Update of node state in the network

[priyambial123]

Hello

How are the node states updated in the network. Is it asynchronous update? I ran the attractor analysis and in the figure, it shows that source nodes determine the next state of the nodes. When we assume it an asynchronous update of nodes, state of the nodes are randomly updated. Are the source node states randomly updated here? Can you explain how the nodes are updated in the attractor analysis

Thanks

Priya

[jcrozum]

By default, pystablemotifs assumes asynchronous update, in which a single node is randomly chosen to be updated at each time step. Updating a source node (like A*=A) will not change its value.

We also consider all possible initial conditions, which is reflected in the different source node values you see in the figure; they correspond to different initial conditions.

[priyambial123]

Is there a way to know how from initial state of the node, the nodes get randomly updated (transition states) and reach a specific attractor state like attractor 1 in the figure.

[jcrozum]

I think you are asking if there is a way to run a simulation in pystablemotifs?

Pystablemotifs is not a simulation library; it exists to give you a "big picture" view of your system and to help you design control strategies. If you want to simulate your system, there are many other tools available.

Probably the simplest one to use with pystablemotifs is pyboolnet because they share the prime dictionary format and pyboolnet is a requirement for pystablemotifs, so you already should have it installed. Look into the pyboolnet.state_transition_graphs module. There are various tools there that I think can accomplish what you want.

[jcrozum]

I'm marking this as closed because simulation is currently not within the project scope for pystablemotifs.