// Declaration of the structure of the hypernetwork organism

create_organism          8        // No. of Cells
threshold_activation     60	  // Threshold for molecular activation
threshold_inhibition     70	  // Threshold for molecular inhibition
mutation_rate_mol_cell   1  	  // MUTPROB ( * 100)
mutation_rate_atom_mol   20	  // PERMUT
molecular_shape_size     20	  // No. of bits by domain

		 // Cell declaration:
create_cell       1  20 rect 5 4 input 0    
		  // No. of cell, No. of Molecules, rectangular, cell type, # of readouts.
	 	  // Cell types are: input, internal1, internal2, and output
n_receptors_cell  1  4   // No. of receptor molecules in cell 1
n_effectors_cell  1  4	 // No. of effector molecules in cell 1
n_internal_cell   1  12  // No. of internal molecules in cell 1
p_inhibitors_cell 1  20	 // Percentaje of inhibitory molecules in cell 1

create_cell       2  20 rect 5 4   input 0
n_receptors_cell  2  4
n_effectors_cell  2  4
n_internal_cell   2  12   
p_inhibitors_cell 2  20

create_cell       3  20 rect 5 4   internal1 0
n_receptors_cell  3   4
n_effectors_cell  3   4 
n_internal_cell   3  12    
p_inhibitors_cell 3  20

create_cell       4   20 rect 5 4 internal1 0
n_receptors_cell  4  4
n_effectors_cell  4  4 
n_internal_cell   4  12   
p_inhibitors_cell 4  20

create_cell       5  20 rect 5 4 output 3
		// This output cell has 3 readouts
create_cell       6  20 rect 5 4 output 3
create_cell       7  20 rect 5 4 output 3
create_cell       8  20 rect 5 4 output 3

n_receptors_cell   5  4
n_effectors_cell   5  4
n_internal_cell    5  12
p_inhibitors_cell  5  20

copy_structure_cell 5 6  // copy the structure of cell 5 into cell 6
copy_structure_cell 5 7  
copy_structure_cell 5 8

// Declaration of cell to cell interactions
 
cell_cell 1  3    // cell 1  -> cell 3
cell_cell 1  4	  // cell 1  -> cell 4

cell_cell 2  3   
cell_cell 2  4

cell_cell 3  5
cell_cell 3  6
cell_cell 3  7
cell_cell 3  8

cell_cell 4  5
cell_cell 4  6
cell_cell 4  7
cell_cell 4  8

fraction_input_vector  2 // usually 2 

minimal_global_error   0.0001

seeds 1001914360 10612
	//or: clock clock
	
end.
