Enter the transition table based on your experimental data for each variable to obtain a polynomial dynamical systems. A table, where the top row consists of the names of the variables, the other rows are the inputs states at time t, and the right most column is the output value at time (t+1). Missing rows are assumed to have output value 0. Entries should be separated by white space. When *continuous* is checked, there will not be any *jumps* in the generated model, i.e., every variable changes its value by at most 1 at every time step.

You can enter a polynomial dynamical systems (PDS), an open polynomial dynamical systems (oPDS), a probabilistic polynomial dynamical systems (or probabilistic Boolean network), a Petri net generated with Snoopy, a logical model generated with GINsim, a stochastic discrete dynamical systems (SDDS), or an open Stochastic Discrete Dynamical Systems (oSDDS).

**Boolean network**: Converts GINsim file to a polynomial system that ADAM will then proceed to analyze. Also outputs the variables and the converted system. Files must be ginml files, if you have an archive (zginml), please unzip it first.

**GINsim File**: Converts GINsim file to a polynomial system that ADAM will then proceed to analyze. Also outputs the variables and the converted system. Files must be ginml files, if you have an archive (zginml), please unzip it first.

**PDS**: Polynomial Dynamical Systems. Operations are interpreted as polynomial addition and multiplication.

**pPDS**: Probabilistic Polynomial Dynamical Systems. Each nodes has several update rules, at each iteration, one is picked at random.

**Petri Net**: A (standard) Petri net generated with Snoopy. The Petri net must be *k*-bounded, and *k* must be entered on the left. This is an experimental feature, if you want to analyze the dynamics of the network, please copy and paste the generated PDS into ADAM.

**SDDS**: Stochastic Discrete Dynamical Systems is a useful tool to generate and analyze mathematical models in systems biology, and it is suitable for cell population simulation. The inputs for SDDS: a file for the (complete) transition table or functions, propensity matrix, an initial state, nodes of interest, the number of states, the number of steps, and the number of simulations.

See an example...

**oPDS**: Open Polynomial Dynamical Systems is used to analyze the (deterministic) open system, which interacts with its environment, under different environmental conditions. In addition to PDS, the user should specify the external parameters that the system interacts with. Update functions can have some external parameters.

**oSDDS**: Open Stochastic Discrete Dynamical Systems is a useful tool to analyze the (stochastic) open models, which interacts with its environment, under different environmental conditions. In addition to SDDS, the user should enter a file for functions, and specify the external parameters that the system interacts with. Update functions can have some external parameters.

Please enter the gene regulatory network as a polynomial dynamical system. ADAM will find the optimal combination of knockouts (that is those with the least cost where the cost is dependent on the inputted weights) using an adaptive genetic algorithm. Please enter the desired steady state and the weight for each respective gene (in numerical order e.g. the first entry would correspond to the first gene) separated by white space.