The first step of constructing a A-Cell model is to draw a cartoon for signal transduction of proteins you are focusing. This cartoon can be a drawing appeared in a paper or your original. So we begin with descriptions of cartoons followed by methods to draw A-Cell models, which are sown below. A-Cell models are classified in Basic, 1st grade, 2nd grade, and 3rd grade as follows:

Basic: Every reaction model is decomposed into 1st order or 2nd order reaction. These two reactions are the bases for all reactions. In this classification, 1st order, 2nd order, and their simple combinations such as chain reaction, forward and backward reaction, and Michaelis-Menten enzymatic reaction are included. For spatio-temporal model, diffusion and diffusion with source are included.

1st grade: This classification includes A-Cell models that can be constructed by simple combinations of the Basic classification. There is neither parallel pathways, feedback pathways nor feed forward pathways. In spatio-temporal model, a simple combination of reaction and diffusion (reaction-diffusion model) is included.

2nd grade: This classification includes reactions with feedback and/or feed forward. In spatio-temporal model, spatial localization is a focus of this classification.

3rd grade: Models for the oscillation and the formation of spatio-temporal pattern are included in this classification. These models are not easy to construct. The analyses of simulation results are also not easy.

The real model is specific to proteins your are focusing, and the following examples may include models you are not interested in. Nonetheless, examples shown here will be helpful for your model construction if you compare structure of your system with that of shown in examples.

Acknowledgement: Examples shown here have been made in collaboration with Drs. Daisuke Ohshima and Ayako Watanabe, who were members of our Lab.

A-Cell models downloadable by buttons at lower half of this page.

Non-spatial model (pathway model)

Basic