BME 303: Introduction to Computing for Biomedical Engineers

• Fall 2009
• Lectures at CPE 2.208, Tuesdays and Thursdays 5:00–6:30pm

• Staff meetings at BME 5.202H, Tuesdays 2:00–3:00pm

• Syllabus


• The textbook is available at the library.


• Drop-In Tutoring


• Important Dates


• Final Exam Date and Time: Thursday, December 10th, 7:00–10:00pm


• Safety


• Health

A Bit of Administration

Introduction: Computation and Biology

From "Mathematics and the Physical World," by M. Kline (Dover, 1981)
Arithmetics and the heart: Numbers were decisive in one of the great achievements of biology (p. 35).

CNN, July 24: Most Lucrative College Degrees

NYTimes, Aug 5: For Today's Graduate, Just One Word: Statistics

Homework 0: Read the syllabus and Chapter 1

Chapter 1: Welcome Aboard

ENIAC: Electronic Numerical Integrator And Computer

Sinclair ZX81: My Brother's First Computer

Homework 1: Computing Platforms

Extra Credit for Homework 1:

1. There is an x-ray machine at MBB. Who built it? What was it used for? (25%)
2. The first photograph is at the Ransom Center. Describe it: What? When? Where? How? (25%)

"Computing with DNA," by L. M. Adleman (Scientific American, 1998)

Chapter 1: Continued

Homework 1 is Due

Chapter 2: Bits, Data Types and Operations

Sexagesimal Numbering System

Homework 2: Bits, Data Types and Operations

Additional Extra Credit for Homework 2:

1. Can a "programmable" coffee maker be programmed to count?
   Add two numbers? Multiply two numbers? If yes, explain how (50%).
2. Thanks, Chris Boronow!: Can Adleman's DNA computer be programmed to count?
   Add two numbers? Multiply two numbers? If yes, explain how (50%).

Chapter 2: Binary Computations

Labs Begin Next Week

Complete the following steps for full functionality in the lab:
Navigate to https://www.engr.utexas.edu/computing/accounts
and click the link Enable your EID Account.

Lab 1: Computer Anatomy

Instructions and Questions

Homework 2 is Due

Chapter 2: Floating Point, ASCII

Homework 3: NAND Logic

Homework 1 Solutions:

1. Thanks, Deidra Garcia!
2. Thanks, Phillip Lin!
3. Thanks, Rebecca Lee!
4. Thanks, Roman Sahota!
5. Thanks, Glendon Plumton!

Chapter 2: Boolean Algebra

Lab 2: Binary Computations

Quiz 1

The computer used in the spacecraft that first carried humans to the moon, the Apollo Guidance Computer, was constructed entirely using NOR gates with three inputs.

Homework 2 Solutions:

1. Thanks, Lindsey Wohlfort!
2. Thanks, Nga Tang!
3. Thanks, Harry Israel!
4. Thanks, Leslie Chang!
5. Thanks, Elaine Ng!
6. Thanks, Glendon Plumton!

Quiz 1 is Due in Class

Chapter 3: Digital Logic Operation Structures

Lab 3: Boolean Algebra and Logical Operators

Lab 1 Solutions:

1. Thanks, Andrew Butler!
2. Thanks, Ytzel Rubalcava!
3. Thanks, Thanks, Jeremy McLain!

Practice Midterm 1

With Kam-Hon Hoi and Bruce (Zhen) Xia

Guest Speaker: Prof. Yale N. Patt

Host: Jordan Dwelle

Chapter 3: Digital Logic Memory Structures

Chapter 4: The von Neumann Computer Architecture

Lab 4: Introduction to Multimedia Logic

Multimedia Logic Freeware

Practice Midterm 1 is Due in Class

Homework 4: United States Patent 4,052,604

"Binary Adder," by D. S. Maitland and B. E. Thayer (United States Patent, 1977).

Extra Credit Due on Thursday, Oct 8:
Prepare a Question for Dr. Drake (40%).

Guest Speaker: Kenneth Drake, Ph.D.
Founder and CEO/CTO, Seralogix, and
Adjunct Associate Professor, Department of Biomedical Engineering

"Entrepreneurial Computational Engineering:
Turning Algorithmic Ideas Into Biomedical Reality"

Host: Jordan Dwelle

2009 Biomedical Engineering Society (BMES) Fall Meeting (Pittsburgh, PA, October 7–10, 2009)

L. Omberg, J. R. Meyerson, K. Kobayashi, L. S. Drury, J. F. X. Diffley and O. Alter, "Global Effects of DNA Replication and DNA Replication Origin Activity on Eukaryotic Gene Expression," Nature Molecular Systems Biology (October 2009)

Lab 5: Implementing Logic Structures in Multimedia Logic

Lab 2 Solutions:

1. Thanks, Taylor Birk!
2. Thanks, Austin Camp!
3. Thanks, Daniel Chou!
4. Thanks, Britton Marlatt!
5. Thanks, George Netscher!

Please bring a copy of Midterm 1 to class!

Homework 4 is Due

Homework 3 Solutions:

1. Thanks, Cristian Ramirez!
2. Thanks, Austin Camp!
3. Thanks, Seung Hoon Choe!
4. Thanks, Anna Lord!
5. Thanks, Aziz Hammoud!

Quiz 1 Solutions:

1. Thanks, Joseph Joo!
2. Thanks, Daniel Proske!
3. Thanks, Courtney Davis!
4. Thanks, Jennifer Nordhauser!
5. Thanks, Aziz Hammoud!

Chapter 5: The LC-3 Operation Commands

Lab 6: The LC-3 Machine Language

LC-3 Guide

Lab 3 Solutions:

1. Thanks, Blake Printy!
2. Thanks, Katherine Owen!
3. Thanks, Thanks, Harry Israel!
4. Thanks, Christine Laramy!
5. Thanks, Kristen Granados!

Midterm 1 is Due

Computation Space

Chapter 5: The LC-3 Data Movement

Data Movement Examples

Chapter 5: The LC-3 Control Commands

Conditional Operations

Practice Midterm 1 Solutions:

1. Thanks, Lindsey Wohlfort!!
2. Thanks, Scott Gorthey!
3. Thanks, Thanks, Rebecca Lee!
4. Thanks, Gary Liu!
5. Thanks, Matthew Bowman!

Chapter 6: Programming

Computation Time

Algorithm Design: How to teach a computer to play your game (tic-tac-toe)?

Homework 4 Solutions:

1. Thanks, Catherine Bacon!
2. Thanks, Gary Ge!
3. Thanks, Katie Cowan!
4. Thanks, Kristin Ward!
5. Thanks, Nicole Ong!

Lab 7: LC-3 Programming of Logic Circuits

Chapter 7: Assembly Language

OXO, a version of tic-tac-toe for the EDSAC from 1952, with a graphical output to a cathode ray tube may well have been the world's first video game.

Extra Credit Homework 5 Due on Tuesday, Nov 3: Design a flowchart for a computer game that performs the trick of predicting the outcome of a tic-tac-toe game, that is, it always forces a draw into the same pattern, up to symmetrical rotations (100%). Hint: the computer always starts, and always in the middle square.

Algorithm Design: How to teach a computer to do your homework?
Part I: How to teach a computer to convert a truth table into a Boolean algebra equation?
1. Vectors and Vector Dot Products
2. Double Loop and Subroutines

Guest Speaker: Prof. Pengyu Ren

Host: Jordan Dwelle

Chapter 8: Input/Output

Chapters 9 and 10: Go To/Subroutines

University of Pennsylvania Biomedical Engineering Seminar (Philadelphia, PA, October 29, 2009)

Lab 8: Assembly Language

Lab 4 Solutions:

1. Thanks, Brock Webberman!
2. Thanks, Alexandra Atalis!
3. Thanks, Justin Hsu!
4. Thanks, Conrad Chao!
5. Thanks, Matthew Mitchell!

Homework 5 is Due

In-Class Discussion of Midterm 2: Is the Four-Cell Game of Life logically complete?

The Game of Life from Wikipedia

Midterm 1 Solutions:

1. Thanks, Simone Siegel!
2. Thanks, Gaurav Chattree!
3. Thanks, Seung Hoon Choe!
4. Thanks, Elda Trevino!
5. Thanks, Nicole Ong!

Algorithm Design: How to teach a computer to do your homework?
Part II: How to teach a computer to identify logical completeness in truth tables?

Lab 9: Introduction to Mathematica

Download to your desktop the executable Mathematica code and change its suffix to .nb: Lab_9.txt

Lab 5 Solutions:

1. Thanks, Justin Long!
2. Thanks, Brock Webberman!
3. Thanks, Katherine Olin!
4. Thanks, Adriel Laya!
5. Thanks, Harry Israel!
6. Thanks, Alexander Lee!
7. Thanks, Sunayna Rajput!
8. Thanks, Glendon Plumton!

Lab 6 Solutions:

1. Thanks, Ansel George!
2. Thanks, Renee Mocha!
3. Thanks, Andres Felipe Perez!
4. Thanks, Renee Keller!
5. Thanks, Jonathan Anthony!
6. Thanks, Glendon Plumton!

Lab 7 Solutions:

1. Thanks, Denny Nguyen!
2. Thanks, Mathew Sides! (Nice Drawings... )
3. Thanks, Sarah Propst!
4. Thanks, Helen Atkins!
5. Thanks, Christopher Miller!

Please bring a copy of Midterm 2 to class!

Practice Quiz 2: Logical Completeness of the Game of Life

Artificial Life I: Cellular Automata and The Game of Life from Mathworld

Artificial Life II: Self-Replicating Computer Programs (see also Lab 9)

Artificial Life III: Self-Portrait of Yariv Alterfin

Lab 10: The Game of Life in Mathematica

Download to your desktop the executable Mathematica code and change its suffix to .nb: Lab_10.txt

Midterm 2 Due-Date Extended to Tuesday, Nov 24

From "The Colossal Book of Mathematics: Classic Puzzles, Paradoxes, and Problems," by M. Gardner (W. W. Norton & Company, 2001)

Extra Credit Homework 6 Due on Tuesday, Nov 24:

1. Is logical completeness important for the design of computer hardware? If yes, explain why (50%).
2. Is logical completeness important for the design of computer software? If yes, explain why (50%).

Practice Quiz 3: The Game of Life in Logic Circuits

Homework 5 Solutions:

1. Thanks, Deidra Garcia!
2. Thanks, Nga Tang!
3. Thanks, Jesus Contreras!
4. Thanks, Sonny Tran!
5. Thanks, Lyndon Lee!

Happy Thanksgiving!

Lab 8 Solutions:

1. Thanks, Whitney Wong!
2. Thanks, Kaili Fan!
3. Thanks, Elizabeth Fischer!
4. Thanks, Elaine Ng!

Lab 9 Solutions

1. Thanks, Hyemin Kim!
2. Thanks, Ashwini Kishore!
3. Thanks, Satyajit Balial!
4. Thanks, Christopher Miller!
5. Thanks, Aziz Hammoud!

Extra Credit Lab 9 Solutions: Self-Replicating Computer Programs

1. Thanks, Satyajit Balial!
2. Thanks, Christopher Miller!
3. Thanks, Aziz Hammoud!

Midterm 2 is Due

Homework 6 is Due

Artificial Life IV: "Origin of Life on Earth," by A. Ricardo and J. W. Szostak (Scientific American, 2009)

Practive Quiz 4: From Flowcharts to LC-3 to Mathematica

Happy Thanksgiving!!!

Lab Review for Final

Lab 10 is Due

Class Review for Final

Practive Quiz 5: Is the 1-Bit Half-Adder Logically Complete?

Mandatory Attendance: End-of-Class Party

What Did We Learn?

Thanks to Our TAs

Private Visit to the Harry Ransom Center

1. The First Photograph and the Dawn of Imaging
2. The Gutenberg Bible and the Invention of Print
3. Other Worlds: Rare Astronomical Works Exhibit Combining Technology with Science