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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

Additional Resources:

  • Frequently Asked Questions (FAQs)
  • Code Repositories
  • Works Cited
MASSpy
  • Overview: module code

All modules for which code is available

  • 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.enzyme_module
  • mass.enzyme_modules.enzyme_module_dict
  • mass.enzyme_modules.enzyme_module_form
  • mass.enzyme_modules.enzyme_module_reaction
  • mass.example_data
  • mass.exceptions
  • mass.io.dict
  • mass.io.json
  • mass.io.sbml
  • mass.simulation.ensemble
  • mass.simulation.simulation
  • 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.dict_with_id
  • mass.util.expressions
  • mass.util.matrix
  • mass.util.qcqa
  • mass.util.util
  • mass.visualization.comparison
  • mass.visualization.phase_portraits
  • mass.visualization.time_profiles

© Copyright 2022, Z. Haiman. Revision 784bda55.

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