB in 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 simulate a model, the software ignores any rate, assignment, or algebraic rules if present in the model.

• If you have DimensionalAnalysis and UnitConversion on for the 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 volume, 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.

  In addition, if you have reactions with stoichiometric coefficients greater than or equal to 2, you need to convert the deterministic rate constants to stochastic rate constants. For example, 2 R -> P has a reaction rate of v=k[R]^2. If R 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 c has units of 1/molecule-second, and c = 2k/NV where N is Avogadro's Number, 6.022e23 molecules/mole, and V is the volume of the model in liters.

• 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, StatesToLog is set to 'all' and all variable parameters are logged. Variable parameters are those that have ConstantValue cleared or false. If you choose the species to log, however, you cannot log the 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.

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 Tag, UserData, and Active are not supported by SBML export.

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 [DNA polymerase+] and [K_DNA polymerase+] 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 i and j are reserved MATLAB characters. Because expressions in abstract kinetic laws, reaction rates, and rules are considered to be MATLAB code, the software evaluates i or j as an imaginary number and not as the value of species i or j. For example, an expression V*S*i/K is interpreted to have three names, V, S, and K, instead of four. Use brackets to protect such variables.

If a variable in a reaction rate equation or rule has the same name as a MATLAB function, the software evaluates the expression as a call to the MATLAB function. In general, when creating variable names, you should 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 species 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. The software 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 MathWorks for help with your conversion.

Version 1.0.1 (R2006a) SimBiology Software

Compatibility Summary for SimBiology Software

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