COMBINE Examples

Here you will find Python Jupyter notebooks that show how to create simple models for each of the COMBINE standards

This notebook creates a model in CellML. The CellML we create here is a simple model for the growth of the number of cancer cells over time.

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This notebook creates a simple model in NeuroML. It adds a single spiking neuron to a population in a network, and then plots the membrane potential.

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OMEX

A COMBINE archive is a bundled package containing all the necessary documents and relevant information for a modeling and simulation project. This notebook is an example for creating a simple COMBINE archive.

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This notebook creates simple models in SBGN. The same biological system is shown in the three different languages of SBGN.

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This notebook creates a simple model in SBML. The SBML model consists of two chemical species and a basic reaction that converts one to the other.

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This notebook illustrates the Synthetic Biology Open Language (SBOL). In this notebook we will be creating a simple sequence and generating a diagram for it.

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This notebook creates a simple SED-ML file. We show how to use SED-ML to specify a simulation of an SBML model.

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If you would like to contribute to the development of these notebooks or if you have spotted a bug, please create a PR or submit an issue to the main examples repo.