System and method for simulating operation of biochemical systems

A method of simulating the operation of a biochemical network, said method comprising the steps of:

• (A) receiving and storing in a computer memory a set of objects, each object representing a biochemical reaction or mechanism in said biochemical network;
• (B) for each of at least a subset of said objects, associating one or more signals with said each object;
• a first subset of said signals representing quantities or concentrations of associated proteins;
• designating a second subset of said signals as output signals;
• (C) for a specified simulation time period, simulating operation of said biochemical network, including (C1) determining reaction probabilities for at least a subset of said biochemical reactions associated with said objects, (C2) selecting ones of said biochemical reactions to simulate in accordance with said determined reaction probabilities, (C3) simulating performance of said selected ones of said biochemical reactions, wherein simulating performance of said selected ones of said biochemical reactions causes associated ones of said signals to be updated, and (C4) redetermining said reaction probabilities in accordance with said updated signals;
• and
• (D) generating output data representing signal values of at least a subset of said output signals during said specified simulation time period.

A biochemical network simulator for simulating the operation of a biochemical network having a multiplicity of biochemical mechanisms, comprising:

• a central processing unit;
• a computer memory, coupled to said central processing unit, for storing data representing said biochemical mechanisms in said genetic network, said stored data including a set of objects, each object representing a biochemical mechanism in said biochemical network;
• said stored data including, for each of at least a subset of said objects, one or more signals associated with said each object;
• a first subset of said signals representing quantities or concentrations of associated proteins;
• said stored data further including output signal designations designating a second subset of said signals as output signals;
• said computer memory further storing a set of methods associated with each object in said set of objects;
• for each of at least a subset of said objects, said associated methods including one or more probability determination methods for determining one or more reaction probabilities for one or more biochemical reactions associated with said object, and one or more reaction simulation methods for simulating performance of one or more associated biochemical reactions;
• a simulation procedure, executed by said central processing unit, that simulates operation of said biochemical network by executing at least a subset of said probability determination methods to determine reaction probabilities for at a subset of said biochemical reactions associated with said objects, selecting ones of said reaction simulation methods to execute in accordance with said determined reaction probabilities, and executing said selected ones of said reaction simulation methods;
• wherein execution of said selected ones of said reaction simulation methods causes associated ones of said signals to be updated;
• and
• an output procedure, executed by said central processing unit, for generating output data representing signal values for ones of said output signals.

A genetic network simulator for simulating the operation of a biochemical network having a multiplicity of biochemical mechanisms, comprising:

• a central processing unit;
• a computer memory, coupled to said central processing unit, for storing data representing said biochemical mechanisms in said genetic network, said stored data including a set of objects, each object representing a biochemical reaction or mechanism in said biochemical network;
• said stored data including, for each of at least a subset of said objects, one or more signals associated with said each object;
• a first subset of said signals representing quantities or concentrations of associated proteins;
• said stored data further including output signal designations designating a second subset of said signals as output signals;
• a simulation procedure, executed by said central processing unit, that simulates operation of said biochemical network by (1) determining reaction probabilities for at least a subset of said biochemical reactions associated with said objects, (2) selecting ones of said biochemical reactions to simulate in accordance with said determined reaction probabilities, (3) simulating performance of said selected ones of said biochemical reactions, wherein simulating performance of said selected ones of said biochemical reactions causes associated ones of said signals to be updated, and (4) redetermining said reaction probabilities in accordance with said updated signals;
• and
• an output procedure, executed by said central processing unit, for generating output data representing signal values for ones of said output signals.