Notebooks

Author: Lukas Breitwieser, Filename: ST01 model-initializer.ipynb

In this tutorial we want to demonstrate different functions to initialize agents in space.

Author: Lukas Breitwieser, Filename: ST02 user-defined-random-number-distribution.ipynb

In this tutorial we demonstrate how to create a random number generator that draws samples from a user-defined distribution.

Author: Lukas Breitwieser, Filename: ST03 agent-reproduction-mortality.ipynb

In this tutorial we want to demonstrate how to add and remove agents from the simulation.

Author: Lukas Breitwieser, Filename: ST04 agent-reproduction-with-behaviors.ipynb

In tutorial `ST3-agent-reproduction-mortality` we have explored how to add and remove agents from the simulation. In this tutorial we want to explore different behavior options to control if a new agent gets a behavior from the original agent, and if a behavior will be removed from the original one.

Author: Lukas Breitwieser, Filename: ST05 agent-reproduction-advanced.ipynb

In the tutorials so far we used `Cell::Divide` to create new agents. In this demo we want to show how to define your own "process" that creates a new agent. Furthermore, we will explain the purpose of the functions `Agent::Initialize` and `Agent::Update`. Assume that we want to create a new agent type `Human` which should be able to `GiveBirth`.

Author: Lukas Breitwieser, Filename: ST06 environment-search.ipynb

In this tutorial we will show how to execute a function for each neighbor of an agent.

Author: Lukas Breitwieser, Filename: ST07 multi-scale-simulation.ipynb

In this tutorial we will show how BioDynaMo support multi-scale simulations. Multi-scale simulation means that simulated processes happen in different time-scales---e.g. substance diffusion and neurite growth.

Author: Lukas Breitwieser, Filename: ST08 histograms.ipynb

In this tutorial we will show how to create a histogram of all agent diameters in the simulation and fit a function to the data.

Author: Lukas Breitwieser, Filename: ST09 timeseries-plotting-basic.ipynb

In this tutorial we show how to collect data during the simulation and plot it at the end.
To this extent, we create a simulation where cells divide rapidly leading to exponential growth.

Author: Lukas Breitwieser, Filename: ST10 timeseries-plotting-and-analysis.ipynb

In this tutorial we show how to collect data during the simulation, and plot and analyse it at the end.
To this extent, we create a simulation where cells divide rapidly leading to exponential growth.

Author: Lukas Breitwieser, Filename: ST11 multiple-experiments-statistical-analysis.ipynb

In this tutorial we show how to collect and analyse data from multiple experiments.
To this extent, we create a simulation where cells divide rapidly leading to exponential growth.

Author: Lukas Breitwieser, Filename: ST12 hierarchical-model.ipynb

Some models require to update certain agents before others. In this tutorial we show how to execute operations first for large agents and afterwards for small ones. Lastly, we demonstrate how to run a different set of operations for large and for small agents.

Author: Lukas Breitwieser, Filename: ST13 dynamic-scheduling.ipynb

This tutorial demonstrates that behaviors and operations can be added and removed during the simulation. This feature provides maximum flexibility to control which functions will be executed during the lifetime of a simulation.

Author: Lukas Breitwieser, Filename: ST14 randomize-iteration-order.ipynb

In this tutorial we show how to randomize the order that BioDynaMo uses in each iteration to process the agents.

Author: Lukas Breitwieser, Filename: ST15 replace-interaction-force.ipynb

This tutorial demonstrates how to replace BioDynaMo's default interaction force with a user-defined one. The interaction force is used to calculate forces between agent pairs that are in physical contact with each other.