The present invention relates to methods, computer systems, and computer
programs for simulating a biological network. The methods of the present
invention facilitate biological network simulations via automated
equation generation based on the concept of a hierarchy of canonical
forms that describe biological processes at various levels of detail. At
each level of hierarchy two classes of canonical forms can be identified:
the input canonical form, that is used to supply information to the
program, and the output canonical form that is produced by a simulator.
The methods in certain preferred embodiments include explicit output
description and flexible user intervention at several steps through the
model generation. Furthermore, preferred embodiments of the present
invention provide the modeling of developmental networks using an
organism-as-a-graph approach using domains and fields.