Difference between revisions of "Assignment 9 Overview: Analyzing yeast images"
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# What mathematical model did Mettetal, ''et. al.'' use for the yeast response network? Express the model in the following forms: transfer function (TF), poles and zeros (ZPK), single differential equation (SDE), and coupled differential equations (CDE). Express the TF, SDE, and ZPK models in terms of the undamped natural frequency, <math>\omega_0</math>, damping ratio <math>\zeta</math>, and/or damped natural frequency <math>\omega_D</math>. | # What mathematical model did Mettetal, ''et. al.'' use for the yeast response network? Express the model in the following forms: transfer function (TF), poles and zeros (ZPK), single differential equation (SDE), and coupled differential equations (CDE). Express the TF, SDE, and ZPK models in terms of the undamped natural frequency, <math>\omega_0</math>, damping ratio <math>\zeta</math>, and/or damped natural frequency <math>\omega_D</math>. | ||
# Find an expression for the step response and plot it over a range of values of <math>\omega_0</math> and <math>\zeta</math>. A hand-drawn plot is fine, but you should probably look into MATLAB's <tt>step</tt> function. | # Find an expression for the step response and plot it over a range of values of <math>\omega_0</math> and <math>\zeta</math>. A hand-drawn plot is fine, but you should probably look into MATLAB's <tt>step</tt> function. | ||
− | # Plot the frequency response (i.e. make a Bode) of the system over a range of <math>\omega_0</math> and <math>\zeta</math> values that includes over damped, critically damped, and under damped. | + | # Plot the frequency response (i.e. make a Bode plot) of the system over a range of <math>\omega_0</math> and <math>\zeta</math> values that includes over damped, critically damped, and under damped. |
# What are two questions that you have about the paper's methodology or how we're going to implement the experiment in 20.309? | # What are two questions that you have about the paper's methodology or how we're going to implement the experiment in 20.309? | ||
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Latest revision as of 21:03, 14 November 2019
Overview
In Assignment 8 you upgraded your microscope to make two-color images, and fabricated a microfluidic device that we used to switch the flow through the device from two fluid reservoirs. In Assignment 10, we'll use this new setup to replicate part of the experiment described in the following paper:
- J. T. Mettetal, D. Muzzey, C. Gomez-Uribe, and A. van Oudenaarden, "The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae," Science, vol. 319, no. 5862, pp. 482–484, 2008
- with its (useful!) supplementary information
In preparation for this experiment, we're going to write the analysis code needed to extract the Hog1 protein's response from images of yeast cells.
To get started, read Mettetal's paper.
Next, head over to Part 1 of this assignment, where you'll answer some questions about the paper and write your analysis code:
Submit your work on Stellar in a single PDF file with the naming convention <Lastname><Firstname>Assignment9.pdf.