Current C functions

-----------------------------------------------------

ODE simulation:

works on: selected items (all items if no items are selected)

writes the model in temp.c, performs the simulation using CVode and outputs the results to the output window and the plot window.  

-----------------------------------------------------

Stochastic simulation:  

works on: selected items (all items if no items are selected)

writes the model in temp.c, performs the naive Gillespie algorithm and outputs the results to the output window and the plot window

-----------------------------------------------------

Load Fill Binding Kinetics:  

works on: selected nodes with "Binding" connections

Generates the full binding/unbinding mass-action model for the Binding interactions that the selected node(s) is involved in.

-----------------------------------------------------

Multi-step Process:  

works on: selected 1-to-1 connections

Converts each reaction into a multi-step reaction with intermediates. Asks the user for the number of intermediate steps.

-----------------------------------------------------

Steady State Plot:  

works on: selected items (or all items if none are selected)

Asks the user for a variable, and performs repeated simulations (ODE) by incrementing that variable each time. Plots all the steady state values (0 if no steady state) as a function of the user selected variable.

-----------------------------------------------------

Values At Time T  :

works on: selected items (or all items if none are selected)

Asks the user for a variable, and performs repeated simulations (ODE or Stochastic) by incrementing that variable each time. Plots all the values at time T (user defined) as a function of the user selected variable. 

-----------------------------------------------------

Find Bistability:  

works on: selected items (or all items if none are selected)

Performs a complicated optimization in order to find the set of parameters that will convert the system into a bistable system (if such parameters exist). 

-----------------------------------------------------