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.