| |
Stochastic Simulation (Gillespie
Algorithm) |
Stochastic modeling based Discrete
event simulation (iSimBioSys) |
Coments |
| 1 |
nitialization: Initialize the number of
molecules in the system, reactions
constants, and random number
generators |
Initialization: Initialize the number
of molecules in the system for each
species, model parameters and
resources and random number
generators |
The initialization steps are similar in both
the algorithms |
| 2 |
Monte Carlo Step: Generate random
numbers to determine the next reaction
to occur as well as the time interval. |
Event modeling and execution: The next
reaction or molecular event is selected
based on the functional logic hardwired
in the simulator.
For each process and its associated
event, a random number is generated
for the event execution time based on
the first and second moment of the event
holding time distribution computed by
the stochastic model. |
In this step, Gillespie and other
stochastic simulation algorithms employ
a Monte Carlo step to determine next
reaction event and time while in our
approach, the next event selection and
random execution time generation are
computed differently. |
| 3 |
Update: Increase the time step by the
randomly generated time in step 1.
Update the molecule count based on the
reaction that occurred. |
Update: The global simulation clock is
increased by the time-step computed in
the previous step as the event holding
time, The resource count of molecules
are updated based on the last event
stochiometry |
The temporal progression takes place in
discrete time-steps based on the random
event holding times computed in the
previous step in our approach. |
| 4 |
Iterate: Go back to Step 1 unless the
number of reactants is zero or the
simulation time has been exceeded. |
Iterate: Go back to Step 1 and repeat
the process. In case a particular event
cannot be executed because of resource
conflicts, it is ignored and simulation
proceeds without the update step |
The handling of reactions/events with
resource conflicts/shortage is different in
our approach |
