simulating time series data for Biomodels model with Copasi

Question

[Zara]

Hello,

I want to test a network reconstruction method. I need to simulate time-series data.

What I have to do is:

1. Find models from Biomodels which contain only mass-action equations. And at most three molecules in each reaction (like AB -> C or A -> B).
2. Add virtual nodes to the network. These virtual nodes are used to perturb some nodes in the existing network. For example I add node E to perturb A, and Add a reaction (E -> B).
3. Simulate different time series experiments in each I have made my perturbation nodes active or inactive. (active means constant value which shows this node is expressing and inactive means this node has concentration of zero so does not influence on node B in the above example.

Can anyone give me any advice about any of these steps?

Thanks a lot in advance.

Answer 1

[Zara]

For 2 and 3 Copasi software was able to handle what I want.

I just added virtual nodes to an existing network and defined reactions like ( P0 -> N0 ) for showing that I want to perturb N0. Now I put a "fixed" value of 1 to P0 and define positive or negative K (for activating or repressing N0) to the reaction. This is a mass action irreversible equation. Using this I can say P0 is an external factor which is having effect on node N0.

For filtering biomodels for using "only mass-action" networks I have not found a way yet.