m = pwAddX(m, *ID, *startValue, fitSetting, minValue, maxValue, unit, ...
compartment, name, description, typeOfStartValue, ...
m = pwAddX(m, interactive)
Adds a dynamic variable to a model.
The dynamic variables comprise all species that are part of the
left hand side of the differential equations. Essentially their
initial value, fitting type and limits have to be specified.
The arguments of pwAddX are properties of x which can also
be specified using pwSetX.
Arguments for pwAddX
1. m struct A model struct (see pwGetEmptyModel)
2. ID ID
3. startValue float initial value for integration (default 0)
4. fitSetting string 'global', 'local', 'fix'
5. minValue float minimal value during fitting
6. maxValue float maximal value during fitting
7. unit string
8. compartment ID
9. name string descriptive name
10. description string
11. typeOfStartValue string 'amount' or 'concentration' (default)
12. designerProps matrix Visualization properties (12 entries per row):
[x y z w h color flipped1 flipped2 upright visible; ...]
13. classname string Custom class name of the variable to define its shape
in the model designer and to group related variables.
For Systems Biology models (compare CellDesigner):
'gene','rna' 'antisense_rna', 'phenotype',
'simple_molecule', 'drug', 'unknown', 'complex',
Alternative function call for interactive specification:
interactive bool If true, the user is prompted to enter the properties
into a user interface.
Not listed dynamic variables which appear in the list of reactions have
a default start value of 0 and are fixed during fitting. The default
compartment is the first specified compartment in the compartment section.
The default fit setting for non-vanishing players is 'local', else 'fix'.
Note that all x variables are treated as concentrations.
If the start value is given as an amount, the corresponding concentration
is calculated. All plotted x trajectories are also concentrations.
The protein classname is useful for visualization in the PW Model Designer
or to exchange the model with CellDesigner.
If the model comprises a set of complexes, the 'or' symbol '|' is
supported in the variable ID as a shortcut to define multiple
x variables at once. E.g.
m = pwAddX(m, 'A_<B|C>_<D|E>', 1);
will be interpreted as
m = pwAddX(m, 'A_B_D', 1);
m = pwAddX(m, 'A_C_D', 1);
m = pwAddX(m, 'A_B_E', 1);
m = pwAddX(m, 'A_C_E', 1);
The explosion of pattern-based IDs can be controlled via the
explodePattern and removeAfterExplosion arguments.
PottersWheel supports arbitrary variable IDs as long as only letters,
numbers and the underscore are used and the first character is not a
numerical value. However, in order to make use of several features
such as sub-reaction-networks and combinatorial complexity, the
following conventions are recommended:
- Basic species start with a capital letter, e.g. Erk and Mek
- Modifications are lower case prefixes, e.g. pErk and ppErk
- Species of a complex are separated by an underscore, e.g. pR_pR and Grb1_Grb2