Tellurium Modeling Platform

The tellurium.notebooks package provides specialized tools designed for use within interactive notebook environments (like Jupyter). It is organized into several functional submodules:

• tellurium.notebooks.notebooktools: General utility tools for notebook interaction.
• tellurium.notebooks.ontologysearch: Tools for searching biological ontologies.
• tellurium.notebooks.parameterslider: Interactive UI components (sliders) for adjusting model parameters dynamically.
• tellurium.notebooks.speciessearch: Tools for searching biological species information.

The tellurium package is organized into several specialized subpackages for systems biology modeling and simulation. Depending on your task, you may need to import from one of the following:

• tellurium.analysis: Tools for analyzing model behavior.
• tellurium.roadrunner: Interface for the RoadRunner simulation engine.
• tellurium.sedml: Support for Systems Entity Description Markup Language.
• tellurium.teio: Input/Output utilities for model files.
• tellurium.teconverters: Converters for different model formats.
• tellurium.visualization & tellurium.plotting: Tools for generating visual representations of models and data.
• tellurium.utils: General utility functions.
• tellurium.notebooks: Support for Jupyter notebook workflows.

The tellurium.sedml package provides tools for working with Systems Biology Evaluation Markup Language (SBML) and related formats. It is organized into several specialized submodules:

• tellurium.sedml.data: Handles data structures and information related to SED-ML.
• tellurium.sedml.mathml: Provides functionality for MathML (Mathematical Markup Language) integration.
• tellurium.sedml.tesedml: Supports TES-EDML (Time-course Experiment Simulation Exchange Data Markup Language).
• tellurium.sedml.utils: Contains utility functions for SED-ML operations.
• tellurium.sedml.xpath: Provides XPath-related utilities for navigating XML-based biological models.
• tellurium.sedml.templates: A subpackage containing templates for generating SED-ML files.

Tellurium supports the following platforms and Python versions:

• Supported Platforms: Windows, Mac, and Linux.
• Supported Python Versions: Python 3.7, 3.8, and 3.9.

Note: New versions of Tellurium do not support Python 2.7. If you require Python 2.7, you must install a previous version of Tellurium.

Antimony is a human-readable, text-based modeling language designed to interconvert between the SBML (Systems Biology Markup Language) standard and a shorthand form. It allows users to define biological models (species, reactions, compartments, events, etc.) without the overhead of working directly with XML.

In Tellurium, Antimony is the primary method for building models. It is particularly useful for:

• Defining reaction networks where processes consume and create elements.
• Packaging and reusing models as modules with defined or implied interfaces.
• Automating model generation from templates (e.g., using TemplateSB).

Tellurium is an integration module that connects several specialized Python packages for systems biology simulation and model handling. When working with Tellurium, you are interacting with a suite of tools that includes:

• tellurium: The main integration module.
• libroadrunner: The SBML ODE / stochastic simulator.
• antimony: Provides a human-readable representation of SBML.
• phrasedml: Provides a human-readable representation of SED-ML.
• libcombine: For reading/writing COMBINE archives.
• sbml2matlab: Utility for converting SBML models to MATLAB ODE simulations.
• simplesbml: Utility for creating SBML models without the complexity of libSBML.
• libsbml: Core library for reading/writing SBML.
• libsedml: Core library for reading/writing SED-ML.

Antimony supports modularity. You can define a reusable module with the model syntax and parentheses to expose specific variables. These modules are then imported into other models.

When a module is imported, its internal species are scoped to that module instance (e.g., A.E and B.E are distinct even if they share the same name in the module definition).

model side_reaction(S, k1)
  J0: S + E -> ES; k1*k2*S*E - k2*ES;
  E = 3;
  ES = E+S;
  k2 = 0.4;
end

model full_pathway
  A: side_reaction(S1, k4)
  S1 = 0
end

The ParameterScan package provides an alternative to standard Tellurium simulation syntax. Instead of passing simulation arguments (like startTime or endTime) directly into a function call, you instantiate a ParameterScan object with a loaded model and set these values as properties. This approach is designed to simplify complex 3D plotting and multi-parameter scans that would otherwise require cumbersome argument handling.

To use it, import it from tellurium after importing the main library.

import tellurium as te
from tellurium import ParameterScan

# Load your model using standard Tellurium methods
rr = te.loadAntimonyModel('...') 

# Initialize ParameterScan with the model
p = ParameterScan(rr)

# Set simulation parameters as properties
p.startTime = 0
p.endTime = 20

# Run a plot
p.plotArray()