Kappa integration (pysb.kappa)

Wrapper functions for running the Kappa programs KaSim and KaSa.

The path to the directory containing the KaSim and KaSa executables can be specified in one of three ways:

  • set the KAPPAPATH environment variable to the KaSim directory
  • move Kappa to /usr/local/share/KaSim (macOS, Linux) or c:Program FilesKaSim (Windows)
  • set the path using the pysb.pathfinder.set_path() function at runtime
class pysb.kappa.SimulationResult
flux_map

Alias for field number 1

timecourse

Alias for field number 0

class pysb.kappa.StaticAnalysisResult
contact_map

Alias for field number 0

influence_map

Alias for field number 1

pysb.kappa.contact_map(model, **kwargs)[source]

Generates the contact map via KaSa.

Parameters:

model : pysb.core.Model

The model for generating the influence map.

**kwargs : other keyword arguments

Any other keyword arguments are passed to the function run_static_analysis().

Returns:

networkx MultiGraph object containing the contact map. For details on

viewing the contact map graphically see run_static_analysis() (notes

section).

pysb.kappa.influence_map(model, **kwargs)[source]

Generates the influence map via KaSa.

Parameters:

model : pysb.core.Model

The model for generating the influence map.

**kwargs : other keyword arguments

Any other keyword arguments are passed to the function run_static_analysis().

Returns:

networkx MultiGraph object containing the influence map. For details on

viewing the influence map graphically see run_static_analysis()

(notes section).

pysb.kappa.run_simulation(model, time=10000, points=200, cleanup=True, output_prefix=None, output_dir=None, flux_map=False, perturbation=None, seed=None, verbose=False)[source]

Runs the given model using KaSim and returns the parsed results.

Parameters:

model : pysb.core.Model

The model to simulate/analyze using KaSim.

time : number

The amount of time (in arbitrary units) to run a simulation. Identical to the -u time -l argument when using KaSim at the command line. Default value is 10000. If set to 0, no simulation will be run.

points : integer

The number of data points to collect for plotting. Note that this is not identical to the -p argument of KaSim when called from the command line, which denotes plot period (time interval between points in plot). Default value is 200. Note that the number of points actually returned by the simulator will be points + 1 (including the 0 point).

cleanup : boolean

Specifies whether output files produced by KaSim should be deleted after execution is completed. Default value is True.

output_prefix: str

Prefix of the temporary directory name. Default is ‘tmpKappa_<model name>_’.

output_dir : string

The directory in which to create the temporary directory for the .ka and other output files. Defaults to the system temporary file directory (e.g. /tmp). If the specified directory does not exist, an Exception is thrown.

flux_map: boolean

Specifies whether or not to produce the flux map (generated over the full duration of the simulation). Default value is False.

perturbation : string or None

Optional perturbation language syntax to be appended to the Kappa file. See KaSim manual for more details. Default value is None (no perturbation).

seed : integer

A seed integer for KaSim random number generator. Set to None to allow KaSim to use a random seed (default) or supply a seed for deterministic behaviour (e.g. for testing)

verbose : boolean

Whether to pass the output of KaSim through to stdout/stderr.

Returns:

If flux_map is False, returns the kasim simulation data as a Numpy ndarray.

Data is accessed using the syntax:

results[index_name]

The index ‘time’ gives the time coordinates of the simulation. Data for the

observables can be accessed by indexing the array with the names of the

observables. Each entry in the ndarray has length points + 1, due to the

inclusion of both the zero point and the final timepoint.

If flux_map is True, returns an instance of SimulationResult, a namedtuple

with two members, timecourse and flux_map. The timecourse field

contains the simulation ndarray, and the flux_map field is an instance of

a networkx MultiGraph containing the flux map. For details on viewing

the flux map graphically see run_static_analysis() (notes section).

pysb.kappa.run_static_analysis(model, influence_map=False, contact_map=False, cleanup=True, output_prefix=None, output_dir=None, verbose=False)[source]

Run static analysis (KaSa) on to get the contact and influence maps.

If neither influence_map nor contact_map are set to True, then a ValueError is raised.

Parameters:

model : pysb.core.Model

The model to simulate/analyze using KaSa.

influence_map : boolean

Whether to compute the influence map.

contact_map : boolean

Whether to compute the contact map.

cleanup : boolean

Specifies whether output files produced by KaSa should be deleted after execution is completed. Default value is True.

output_prefix: str

Prefix of the temporary directory name. Default is ‘tmpKappa_<model name>_’.

output_dir : string

The directory in which to create the temporary directory for the .ka and other output files. Defaults to the system temporary file directory (e.g. /tmp). If the specified directory does not exist, an Exception is thrown.

verbose : boolean

Whether to pass the output of KaSa through to stdout/stderr.

Returns:

StaticAnalysisResult, a namedtuple with two fields, contact_map and

influence_map, each containing the respective result as an instance

of a networkx MultiGraph. If the either the contact_map or influence_map

argument to the function is False, the corresponding entry in the

StaticAnalysisResult returned by the function will be None.

Notes

To view a networkx file graphically, use draw_network:

import networkx as nx
nx.draw_networkx(g, with_labels=True)

You can use graphviz_layout to use graphviz for layout (requires pydot library):

import networkx as nx
pos = nx.drawing.nx_pydot.graphviz_layout(g, prog='dot')
nx.draw_networkx(g, pos, with_labels=True)

For further information, see the networkx documentation on visualization: https://networkx.github.io/documentation/latest/reference/drawing.html

pysb.kappa.set_kappa_path(path)[source]

Set the path to the KaSim and KaSa executables.

Deprecated. Use pysb.pathfinder.set_path() instead.

Parameters:

path: string

Directory containing KaSim and KaSa executables.