Quantitative Biology of the Living Cell

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'''Prof Jenna Rickus'''
'''Prof Jenna Rickus'''
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BMED 2029
 
rickus@purdue.edu
rickus@purdue.edu
==Course Description==
==Course Description==
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In this class you will conduct a cellular design projectYou 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.
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This course is an introduction to cellular engineeringWe will explore frameworks, possibilities, ethics, and tools for engineering living cells.
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[[Media:Biol295F_Fall_2007_Syllabus.doc | Syllabus]]
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==Assignments and Class Schedule==
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All grades are posted in [http://www.itap.purdue.edu/tlt/ecourses/ WebCT]
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'''August 28th'''
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==Usfeul References==
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In Class. Go over syllabus, course goals, openwetware, and software
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[http://portal.isiknowledge.com/ Web of Science]- for literature review
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Assignment.  complete before next week.
 +
# Create an account on Openwetware
 +
# Read the [http://www.openwetware.org/wiki/Help wiki help] on openwetware
 +
# Create your own wiki page that links to this course page.  Name your page "Biol295F_LASTNAME"
 +
# Download and Install [http://sys-bio.org/ Systems Biology Workbench] and [http://www.systems-biology.org/cd/  Cell Designer]
 +
# Start reading [http://stemcells.nih.gov/info/basics/ NIH Stem Cell Basics]
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[http://www.ncbi.nlm.nih.gov/sites/entrez PubMed] - for literature review
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'''Sept 4th'''
-
[http://www.ncbi.nlm.nih.gov/sites/gquery Entrez] - quick keyword based search across literature, protein, gene, etc databases simultaneously
+
In Class.
 +
# Quest Speaker. 5 minutes. Jennifer Nordland. Soybean Competition
 +
# Frit-O-Lay Visit.  10 minutes
 +
# Big Picture:  Cellular Engineering
 +
# '''Assignment''': 
 +
Look up one of these 6 entities. Report on the who, what, where, when, and how of what these companies do. What is their status today?
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[http://ca.expasy.org/ ExPASy Protein Database]
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Biobricks Foundation (Cambridge Mass), Blue Heron Biotechnology (Bothel Washington), Amyris Biotechnologies (Emeryville, CA), Codon Devices (Cambridge, Mass), Foundation for Applied Molecular Evolution (Gainesville, FL), Synthetic Genomics (Rockville, Md)
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link to [http://www.ncbi.nlm.nih.gov/Genbank/  Genbank] - "GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences"
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1 page written.
 +
5 minutes oral to the class.
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[http://www.biobricks.org/ BioBricks]
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Due next week.
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==Primary Steps to the Design Process==
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'''Sept 11'''
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#define the problem
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# Student reports from last week's assignment
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#create specific and quantifiable design criteria
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# test of email list
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#quantify the potential impact/market
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# blackboard
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#summary of prior art
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# continue cellular engineering slides
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#generate a novel solution to meets some or all of the design criteria
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# begin stem cells
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##[http://openwetware.org/wiki/Synthetic_Biology:Abstraction_hierarchy abstraction]: generate a high level design
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# stem cell policy
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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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# introduce bioethics essay assignment
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#model the system to predict performace
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# Begin CellDesigner
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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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Due next week:  a typed outline or listing of your thoughts regarding "do biological engineers need a code of ethics?"
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==In Class Activities==
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'''Sept 18'''
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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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# Dr. Rickus' rules of writing :)
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# Create a CellDesigner model of glycolysis
 +
# One on one - go over last weeks graded writing assignments
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[[Media:2007_writing_assgn_1.doc | '''Assignment 1''']] due Aug 30 in class
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Due next week: a first draft of your essay regarding "do biological engineers need a code of ethics?"
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'''Aug 30  - Step 1 Defining the Problem'''
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'''Sept 25'''
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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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# Peer Review of Bioethics essays
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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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# Introduction to BioModels Database
 +
# In class .... BioModels Assignment - finding glycolysis models
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The class decided on 2 problems
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CHANGE!!!  Draft #2 of Bioethics Essay is now due Oct 9th.
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'''Team 1 - Environmental Toxins Related to Katrina'''
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'''Oct 2'''
 +
#discussion / lecture of biological oscillations
 +
# In class .... Cell Designer Assignment - Create Structure of Goldbeter PER TIM model
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'''Team 2 - Nutrition and Famine'''
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Remember ... Final Draft of Bioethics Essay due Oct 9th in class.
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'''Assignment 2''' - due Sept 6 in class
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'''Oct 9'''
 +
#Class canceled
 +
#email final bioethics essays to Dr. Rickus
 +
#finish your Goldbeter Period Timeless Model structure and email it to Dr. Rickus
 +
#Register for IBE student conference for BONUS Points  [http://www.engineering.purdue.edu/~ibe click here to register]
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- Each team turn in one assignment
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'''Oct 16'''
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- Define the specific problem that you want to solveThis 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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# in class lectureprimer in biochemical kinetics
 +
# class lecture notes posted in Web CT
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'''Literature Review to Define the Problem and Prior Art'''
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'''Oct 23'''
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link to [http://portal.isiknowledge.com/ Web of Science]
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# kinetic rate equations in the Goldbeter Period Model
 +
# class lecture notes posted in Web CT
 +
# Reference. "A model for circadian oscillations in the Drosophila period protein (PER)."  Albert Goldbeter 1995.  Proc. R. Soc. Lond. vol 261. pages 319-324
 +
# create and simulate PER model in Cell Designer
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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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'''Oct29'''
 +
#Seminar.  [http://thedoylegroup.org/ Dr. Frank Doyle].  BME 1001 9:30 - 10:30 am
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#Write a 1 page summary of Dr. Doyle's talk
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#If you could not attend seminar.  1 page summary on Science paper.  See Dr. Rickus
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'''Sept 27 - Step 4'''
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'''Oct 30'''
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No class to make up for time at seminar
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'''Oct 4'''
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'''Nov 6'''
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#Finish Simulations of Goldbeter Period Model
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'''Oct 11'''
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"Nov 13"
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No class to make up for time at seminar
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'''Oct 18'''
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'''Nov 19'''
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# SEMINAR.  [http://mpf.biol.vt.edu/Tyson%20Lab.html Dr. John Tyson]  BME 1001 9:30 - 10:30 am
 +
#Write a 1 page summary of Dr. Tyson's talk
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'''Oct 25'''
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'''Nov 20'''
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cell cycle quiz on reading from book
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'''Nov 1'''
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'''Nov 27'''
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thanksgiving
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'''Nov 8'''
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'''Dec 4'''
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Cell Cycle lecture
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introduction
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begin Tyson Cell Cycle model lab
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'''Nov 15'''
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'''Dec 11'''
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finish Tyson Cell Cycle model lab
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'''Nov 22'''
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'''Dec 18'''
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finals week
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no final exam.
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finish
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'''Nov 29'''
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==References==
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'''Dec 6'''
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'''Stem Cell Biology'''
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# [http://stemcells.nih.gov/info/basics/ NIH Stem Cell Basics]
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==Team Project Pages==
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'''Policy and Ethics'''
 +
# U.S. Policy on Use of Stem Cells.  [http://stemcells.nih.gov/ NIH link]
 +
# Article arguing for a code of ethics for Biological Engineers.  [[IBE:Code of Ethics | IBE code of ethics]]
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# AAAS Report on Stem Cell Policy and Ethics [http://www.aaas.org/spp/cstc/briefs/stemcells/index.shtml]
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'''[[Rickus Biol295F Team 1 | Team 1 - Biological Engineering Solutions to Water Contamination]]'''
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==Useful Links==
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'''[[Rickus Biol295F Team 2 | Team 2 - Nutrition and Famine]]'''
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[http://www.openwetware.org/wiki/Help  Help Editing Wiki's]
 +
 
 +
[http://en.wikipedia.org/wiki/Wikipedia:Tutorial  Wikipedia's Tutorial on Editing Wiki's]
 +
 
 +
[http://portal.isiknowledge.com/ Web of Science]- for literature review
 +
 
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez PubMed] - for literature review
 +
 
 +
[http://www.ncbi.nlm.nih.gov/sites/gquery Entrez] - quick keyword based search across literature, protein, gene, etc databases simultaneously
 +
 
 +
[http://ca.expasy.org/ ExPASy Protein Database]
 +
 
 +
link to [http://www.ncbi.nlm.nih.gov/Genbank/  Genbank] - "GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences"
 +
 
 +
[http://www.biobricks.org/ BioBricks]
 +
 
 +
[http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=home BioModels Database]  this site is a searchable database of published annotated models.  These models can be accessed and used within CellDesigner
==Class Discussion Board==
==Class Discussion Board==
post any comments, questions etc. here
post any comments, questions etc. here
 +
 +
==Links to Student Pages==
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*[[Biol295F_STINE|Janie's Page]]
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*[[Biol295F_FORTENER|Emily's Page]]
 +
*[[Biol295F_MEIER|Tim's Page]]
 +
*[[Biol295F_HOUCK|Dylan's Page]]
 +
*[[Bio1295F_Woojun Kim|Kim's Page]]
 +
*[[Bio1295F_Piper|Corey's Page]]
 +
*[[Bio1295F_Gudeman|Josh's Page]]
 +
*[[Biol295F_Wooddell|Jacob's Page]]

Current revision

Click here to return to main Rickus Lab page

Contents

Instructor

Prof Jenna Rickus rickus@purdue.edu

Course Description

This course is an introduction to cellular engineering. We will explore frameworks, possibilities, ethics, and tools for engineering living cells.

Assignments and Class Schedule

August 28th

In Class. Go over syllabus, course goals, openwetware, and software

Assignment. complete before next week.

  1. Create an account on Openwetware
  2. Read the wiki help on openwetware
  3. Create your own wiki page that links to this course page. Name your page "Biol295F_LASTNAME"
  4. Download and Install Systems Biology Workbench and Cell Designer
  5. Start reading NIH Stem Cell Basics

Sept 4th

In Class.

  1. Quest Speaker. 5 minutes. Jennifer Nordland. Soybean Competition
  2. Frit-O-Lay Visit. 10 minutes
  3. Big Picture: Cellular Engineering
  4. Assignment:

Look up one of these 6 entities. Report on the who, what, where, when, and how of what these companies do. What is their status today?

Biobricks Foundation (Cambridge Mass), Blue Heron Biotechnology (Bothel Washington), Amyris Biotechnologies (Emeryville, CA), Codon Devices (Cambridge, Mass), Foundation for Applied Molecular Evolution (Gainesville, FL), Synthetic Genomics (Rockville, Md)

1 page written. 5 minutes oral to the class.

Due next week.

Sept 11

  1. Student reports from last week's assignment
  2. test of email list
  3. blackboard
  4. continue cellular engineering slides
  5. begin stem cells
  6. stem cell policy
  7. introduce bioethics essay assignment
  8. Begin CellDesigner

Due next week: a typed outline or listing of your thoughts regarding "do biological engineers need a code of ethics?"

Sept 18

  1. Dr. Rickus' rules of writing :)
  2. Create a CellDesigner model of glycolysis
  3. One on one - go over last weeks graded writing assignments

Due next week: a first draft of your essay regarding "do biological engineers need a code of ethics?"

Sept 25

  1. Peer Review of Bioethics essays
  2. Introduction to BioModels Database
  3. In class .... BioModels Assignment - finding glycolysis models

CHANGE!!! Draft #2 of Bioethics Essay is now due Oct 9th.

Oct 2

  1. discussion / lecture of biological oscillations
  2. In class .... Cell Designer Assignment - Create Structure of Goldbeter PER TIM model

Remember ... Final Draft of Bioethics Essay due Oct 9th in class.

Oct 9

  1. Class canceled
  2. email final bioethics essays to Dr. Rickus
  3. finish your Goldbeter Period Timeless Model structure and email it to Dr. Rickus
  4. Register for IBE student conference for BONUS Points click here to register

Oct 16

  1. in class lecture. primer in biochemical kinetics
  2. class lecture notes posted in Web CT

Oct 23

  1. kinetic rate equations in the Goldbeter Period Model
  2. class lecture notes posted in Web CT
  3. Reference. "A model for circadian oscillations in the Drosophila period protein (PER)." Albert Goldbeter 1995. Proc. R. Soc. Lond. vol 261. pages 319-324
  4. create and simulate PER model in Cell Designer


Oct29

  1. Seminar. Dr. Frank Doyle. BME 1001 9:30 - 10:30 am
  2. Write a 1 page summary of Dr. Doyle's talk
  3. If you could not attend seminar. 1 page summary on Science paper. See Dr. Rickus

Oct 30 No class to make up for time at seminar

Nov 6

  1. Finish Simulations of Goldbeter Period Model

"Nov 13" No class to make up for time at seminar

Nov 19

  1. SEMINAR. Dr. John Tyson BME 1001 9:30 - 10:30 am
  2. Write a 1 page summary of Dr. Tyson's talk

Nov 20 cell cycle quiz on reading from book

Nov 27 thanksgiving

Dec 4 Cell Cycle lecture introduction begin Tyson Cell Cycle model lab

Dec 11 finish Tyson Cell Cycle model lab

Dec 18 finals week no final exam. finish

References

Stem Cell Biology

  1. NIH Stem Cell Basics

Policy and Ethics

  1. U.S. Policy on Use of Stem Cells. NIH link
  2. Article arguing for a code of ethics for Biological Engineers. IBE code of ethics
  3. AAAS Report on Stem Cell Policy and Ethics [1]

Useful Links

Help Editing Wiki's

Wikipedia's Tutorial on Editing Wiki's

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

BioModels Database this site is a searchable database of published annotated models. These models can be accessed and used within CellDesigner

Class Discussion Board

post any comments, questions etc. here

Links to Student Pages

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