Examples

PathwayLab Research Edition's integration with Mathematica provides a powerful environment for modeling and computational analysis of biochemical reaction networks. A pathway model defined in PathwayLab Research Edition can be easily exported to Mathematica. PathwayLab Research Edition provides the functions to extract the information from the model, and the built-in capabilities of Mathematica can then be utilized for further analysis, including transient and steady-state, stability, sensitivity, and parameter estimation.

Here are a few examples that demonstrate the process.

	BioCircuit This example is a purely artificial biochemical network that illustrates different pathway modeling objects and how they are transformed into mathematical expressions. Download example as  Mathematica notebook*
	A MAPK Cascade The model in this example is taken from "Untangling the Wires: A Strategy to Trace Functional Interactions in Signaling and Gene Networks." Once the model equations are available in Mathematica, this example shows how easy it is to perform further computational analysis, in particular steady state analysis. Download example as  Mathematica notebook*
	Integral Feedback Control This example illustrates how robust perfect adaptation (integral feedback control) can be implemented by a small reaction network. The pathway model is taken from "Robust Perfect Adaptation in Bacterial Chemotaxis through Integral Feedback Control." Download example as  Mathematica notebook*
	Cell Cycle Control in Xenopus Frog Eggs This example uses the model presented in "Modeling the Cell Division Cycle: M-Phase Trigger, Oscillations, and Size Control" and illustrates oscillations in concentration of biochemical entities involved in cell cycle control. Download example as  Mathematica notebook*

* Note: If you do not own a copy of Mathematica, you will need to download a trial version in order to view the above notebook documents.