Quantitative Biology of the Living Cell: Difference between revisions

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==Course Description==
==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==
==Assignments and Class Schedule==


'''August 28th'''
'''August 28th'''
In Class. Go over syllabus, course goals, openwetware, and software
In Class. Go over syllabus, course goals, openwetware, and software


Line 21: Line 24:


'''Sept 4th'''
'''Sept 4th'''
In Class.   
In Class.   
# Quest Speaker.  5 minutes.  Jennifer Nordland.  Soybean Competition
# 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?
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'''
#  Student reports from last week's assignment
#  test of email list
#  blackboard
#  continue cellular engineering slides
#  begin stem cells
#  stem cell policy
#  introduce bioethics essay assignment
#  Begin CellDesigner
Due next week:  a typed outline or listing of your thoughts regarding "do biological engineers need a code of ethics?"
'''Sept 18'''
# Dr. Rickus' rules of writing :)
# Create a CellDesigner model of glycolysis
# 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'''
# Peer Review of Bioethics essays
# Introduction to BioModels Database
# In class .... BioModels Assignment - finding glycolysis models
CHANGE!!!  Draft #2 of Bioethics Essay is now due Oct 9th.
'''Oct 2'''
#discussion / lecture of biological oscillations
# 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'''
#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]
'''Oct 16'''
# in class lecture.  primer in biochemical kinetics
# class lecture notes posted in Web CT
'''Oct 23'''
# 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
'''Oct29'''
#Seminar.  [http://thedoylegroup.org/ Dr. Frank Doyle].  BME 1001 9:30 - 10:30 am
#Write a 1 page summary of Dr. Doyle's talk
#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'''
#Finish Simulations of Goldbeter Period Model
"Nov 13"
No class to make up for time at seminar
'''Nov 19'''
# 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
'''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==
==References==


'''Stem Cell Biology'''
# [http://stemcells.nih.gov/info/basics/ NIH Stem Cell Basics]
# [http://stemcells.nih.gov/info/basics/ NIH Stem Cell Basics]
'''Policy and Ethics'''
# U.S. Policy on Use of Stem Cells.  [http://stemcells.nih.gov/ NIH link]
# 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]]
# AAAS Report on Stem Cell Policy and Ethics [http://www.aaas.org/spp/cstc/briefs/stemcells/index.shtml]


==Useful Links==
==Useful Links==
Line 46: Line 152:


[http://www.biobricks.org/ BioBricks]
[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==

Latest revision as of 10:26, 18 December 2008

Click here to return to main Rickus Lab page

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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