MASSpy
v0.1.1

Installation and Setup

  • Quick Start Guide
  • Optimization Solvers
  • Using MASSpy with Docker
  • Advanced Docker Usage

Step-by-Step Tutorials

  • 1. Getting Started with MASSpy
  • 2. Constructing Models
  • 3. Reading and Writing Models
  • 4. Dynamic Simulation of Models
  • 5. Plotting and Visualization
  • 6. Enzyme Modules
  • 7. Thermodynamic Feasibility and Sampling of Metabolite Concentrations
  • 8. Ensemble Modeling
  • 9. Network Visualization
  • 10. Checking Model Quality
  • 11. Global Configuration
  • 12. Using COBRApy with MASSpy
  • 13. Modeling Volumes and Multiple Compartments
  • 14. Import and Export of Optimization Problems

Gallery

  • Visualization
  • Workflows

Educational Resources

  • Systems Biology: Simulation of Dynamic Network States

API

  • API Reference
    • mass

Additional Resources:

  • Frequently Asked Questions (FAQs)
  • Code Repositories
  • Works Cited
MASSpy
  • Docs »
  • API Reference
  • Edit on GitHub

API ReferenceΒΆ

This page contains auto-generated API reference documentation 1.

  • mass
    • mass.core
      • mass.core.mass_configuration
      • mass.core.mass_metabolite
      • mass.core.mass_model
      • mass.core.mass_reaction
      • mass.core.mass_solution
      • mass.core.units
    • mass.enzyme_modules
      • mass.enzyme_modules.enzyme_module
      • mass.enzyme_modules.enzyme_module_dict
      • mass.enzyme_modules.enzyme_module_form
      • mass.enzyme_modules.enzyme_module_reaction
    • mass.io
      • mass.io.dict
      • mass.io.json
      • mass.io.sbml
    • mass.simulation
      • mass.simulation.ensemble
      • mass.simulation.simulation
    • mass.test
    • mass.thermo
      • mass.thermo.conc_sampling
        • mass.thermo.conc_sampling.conc_achr
        • mass.thermo.conc_sampling.conc_hr_sampler
        • mass.thermo.conc_sampling.conc_optgp
        • mass.thermo.conc_sampling.conc_sampling
      • mass.thermo.conc_solution
      • mass.thermo.conc_solver
    • mass.util
      • mass.util.dict_with_id
      • mass.util.expressions
      • mass.util.matrix
      • mass.util.qcqa
      • mass.util.util
    • mass.visualization
      • mass.visualization.comparison
      • mass.visualization.phase_portraits
      • mass.visualization.time_profiles
      • mass.visualization.visualization_util
    • mass.exceptions
1

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