Quantitative Biology of the Living Cell

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(Course Description)
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==Course Description==
==Course Description==
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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 goalsThe particular topics will be driven by the project.
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==Assignments==
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'''August 28th'''
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# Create an account on Openwetware
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# Create your own wiki page that links to this course pageName your page "Biol295F_LASTNAME"
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# Download and Install Systems Biology Workbench and Cell Designer
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==Software==
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[http://www.systems-biology.org/cd/ read about cell designer here]
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[http://www.systems-biology.org/cd/download.html Instructions to Download Cell Designer]
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All grades are posted in [http://www.itap.purdue.edu/tlt/blackboard/ Blackboard]
 
==Usfeul References==
==Usfeul References==
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[http://www.biobricks.org/ BioBricks]
[http://www.biobricks.org/ BioBricks]
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==Primary Steps to the Design Process==
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==Class Schedule==
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#define the problem
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#create specific and quantifiable design criteria
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#quantify the potential impact/market
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#summary of prior art
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#generate a novel solution to meets some or all of the design criteria
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##[http://openwetware.org/wiki/Synthetic_Biology:Abstraction_hierarchy abstraction]: generate a high level design
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##create a detailed, quantitative design of your system by drilling down into more detailed sublayers of your high level design
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#model the system to predict performace
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#compare model predictions to design criteria and prior art
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#build the system
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#experimentally test the prototype system with comparison to predictions and design criteria
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#if your design did not accomplish and perform up to the original criteria return to steps 5-10
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in this class you will conduct steps 1-7
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==In Class Activities==
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'''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.
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[[Media:2007_writing_assgn_1.doc | '''Assignment 1''']] due Aug 30 in class
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'''Aug 30  - Step 1 Defining the Problem'''
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The class brainstormed on large problems that they would like to be part of a solution for.
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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
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The class decided on 2 problems
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'''Team 1 - Environmental Toxins Related to Katrina'''
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'''Team 2 - Nutrition and Famine'''
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'''Assignment 2''' - due Sept 6 in class
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- Each team turn in one assignment
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- 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?
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'''Literature Review to Define the Problem and Prior Art'''
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link to [http://portal.isiknowledge.com/ Web of Science]
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'''Sept 6''' - class cancelled.
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'''Sept 13 - Step 2,3''' - Setting Quantifiable Design Criteria, Quantifying the Potential Impact
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'''Sept 27 - Step 4'''
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'''Oct 4'''
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'''Oct 11'''
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'''Oct 18'''
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'''Oct 25'''
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'''Nov 1'''
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'''Nov 8'''
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'''Nov 15'''
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'''Nov 22'''
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'''Nov 29'''
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'''Dec 6'''
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==Team Project Pages==
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'''[[Rickus Biol295F Team 1 | Team 1 - Biological Engineering Solutions to Water Contamination]]'''
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'''[[Rickus Biol295F Team 2 | Team 2 - Nutrition and Famine]]'''
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==Class Discussion Board==
==Class Discussion Board==
post any comments, questions etc. here
post any comments, questions etc. here

Revision as of 10:37, 28 August 2008

Click here to return to main Rickus Lab page

Contents

Instructor

Prof Jenna Rickus

BMED 2029 rickus@purdue.edu

Course Description

Assignments

August 28th

  1. Create an account on Openwetware
  2. Create your own wiki page that links to this course page. Name your page "Biol295F_LASTNAME"
  3. Download and Install Systems Biology Workbench and Cell Designer

Software

read about cell designer here

Instructions to Download Cell Designer


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

Class Schedule

Class Discussion Board

post any comments, questions etc. here

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