BE 240, Spring 2020

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Open Source Tools for Biological Circuit Design


  • Richard Murray (CDS/BE),
  • Ayush Pandey (CDS)
  • Cindy Ren (CDS)
  • William Poole (CNS)

Class meetings

  • Lectures: TBD
  • Recitations: TBD
  • Office hours: TBD

This is the course homepage for BE 240, Spring 2020.

This course covers the use of open source tools developed at Caltech for use in modeling and simulation of engineered biological circuits. Participants in the course will develop working knowledge of modeling, simulation, and design tools that are available for biological circuits and apply that knowledge to a circuit relevant to your research. Students will also gain insights into modeling and design choices, including what level of detail to include in a model based on the questions you are trying to ask. Finally, the course aims to expand the available applications of model-based design of biological circuits and/or the available tools for biological circuit design through open source implementations.

Lecture Schedule

Date Topic Lecturer Tools
W1 - 30 Mar Organizational week Richard Anaconda, Jupyter, Git
W2 - 6 Apr CRNs and simulating them with Bioscrape William Bioscrape
W3 - 13 Apr Model reduction in bioscrape via non-mass-action propensities and rules Ayush Bioscrape
W4 - 20 Apr BioCRNpyler for generating large CRN models from parts William BioCRNpyler
W5 - 27 Apr Compartments as orthogonal CRNs connected by diffusion reactions and SubSBML Ayush Sub-SBML
W6 - 4 May Spatial systems and signalling Cindy Gro
W7 - 11 May Cells and Growth/death regulation Cindy Gro
W8 - 18 May System ID: Bioscrape inference tools Ayush Bioscrape Inference
W9 - 25 May Bioscrape Lineages as a well-mixed version of GRO William Bioscrape Lineages
W10 - 1 Jun Advanced: Automated Model Reduction Ayush Auto-Reduce


This class is graded pass/fail. To pass the class, you must participate in at least 80% of the lectures and recitations and submit a final project report consisting of a Jupyter notebook demonstrating the use of two or more of the tools in the class on a problem of interest to your research.

Collaboration Policy