Using Strengths

The following sections try to explain how to deal with various aspects of the Strengths package. Each section is quite independent from the order and you can be approached in any order.

The first section explains how to install and import the package. The second section shows how to build reaction-diffusion systems and perform system trajectory simulations. The third section explains how the UnitValue and UnitArray classes, which represent physical quantities, work. The Fourth section deals with simulation engines, explaining how they work and which ones are available. The Last section just tells which external packages are needed to have strengths running.

• Installing and importing Strengths
• The fundamental concepts
  • Object concepts
    • Species (Species class)
    • Reaction (Reaction class)
    • Network (RDNetwork class)
    • Space (RDSpace class)
    • System (RDSystem class)
    • Script (RDScript class)
    • Engine (RDEngineBase derived class)
    • Trajectory (RDTrajectory class)
  • Other concepts
    • Cells
    • Environments
    • Chemostats
• Building and simulating a reaction-diffusion system
  • A simple example without diffusion
  • Alternative ways to define a reaction-diffusion system
    • Through a JSON File
    • With multiple JSON files
    • With a Python dictionary
    • Using object construction
  • Alternative ways to script a simulation
    • Creating the script
    • Simulating the script
  • Another example featuring diffusion
  • A Third Example with chemostats
  • A fourth example with environments
  • Defining boundary conditions
  • References
• Setting up initial conditions
  • Setting up the initial state
  • Setting up the chemostates
  • Changing the Species.density attribute
  • Changing the Species.chstt attribute
• Working the simulation output
  • What is in the simulation output?
  • Accessing trajectory data
  • Examples
    • use case 1: Plotting a trajectory
    • use case 2: Plotting a sampled system state
• Working with units
  • UnitsValue, UnitArray and Units
  • Operations on UnitValue and UnitArrays
    • addition and subtraction
    • division and multiplication
    • modulo
    • power
    • comparison
• Using Strengths with SciPy’s integration ODE methods
• References
• Simulation Engines
  • What is a simulation engine
  • Engine implementations installed with Strengths
  • References
• Diffusion in graph spaces
• References
• Array indexing
  • Space cell index
  • System state and system chemostats
  • State trajectory data
• Building Strengths from source
• Dependencies
  • NumPy
  • Matplotlib