Quantitative Biology of the Living Cell
Prof Jenna Rickus firstname.lastname@example.org
This course is an introduction to cellular engineering. We will explore frameworks, possibilities, ethics, and tools for engineering living cells.
Assignments and Class Schedule
In Class. Go over syllabus, course goals, openwetware, and software
Assignment. complete before next week.
- Create an account on Openwetware
- Read the wiki help on openwetware
- Create your own wiki page that links to this course page. Name your page "Biol295F_LASTNAME"
- Download and Install Systems Biology Workbench and Cell Designer
- Start reading NIH Stem Cell Basics
- Quest Speaker. 5 minutes. Jennifer Nordland. Soybean Competition
- Frit-O-Lay Visit. 10 minutes
- Big Picture: Cellular Engineering
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.
- Student reports from last week's assignment
- test of email list
- 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?"
- 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?"
- 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.
- 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.
- 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 click here to register
- in class lecture. primer in biochemical kinetics
- class lecture notes posted in Web CT
- 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
- Seminar. 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
- Finish Simulations of Goldbeter Period Model
"Nov 13" No class to make up for time at seminar
- SEMINAR. 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
Stem Cell Biology
Policy and Ethics
- U.S. Policy on Use of Stem Cells. NIH link
- Article arguing for a code of ethics for Biological Engineers. IBE code of ethics
- AAAS Report on Stem Cell Policy and Ethics 
Web of Science- for literature review
PubMed - for literature review
Entrez - quick keyword based search across literature, protein, gene, etc databases simultaneously
link to Genbank - "GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences"
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