BE 240, Spring 2020

Open Source Tools for Biological Circuit Design
Instructors Richard Murray (CDS/BE), murray@cds.caltech.edu 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

Grading

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

Collaboration is encouraged in figuring out how to use all of the tools of this course. The final project report should represent your individual understanding of how to apply the tools demonstrated in this course to a problem of interest to your research. Obtaining feedback and advice from the instructors, course participants, or others on the final project is allowed, but the final code included in the project should be written up individually, citing any sources of code snippets that are included in the notebook.