BE 240, Spring 2020

Open Source Tools for Biological Circuit Design
Instructors Richard Murray (CDS/BE), murray@cds.caltech.edu Ayush Pandey (CDS), apandey@caltech.edu Cindy Ren (CDS), xrren@caltech.edu William Poole (CNS), wpoole@caltech.edu	Class meeting times Lectures (overview of the tool via Zoom): Thu, 3-4:30 pm PDT Recitations (group debugging of student examples via Zoom): Tue, 3-4:30 pm PDT Office hours (individual help via Slack): Fri, 1-5 pm PDT

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

Each week of the course will cover a different topic and/or tool. The first class meeting of the week (Thu session) will be a description of the use of that tool on a representative problem, carried out using a Jupyter notebook that students can download and follow along with the instructor. The second class meeting of the week (the following Tue) will consist of problems brought forth by students in the class as they have tried to implement the tools on their own problems. These problems will be discussed and solved in a group setting. Weekly office hours will be offered between the lectures to allow students to ask questions about individual tools and problem and receive help via Slack and/or Zoom.

Date	Topic	Lecturer	Tools	Notes
W1 - 31 Mar	Organizational week	Richard	Anaconda, Jupyter, GitHub	Computer setup instructions
W2 - 7 Apr	CRNs and simulating them with Bioscrape	William	Bioscrape	W2_bioscrape.ipynb (Jupyter notebook)
W3 - 16 Apr	Intro to SBML and non-mass-action propensities & rules in bioscrape	Ayush	Bioscrape	W3_sbml_p1.ipynb, W3_sbml_p2.ipynb (Jupyter notebook), repressilator_sbml.xml
W4 - 23 Apr	BioCRNpyler for generating large CRN models from parts	William	BioCRNpyler	W4_biocrnpyler.ipynb (Jupyter notebook), parameters.txt
W5 - 30 Apr	Compartments as orthogonal CRNs connected by diffusion reactions and SubSBML	Ayush	Sub-SBML	W5_subsbml.ipynb, subsbml_generate_models.ipynb (Jupyter notebooks),
W6 - 7 May	Spatial systems and signalling	Cindy	gro	W6_gro-07May2020.pdf
W7 - 14 May	Cells and Growth/death regulation	Cindy	gro	W7_gro-14May2020.pdf
W8 - 21 May	Bioscrape Lineages as a well-mixed version of gro	William	Bioscrape Lineages	W8_lineages-21May2020.ipynb, RepressillatorCRN.sbml, ToggleCRN.sbml
W9 - 28 May	System ID: Bioscrape inference tools	Ayush	Bioscrape Inference	W9_inference-28May2020.ipynb
W10 - 4 Jun	TBD	TBD	TBD

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.