UQ-bio Summer School

3.5 – TASEP Models (William Raymond)

Lecture 3.5

Title: Tutorial — Totally Asymmetric Simple Exclusion Process models for single-mRNA Translation

Lecturer: Will Raymond

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

Lecturer Email: wsraymon@rams.colostate.edu

Learning Objectives:

      • Examine simple TASEP processes.

      • Produce a flow density diagram and describe each canonical flow regime.

      • See how TASEP process naturally extends to mRNA translation (and other biological processes).
      • Test out the rSNAPsim package and examine some of its TASEP trajectories.
      • Learn how to read Kymographs.

Will Raymond graduated in May 2017 from Colorado State University with a Bachelors in Biomedical Engineering and a Bachelors in Chemical and Biological Engineering.

Will has been a PhD student in Dr. Munsky’s lab since 2019 working on a myriad of projects. He is currently the lead developer on the rSNAPsim, an open source Python TASEP mRNA simulation package. In addition to that, he also works on implementing machine learning for nascent chain tracking fluorescent spot identification. Additionally, a recent area of focus has been modeling tRNA abundances and their effect on translation dynamics.

His primary area of interest is the intersection of machine learning, bioinformatics, and RNA biology. He is most excited about novel ncRNA discovery and advancements in RNA structural identification and disease classification. 

Title: Totally Asymmetric Simple Exclusion Process models for single-mRNA Translation

Abstract: In this tutorial we will work through the TASEP notebook and provide hands on instruction to the students. We will start with a very simple canonical tasep and work through adding different features and processes, concluding with simulating mRNA translation with the rSNAPsim.

Suggested Reading or Key Publications:

Links to Relevant Software: 

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