pwAddX


 m = pwAddX(m, *ID, *startValue, fitSetting, minValue, maxValue, unit, ...
            compartment, name, description, typeOfStartValue, ...
            designerProps, classname)
 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):
                               'protein.generic', 'protein.receptor',
                               'protein.ion_channel', 'protein.truncated',
                               'gene','rna' 'antisense_rna', 'phenotype',
                               'simple_molecule', 'drug', 'unknown', 'complex',
                               'ion', 'degraded'

 Alternative function call for interactive specification:
 interactive   bool    If true, the user is prompted to enter the properties
                       into a user interface.

 

Description

 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.

 

Rule-based definition

 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.

 

Naming convention

 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

 

Example

 m = pwAddX(m, 'Stat', 1.7, 'local', 0, 100);
 m = pwAddX(m, 'pStat');

See also

pwGetX
pwSetX
pwAddR
pwAddY
pwAddZ
pwAddU