UQ-bio Summer School

3.2 – Stochastic simulation Tutorial (Lisa Weber)

Lecture 3.2

Title: Tutorial — Write your own Stochastic Simulation Algorithm in Python

Lecturer: Lisa Weber 

Lecturer Website: https://www.engr.colostate.edu/~munsky/

Lecturer Email: llweber@rams.colostate.edu

Learning Objectives:

      • Learn how to define the stoichiometry vectors and propensity functions for stochastic chemical reactions

      • Write your own Gillesspie’s Stochastic Simulation algorithm in Python

Lisa Weber is currently an Instructor and PhD Candidate in Chemical Engineering at Colorado State University. She received a BS in Chemical Engineering from the University of Colorado-Boulder, an MS in Mechanical Engineering with a biological emphasis from the University of Denver, and has engineering experience in multiple industries (Oil and Gas, Pharmaceuticals, and Aerospace). Her research involves performing computational modeling of various biological processes, including aspects of gene expression and DNA/Oligonucleotide binding interactions in relation to multiple experimental variables, integrating computational methods with experimental data. She also has an interest in helping engineering students foster more inclusive professional identities by (performing research on) implementing and teaching implicit bias, inclusion, and diversity-related topics to undergraduate engineering students. In addition, she was a Graduate Teaching Fellow from 2017-2019, and she is currently the Instructor for CBE 160: Introduction to MATLAB for Chemical and Biological Engineers (from 2018-Present). 

Title: Write your own Stochastic Simulation Algorithm in Python

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Suggested Reading or Key Publications:

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