Inchman User Guide

Contents:

• Introduction
  • Overview
  • Reaction-Drift-Diffusion Systems
  • Gillespie-Multiparticle Algorithm
  • GPU Implementation
  • Basic Workflow
  • References
• Installation
  • Linux
  • Mac OS X
• Editor
  • Running the editor
  • File Panel
  • Options
  • Parameters
  • Compartments
  • Species
  • Reactions
  • Initialization
  • Drift-Diffusivity Method
  • Events
  • Update Fields
  • New Individuals
• Running Inchman
  • Invoke Inchman from the Editor
  • Invoke Inchman from the Command Line
• Analyzing the simulation output
  • Inchman output files
  • The HDF5 File
• Tutorials
  • The Belousov-Zhabotinsky reaction
  • Migration of neurons in the brain
  • References

Inchman Reference

• Examples
  • Simple Reaction Network
  • Simple Reaction Network with Individuals
  • Simple Reaction Network with Individuals (using New Individuals Method)
  • Fisher Problem
  • Fisher Problem with Individuals
  • Homogeneous Diffusion
  • Homogeneous Diffusivity and Drift
  • Homogeneous Diffusivity and Drift with Field Parameter
  • Homogeneous Diffusivity and Drift (Individuals)
  • Multiplicative Noise (Geometric Brownian Motion)
  • Non-linear Drift Field
  • Ornstein-Uhlenbeck Process
  • A+B Annihilation
  • A+B Annihilation with Drift
  • Random Drift Field
  • Intracellular Calcium Distribution
  • Oregonator Model of the Belousov-Zhabotinsky Reaction
  • Chemotaxis of Neurons in the Brain
• Inchman SBML Annotations
  • SBML Container
  • Model
  • Compartment
  • Species
  • Parameters
  • Reactions
• Structure of the HDF5 File
  • Model Group
  • Parameters Group
  • Runs Group
• Individual Solver
  • Particle creation and annihilation
  • References