physioblocks 1.1.3

Physioblocks allows the simulation of dynamical models of physiological systems

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 -t -s QuickStart

# This can take some time.

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

• the csv file contains the simulation results.
• the html allows you to visualize the results.
• the log and json files are here for debug purposes.