Model formulation

This section will cover how to formulate mathematical models, including the components of ordinary differential equations.

What is a state?

This video introduces you to the concept of a state in an ODE-based model, useful e.g. in a systems biology project. It allows you know its basic properties, and to identify the states in three versions of writing up a model: state-space form, reaction form, and interaction-graph form.

What are the parameters?

In this video we ask the question: "What are the parameters?", and find that there are three types of them in a state-space model: the kinetic parameters, the initial conditions, and the measurement parameters.

What are the inputs and outputs?

In this video we ask the question: "What are the inputs and outputs?", and find that the inputs are things that we do to the system, and that the outputs are things that we can measure.

Model from an interaction graph

In this video we get to the core of the model formulation task: "How do you write a model in state-space form, from a given interaction-graph?". This video describes the essence of how to formulate a model from an interaction-graph.