CellML Specification Overview Entire Specification Introduction Fundamentals Model Structure Mathematics Units Grouping Reactions Metadata Framework |
## 7 Reactions## 7.1 IntroductionCellML is intended to be used to represent many different types of models. Therefore, its basic structure is rather general, and models are primarily specified by explicitly defining mathematics using MathML. It will always be possible to specify a model purely in terms of mathematics, without using any of the elements defined in this section of the specification. However, in some types of models, information is lost in reducing the model to pure mathematics. For instance, in biochemical pathway models it will not always be straightforward, or even possible, to unambiguously determine from the mathematical rate laws which variables represent inhibitors or activators in the reactions. Therefore, some additional elements were needed in CellML to fully capture the information in biochemical pathway models. ## 7.1.1 Pathway model representations supported by CellMLThree fundamental representations of reaction/pathway models must be supported by CellML: -
**Mathematical Equations**: these are any valid mathematical equations that describe the model. For example, they may be ordinary differential equations that define kinetic reaction rate laws and the rate of change of the concentration of species participating in the modelled reactions. -
**Chemical Expressions**: these are the stoichiometric expressions (such as`A + B <-> 2C + D` ) used by chemists to represent reactions. -
**Pathway Diagrams**: these are the stylised drawings commonly used by biochemists and cell biologists to represent interactions among participants in reactions. Some examples of pathway diagrams are shown in Section 7.3.
It is important that CellML be able to store the information needed to unambiguously reproduce any of these representations of a model. It is also important to minimise duplication of information within the model definition, because duplication can lead to inconsistencies. Therefore, we must integrate the information needed to support the three types of model representation.
The integration process has resulted in the introduction of a CellML syntax that implies a mathematical relationship between variables in the current component. In this section of the specification, ## 7.1.2 Qualitative vs. quantitative pathway models
CellML supports both quantitative and qualitative pathway models. Many types of models are commonly referred to as "qualitative". Some of these are mathematically specified, while others are not. For the purposes of this specification, Any model in which the change of concentration of a chemical species participating in a reaction is implicitly or explicitly defined is quantitative. All others are qualitative. ## 7.2 Basic Structure
The
The reaction element contains multiple
Each
The
There are three uses for equations inside -
If the
`role` attribute value is`"` `rate` `"` , any enclosed equations calculate the kinetic rate law (i.e., calculate the value of the referenced variable) and the value of intermediate variables used in the rate law equation. -
If the
`role` attribute value is`"` `reactant` `"` or`"` `product` `"` , the equations calculate the relationship between the general reaction rate and the rate of change of the species represented by the referenced variable (i.e., calculate the value of the variable named in the`delta_variable` attribute), and calculate any intermediate variables used in this relationship. -
In all other cases, the equations relate an intermediate variable used in the rate calculation to the variable referenced by the containing
`<variable_ref>` element. For instance, it would be appropriate to calculate an effective concentration of a catalyst inside the`<role>` element contained by the`<variable_ref>` element that references the variable representing the actual concentration of the catalyst.
Note that CellML processing applications are not required to be able to deduce the stoichiometry of a reaction from explicit mathematics. Therefore, it is strongly recommended that the ## 7.3 Examples
This section contains two examples demonstrating the recommended use of the Figure 13 shows a pathway diagram representation of the following reversible reaction:
Figure 14 demonstrates the use of CellML to define this reaction. There are five Figure 15 shows the pathway diagram for the following irreversible, catalyzed reaction, which exhibits product-inhibition:
The CellML definition of this reaction is shown in Figure 16.
The ## 7.4 Rules for CellML Documents## 7.4.1 The
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