WOLFRAM SYSTEMMODELER

BioChem

A library for modeling, simulation, and visualization of biological and biochemical systems

Package Contents

Examples

Package with examples of BioChem models

Compartments

Package with basic compartments

Reactions

Package with commonly used reactions

Substances

Package with substance nodes

Constants

Package with mathematical constants and constants of nature

Interfaces

Package with connection points and icons

Math

Package with mathematical functions

Types

Package with BioChem specific types

Units

Package with definitions of units that are common in biochemical models

Icons

Package containing icons

Information

The BioChem library is an extendable, general purpose Modelica library for modeling, simulation, and visualization of biological and biochemical systems. The library is designed to be used together with Wolfram SystemModeler, which enables several extra features such as systems biology markup language (SBML) import and export.

The Fig. 1 below shows a simple reaction network modeled using the BioChem library. For more information on how you can use the library, please have a look at the examples in the Examples package.


Fig. 1 a simple reaction network, where the concentration of substance 'D' inhibits the reaction between A+B and C.

 


Release Notes (BioChem 1.2)

Updates:

Update models from BioChem 1.1:

To update a model/package based on substance, reaction, and compartment classes from BioChem 1.1, please open the model/package in a text editor and replace all instances of the following two classes:

  • Compartments.Compartment
  • Compartments.MainCompartment

with Compartments.ConstantCompartment. Finally, update the mainCompartment parameter to "true" in all previous MainComparment models.