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from pysb import * # Model, Monomer, Parameter, Initial, Rule, Observable from pysb.macros import * 2) Create an instance of the model class. This creates an empty model to be defined interactively. In [3]: Model Out[3]:

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The pysb.pkpd.macros module currently defines the following macros encoding PK, PD, and dosing functions:. PK functions: drug_monomer - adds a simple monomer species for the drug to the model. If the drug needs binding sites or other state variables then you should directly use the PySB Monomer class instead.; one_compartment - adds one compartment to the model for a …

PySB documentation¶. PySB is a framework for building mathematical rule-based models of biochemical systems as Python programs. PySB abstracts the complex process of creating equations describing interactions among multiple proteins (or other biomolecules) into a simple and intuitive domain specific language embedded within Python.

detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage thework of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.

Programming biological models in Python using PySB Carlos F Lopez1,3, Jeremy L Muhlich2,3, John A Bachman2,3 and Peter K Sorger2,* 1 Department of Cancer Biology, Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA and 2 Department of Systems Biology, Center for Cell Decision Processes, Harvard Medical School, …

class pysb.core. Model (name = None, base = None, _export = True) [source] ¶. A rule-based model containing monomers, rules, compartments and parameters. Parameters: name string, optional. Name of the model. If not specified, will be set to the name of the file from which the constructor was called (with the .py extension stripped).

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The pysb.pkpd.macros module currently defines the following macros encoding PK, PD, and dosing functions:. PK functions: drug_monomer - adds a simple monomer species for the drug to the model. If the drug needs binding sites or other state variables then you should directly use the PySB Monomer class instead.; one_compartment - adds one compartment to the model for a …

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PySB Models. Biochemical systems models encoded using the PySB framework: PAR2 Activation and calcium signaling Reaction Model (PARM) Models of agonist-induced activation of PAR2 and calcium signaling via the phospholipase C and IP3 pathway. Type: Dynamical differential equation-based (ODE/SDE) model.

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The Model class has a container for each component type, for example monomers holds the monomers. These component objects are the very same ones you defined in your model script – they were implicitly added to the model's monomers container by the self-export system. This container is a ComponentSet, a special PySB class which acts like a list, a dict and a set rolled …

Within that group, a dataset "_model" has a JSON version of the PySB model. SimulationResult are stored as groups within the model group. The file hierarchy under group_name/dataset_name/ then consists of the following HDF5 gzip compressed HDF5 datasets: trajectories, param_values, initials, tout, observables (optional) and expressions ...

PySB Modules Reference¶. PySB core (pysb.core)ANY; Compartment; CompartmentAlreadySpecifiedError; ComplexPattern

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