Rule-based modeling
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Rule-based modeling is a
modeling A model is an informative representation of an object, person or system. The term originally denoted the plans of a building in late 16th-century English, and derived via French and Italian ultimately from Latin ''modulus'', a measure. Models c ...
approach that uses a set of rules that indirectly specifies a mathematical model. The rule-set can either be translated into a model such as
Markov chains A Markov chain or Markov process is a stochastic process, stochastic model describing a sequence of possible events in which the probability of each event depends only on the state attained in the previous event. Informally, this may be thought ...
or differential equations, or be treated using tools that directly work on the rule-set in place of a translated model, as the latter is typically much bigger. Rule-based modeling is especially effective in cases where the rule-set is significantly simpler than the model it implies, meaning that the model is a repeated manifestation of a limited number of patterns. An important domain where this is often the case is biochemical models of living organisms. Groups of mutually corresponding substances are subject to mutually corresponding interactions. BioNetGen is a suite of software tools used to generate mathematical models consisting of
ordinary differential equation In mathematics, an ordinary differential equation (ODE) is a differential equation whose unknown(s) consists of one (or more) function(s) of one variable and involves the derivatives of those functions. The term ''ordinary'' is used in contrast w ...
s without generating the equations directly. For example below is an example rule in the BioNetGen format: A(a,a) + B(b) -> A(a!1). B(b!1) Where: # A(a,a): Represents a model species A with two free binding sites a # B(b): Represents a model species B with one free binding site # A(a!1).B(b!1): Represents model species where at least one binding site of A is bound to the binding site of B With the above line of code, BioNetGen will automatically create an ODE for each model species with the correct mass balance. Additionally, an additional species will be created because the rule above implies that two B molecules can bind to a single A molecule since there are two binding sites. Therefore, the following species will be generated: 4. A(a!1,a!2).B(b!1).B(b!2): Molecule A with both binding sites occupied by two different B molecules.


For biochemical systems

Early efforts to use rule-based modeling in simulation of biochemical systems include the stochastic simulation systems StochSim A widely used tool for rule-based modeling of biochemical networks is BioNetGen It is released under the
GNU GPL The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the four freedoms to run, study, share, and modify the software. The license was the first copyleft for general us ...
, version 3. BioNetGen includes a language to describe chemical substances, including the states they can assume and the bindings they can undergo. These rules can be used to create a reaction network model or to perform
computer simulation Computer simulation is the process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be dete ...
s directly on the rule set. The biochemical modeling framework
Virtual Cell Virtual Cell (VCell) is an open-source software platform for modeling and simulation of living organisms, primarily cells. It has been designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophys ...
includes a BioNetGen interpreter. A close alternative is the Kappa language. Another alternative is BioChemical Space language.Děd et al. (2016
Formal Biochemical Space with Semantics in Kappa and BNGL
ENTCS 326:27-49.


References

Systems biology Molecular biology Stochastic simulation Free science software {{molecular-cell-biology-stub