Types
The MASS Toolbox relies heavily on data types and custom notation to facilitate the process of model construction, manipulation, and analysis.
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It is very important to make clear that although metabolites (and many of the following data types) are displayed in a human readable format (e.g
atpc), the internal representation is conserved,
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and is in this respect very similar to other
Mathematica definitions, e.g.,
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It is possible to use "Evaluation-> Evaluate in place" in the menu (or Cmd + Shift + Enter or the mouse context menu) for inplace replacements (select the next line and try it)
Select the following code and hit Cmd + Shift + Enter (metabolite["atp","cytosol"] should be converted to
atpcytosol)
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Species
In order to define a model of biochemical process one has to define the participating species. The Toolbox provides a series of species type definitions.
| species["id"] | a species |
| species["id", "compartment"] | a species in a particular compartment |
| species["id", _] | a species in any compartment |
| metabolite["id", "compartment"] | a small compound in a particular compartment |
| m["id", "compartment"] | shorthand for metabolite["id", "compartment"] |
| enzyme["ID"→"id", "Compartment"→"compartment",opts] | a enzyme in a particular compartment |
Toolbox species types
This defines adenosine triphosphate (ATP) in the cytosol
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This defines adenosine triphosphate (ATP) using a slightly shorter notation
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However, the full type expression (metabolite) is used internally
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Reactions
Chemical reactions are defined in the following way:
| reaction["id", substrates, products, stoichiometry] | a reversible reaction |
| reaction["id", substrates, products, stoichiometry, False] | an irreversible reaction |
| r[args] | a shorthand for reaction |
Toolbox reactions
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Define an irreversible reaction
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Query data types
Toolbox typical accessor function
Query the ID and compartment of a metabolite
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Query the ID and compartment of an reaction
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Textual input
| str2mass["ID"] | a metabolite (ID) |
| str2mass["ID[Comp]"] | a metabolite in a particular compartment (IDComp) |
| str2mass["ID: 2 x <=> y + z"] | a reversible reaction ( ) |
| str2mass["ID: 2 x[c] --> y[c] + z[c]"] | an irreversible reaction ( ) |
| str2mass["Keq_ID"] | an equilibrium constant for reaction ID ( ) |
| str2mass["k_ID_fwd"] | forward rate constant |
| str2mass["k_ID_rev"] | reverse rate constant |
Use textual input to declare species, parameters, reactions etc.
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Parse a metabolite with a specific compartment
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Facilitate
str2mass to quickly define a model
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