jgerardin / persistence-detection Goto Github PK

Hello!

Could you please add an example of writing the parameter file (paramfile) for running simulations?

In other words, it is somewhat difficult for me to understand and utilize runSimulations.py.

In simualte.cc, I've found a code snippet below:

else // node is under AND logic
{
	if (i != 0) // node is not input node
	{
		double in1 = 0, in2 = 0, in3 = 0;
		int sign1 = 1, sign2 = 1, sign3 = 1;
		if (Ks[i * (NUMNODES + 1) + 0] > 0) // if there's regulation by A on node i
		{
			in1 = ks[i * (NUMNODES + 1) + 0] * nodes[0] / (conc[i * (NUMNODES + 1) + 0] + Ks[i * (NUMNODES + 1) + 0] + nodes[0]);
			if (ks[i * (NUMNODES + 1) + 0] < 0)
				sign1 = -1;
		}

From my understanding, Ks represents Michaelis constant, and it cannot have a sign.

So, is the code, Ks[i * (NUMNODES + 1) + 0] > 0 , a typo?
Or, is it just checking whether the corresponding link exists? (i.e., Ks > 0 equals Ks != 0, which means the link exists.)