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− | As already mentioned, traditional stochastic or ODE-solver simulation methods require every possible reaction to be defined, with all possible molecular states being named. The valences of the constructs that we are interested in, have the chance to form a very complex and connected network. It would be impossible to define this network beforehand. Since more systems are too complex to simulate with the traditional stochastic or ODE-solver simulation methods, researchers have begun to develop another modeling language, for example the BioNetGen Language (BNGL). The main advantage of BNGL is that the specification of reaction rules is required, but not the specification of all reactions. To make this possible, the molecules need to be specified in another way, namely with the different components and states that it can be in. The components can form a bond with components of another molecule and the states can change, which may be required for binding with another molecule. In short, rule-based-modelling requires the definition of rules, and the computer will figure out the rest.<h7>[1]</h7> | + | <h6>As already mentioned, traditional stochastic or ODE-solver simulation methods require every possible reaction to be defined, with all possible molecular states being named. The valences of the constructs that we are interested in, have the chance to form a very complex and connected network. It would be impossible to define this network beforehand. Since more systems are too complex to simulate with the traditional stochastic or ODE-solver simulation methods, researchers have begun to develop another modeling language, for example the BioNetGen Language (BNGL). The main advantage of BNGL is that the specification of reaction rules is required, but not the specification of all reactions. To make this possible, the molecules need to be specified in another way, namely with the different components and states that it can be in. The components can form a bond with components of another molecule and the states can change, which may be required for binding with another molecule. In short, rule-based-modelling requires the definition of rules, and the computer will figure out the rest.</h6><h7>[1]</h7> |
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− | The BNGL can be applied using a Network-Free Stochastic Simulator (NFsim). NFsim is especially useful for the simulation of systems with large reaction networks and a high degree of combinatorial complexity.It keeps track of the state of the system that actually exists and does not consider every possible configuration.<h7>[2]</h7 | + | <h6>The BNGL can be applied using a Network-Free Stochastic Simulator (NFsim). NFsim is especially useful for the simulation of systems with large reaction networks and a high degree of combinatorial complexity.It keeps track of the state of the system that actually exists and does not consider every possible configuration.</h6><h7>[2]</h7> |
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<h2>Defining the rules</h2> | <h2>Defining the rules</h2> |
Revision as of 17:47, 20 October 2017