PhysioBlocks

PhysioBlocks allows the simulation of dynamical models of physiological systems.

User Levels

They are several use cases for PhysioBlocks depending on the user profile:

• Level 1: Configure and run physiological systems simulation (for pre-existing systems)
• Level 2: Create new systems with existing blocks without writing code
• Level 3: Write and add new blocks to the library.

Principle

• A Net (system) is built from Nodes and Blocks connected by those nodes.
• At each node in the net, connected blocks share Degrees of Freedom (ex: pressure) and send Fluxes that verify Kirchhoff Law.
• ModelComponents concatenate blocks equations to the global system (if necessary, for modularity purposes within the block)

Interactions

Level 1: Configure and run a simulation: JSON

• Update the model parameters

Level 2: Create Nets: JSON

• Declare the nodes, the blocks, and the block - nodes connections

Level 3: Write and add models to the library: Python

• Declare the quantities to use in the model
• Write the fluxes and equations

Documentation

Here are the links to the sections of the full documentation:

• Installation
• User Guide
• Library
• API Reference

Quick start

Complete instructions are available in the documentation. This instructions will enable you to launch a reference simulation.

Installation

This project requires a recent version of python installed. Then:

    pip install physioblocks

Configuration

To configure PhysioBlocks Launcher:

# Create an empty folder where you want to store simulations results.
mkdir $LAUNCHER_FOLDER_PATH$

# Configure the folder
python -m physioblocks.launcher.configure -d $LAUNCHER_FOLDER_PATH$ -v

Launch a simulation

With a Launcher folder configured:

# Move to your configured launcher folder
cd $LAUNCHER_FOLDER_PATH$

#  Launch a reference simulation
python -m physioblocks.launcher references/spherical_heart_sim.jsonc -v -s QuickStart

Results will be available in the $LAUNCHER_FOLDER_PATH/simulations/QuickStart series folder:

• the csv files contain the simulation results.
• the html files allow you to visualize the results.
• the log and json files are here for debug purposes.