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:
- setting the KAPPAPATH environment variable to the KaSim directory
- setting the path using the
set_kappa_path()function at runtime - adding the path to the KaSim directory to the system PATH environment variable
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class
pysb.kappa.SimulationResult¶ -
flux_map¶ Alias for field number 1
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timecourse¶ Alias for field number 0
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class
pysb.kappa.StaticAnalysisResult¶ -
contact_map¶ Alias for field number 0
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influence_map¶ Alias for field number 1
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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: pygraphviz AGraph object containing the contact map.
The contact map can be rendered as a pdf using the dot layout program
as follows:
contact_map.draw('contact_map.pdf', prog='dot')
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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: pygraphviz AGraph object containing the influence map.
The influence map can be rendered as a pdf using the dot layout program
as follows:
influence_map.draw('influence_map.pdf', prog='dot')
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pysb.kappa.run_simulation(model, time=10000, points=200, cleanup=True, output_prefix=None, output_dir=None, flux_map=False, perturbation=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 -t 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. Identical to the -p argument when using KaSim at the command line. 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).
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 pygraphviz AGraph containing the flux map. The flux map can be rendered
as a pdf using the dot layout program as follows:
fluxmap.draw('fluxmap.pdf', prog='dot')
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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 pygraphviz AGraph. 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.