Quantitative Biology of the Living Cell

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Contents

Instructor

Prof Jenna Rickus

BMED 2029 rickus@purdue.edu

Course Description

In this class you will conduct a cellular design project. You will create a design to engineer cells to accomplish a task or solve a problem. You will define the problem that you will work on. In class we will explore and apply the necessary topics and models applying your previous and current coursework in thermodynamics, kinetics, transport etc that will be necessary to achieve your goals. The particular topics will be driven by the project.

Syllabus

All grades are posted in WebCT

Usfeul References

Web of Science- for literature review

PubMed - for literature review

Entrez - quick keyword based search across literature, protein, gene, etc databases simultaneously

ExPASy Protein Database

link to Genbank - "GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences"

BioBricks

Primary Steps to the Design Process

  1. define the problem
  2. create specific and quantifiable design criteria
  3. quantify the potential impact/market
  4. summary of prior art
  5. generate a novel solution to meets some or all of the design criteria
    1. abstraction: generate a high level design
    2. create a detailed, quantitative design of your system by drilling down into more detailed sublayers of your high level design
  6. model the system to predict performace
  7. compare model predictions to design criteria and prior art
  8. build the system
  9. experimentally test the prototype system with comparison to predictions and design criteria
  10. if your design did not accomplish and perform up to the original criteria return to steps 5-10

in this class you will conduct steps 1-7

In Class Activities

Aug 23 Group Brainstorm: Define the problem(s) that cells face and must find solutions to in their native environments. What are the design criteria? What are the constraints? What are the size scales? What are the processes that occur and how do they relate to topics of thermodynamics, kinetics, and transport? We will have a group discussion following. You do not have to turn anything in for this, but the thought process will be useful for the writing assignment below.

Assignment 1 due Aug 30 in class

Aug 30 - Step 1 Defining the Problem The class brainstormed on large problems that they would like to be part of a solution for. some of these included: famine, malnutrition, athletic injury, cancer, environmental toxins from huricane Katrina, lack of organs for transplants, lack of sustainable processes for producing retail products, lack of heathy foods that taste good, antibiotic resistence

The class decided on 2 problems

Team 1 - Environmental Toxins Related to Katrina

Team 2 - Nutrition and Famine

Assignment 2 - due Sept 6 in class

- Each team turn in one assignment - Define the specific problem that you want to solve. This should be 1-2 paragraphs that includes preliminary information on the number of people, dollars impacted; what is the potential specific cause of the problem; what types of information are currently known about the problem; what type of design criteria will be needed?

Literature Review to Define the Problem and Prior Art link to Web of Science

Sept 6 - class cancelled.

Sept 13 - Step 2,3 - Setting Quantifiable Design Criteria, Quantifying the Potential Impact

Sept 27 - Step 4

Oct 4

Oct 11

Oct 18

Oct 25

Nov 1

Nov 8

Nov 15

Nov 22

Nov 29

Dec 6

Team Project Pages

Team 1 - Biological Engineering Solutions to Water Contamination

Team 2 - Nutrition and Famine

Class Discussion Board

post any comments, questions etc. here

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