Pycotools
develop
  • PyCoTools
  • Getting started
    • Build a model with antimony
    • Create an antmiony string from an existing model
    • Simulate a time course
    • Visualise a time course
    • Run Parameter Estimation
  • Tutorials
    • Running Time-Courses
      • Create a model
      • Deterministic Time Course
      • Visualization
        • Plot in Phase Space
        • Save to file
      • Alternative Solvers
        • Stochastic MM
      • Run a Time Course Using Direct Method
      • Plot stochastic time course
    • Insert Parameters
      • Build a demonistration model
      • Insert Parameters from Python Dictionary
      • Insert Parameters from Pandas DataFrame
      • Insert Parameters from Parameter Estimation Output
      • Insert Parameters using the model.Model().insert_parameters method
      • Change parameters using model.Model().set
    • Parameter Scan
      • Two Way Parameter Scan
      • Repeat Scan Items
    • Parameter Estimation
      • Build a Model
      • Collect some experimental data
      • The Config Object
      • Running multiple parameter estimations
    • A shortcut for configuring the ParameterEstimation.Config object
  • Examples
    • Working with an existing copasi model
      • Create a PyCoTools model from an existing model
      • Extracting the antimony string associated with a copasi model
    • Integration with Tellurium
    • Simple Parameter Estimation
    • Simple Parameter with Steady State Data
    • Parameter Estimation using Prefix Argument
    • Parameter Estimation with Independent Variables
    • Advanced Parameter Estimation
      • Models
      • Datasets
      • Items
      • Settings
      • Building a ParameterEstimation.Config object
      • Using a ParameterEstimation.Context as a template
    • Multiple Parameter Estimations
      • Increasing Parameter Estimation Throughput
    • Parameter estimation with multiple models
    • Working from the model.Model class directly
      • Inserting parameters
      • Simulating a time course
      • Sensitivities
    • Profile Likelihoods
    • Cross validation
  • API documentation
    • The model module
      • pycotools3.model.Model
      • pycotools3.model.ImportSBML
      • pycotools3.model.InsertParameters
      • pycotools3.model.BuildAntimony
      • pycotools3.model.Build
    • The tasks module
      • pycotools3.tasks.TimeCourse
      • pycotools3.tasks.ParameterEstimation.Config
      • pycotools3.tasks.ParameterEstimation
      • pycotools3.tasks.ParameterEstimation.Context
      • pycotools3.tasks.Sensitivities
      • pycotools3.tasks.Scan
      • pycotools3.tasks.Reports
    • The viz module
      • pycotools3.viz.Parse
      • pycotools3.viz.PlotTimeCourse
      • pycotools3.viz.Boxplots
Pycotools
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  • API documentation
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API documentationΒΆ

Here you will find detailed information about every module class and method in the pycotools3 package.

  • The model module
    • pycotools3.model.Model
    • pycotools3.model.ImportSBML
    • pycotools3.model.InsertParameters
    • pycotools3.model.BuildAntimony
    • pycotools3.model.Build
  • The tasks module
    • pycotools3.tasks.TimeCourse
    • pycotools3.tasks.ParameterEstimation.Config
    • pycotools3.tasks.ParameterEstimation
    • pycotools3.tasks.ParameterEstimation.Context
    • pycotools3.tasks.Sensitivities
    • pycotools3.tasks.Scan
    • pycotools3.tasks.Reports
  • The viz module
    • pycotools3.viz.Parse
    • pycotools3.viz.PlotTimeCourse
    • pycotools3.viz.Boxplots
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© Copyright 2017, Ciaran Welsh Revision c7238882.

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