Welcome to the Cytocalc documentation!

This project aims to develop tools for analyzing simulations run using cytosim.

Note

This project is under development.

Contents

• Installation
• Using Scripts
  • Example
• Creating Scripts
  • General idea
  • Example 1: MSD of beads
  • Example 2: Contraction of network
• Developer’s Guide
  • Development Environment
    • Prerequisites
    • Getting Started
  • Code architecture
    • Class context for parsing cytosim report files
  • Development Workflow
    • Branch Naming Convention
    • Code Standards and Style
    • Testing
    • Making Changes
  • Merge Request Process
  • Documentation
  • Getting Help
  • License

Reference

• cytocalc package
  • Submodules
    • cytocalc.csmframe module
      • CSMFrame
    • cytocalc.csmparser module
      • CSMParser
      • CYMParser
    • cytocalc.csmsimulation module
      • CSMSimulation
    • cytocalc.helper module
      • theoretical_cont_rate()
    • cytocalc.microrheology module
      • _msd_to_g_star_evans()
      • _msd_to_g_star_mason()
      • msd_to_g_star()