The purpose of this page is to serve as an introduction to the use of CellDesigner and Complex Pathway Simulator (COPASI) for modeling immunity.
CellDesigner is a structured diagram editor for drawing gene-regulatory networks. MIEP uses this software to create the structural model. If you are interested in using CellDesigner to build your structural models you can download and install the program.
In addition, CellPublisher can be used to generate and publish the CellDesigner structure model onto Web using google map APIs. The CellPublisher map is interactive and user-friendly. Users can navigate through different species and reactions on the map and get useful information though the info windows. This is an example of CellPublisher models we published on our website.
COPASI is a software application for simulation and analysis of complex intracellular networks and their dynamics. An overview of the program’s applications and abilities can be seen in this basic video tutorial. If you are interested in using COPASI for your own models, the first step is to download and install the program.
The three above mentioned software packages are able to exchange the model seamlessly by using the Systems Biology Markup Language (SBML).
COPASI Documentation
A basic description of the steps involved in model building and analysis is available in this tutorial.
The full COPASI online user manual is available, but if you are new to COPASI or modeling in general, the key steps for getting started are:
1. Understanding the GUI interface
2. Using the General Model Settings to name your model and choose units.
3. Adding Compartments, Species and Reactions to your model.
4. Using Parameter View to view and edit all parameters in one place.
5. Using Pre-Determined Reports to read your model’s output.
