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Systems biology practical on writing simulators with F# and Z3
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Brownian dynamics.ipynb
Introduction.ipynb
LICENSE.md
NegativeFeedBackLoops.ipynb
ProgrammingInFsharp.ipynb
README.md
Simple Z3 example.ipynb
Single Progenitor.ipynb
Timing Z3 example.ipynb

README.md

Writing simulation and analysis tools using F# and Z3

Introduction

This practical is intended as a brief introduction to the F# programming language and the SMT solver Z3. In the course of this practical you will be performing two types of biological simulation; you will be writing a small Gillespie simulator for the single progenitor model of epithelial stem cells, and editing and exploring logical models of small biological networks. This practical builds on the discussions of F# and Z3 in lecture 4, and the demonstrations in the associated supervision. The goal of this practical is to allow you to see how you model different systems using a functional programming language (F#) and formal logic (using Z3). The final questions in each section are more open ended so aim to spend about 1.5 hours on each component.

Parts of this tutorial are available as an Azure Notebook:

Azure Notebooks

Getting started

I recommend looking at

https://notebooks.azure.com/Microsoft/libraries/samples/html/FSharp%20for%20Azure%20Notebooks.ipynb

as a reference for using F# in jupyter notebooks.

Z3 for logical models

Reread "Simple Z3 example" and "Timing Z3 example", before working on to "NegativeFeedbackLoops"

F# for stochastic simulation

Complete the code in the Single Progenitor notebook, following the instructions

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