2012F001
From CDS 130
1. Tuesday, Dec. 18th
 Final exam (10:30 am ~ 12.45 pm), IN 318
2. Tuesday, Dec. 11th
 Review Quiz #3 problems
 Discuss computational projects
 Final exam review
 Final exam sample
 Help sessions will be available on this Thursday.
3. Thursday, Dec. 6th
 Polulation growth (Additional learning materials have been uploaded to Blackboard).
 Population growth Exercises
 Review homework 9 problems
 Review Quiz #3
 Discuss computational projects.
 Help sessions will be held next week. Time and location will be announced by email.
4. Tuesday, Dec. 4th
 The final exam is scheduled on Dec. 18th.
 The final exam will be noncumulative. (Note: This is different from what's said in the syllabus).
 Computational projects have been posted on Blackboard (Due on Dec. 18th)
 matrix A for your project. To read A.dat to your matlab code try:
clear all; clc; urlwrite('http://cds130.org/wiki/images/A.dat', 'A.dat'); A=importdata('A.dat');
5. Thursday, November 29th
 if statements
 while loops
 integration
 Assign homework 9
 Computational projects will be posted on Blackboard.
6. Tuesday, November 20th
 Assign homework 8, due on Nov. 29th (next Thursday).
7. Thursday, November 15th
 Review homework and quiz problems.
 Examples of images and plots

Assign homework 8
8. Tuesday, November 13th
 Review Iterations, images, and plots
 inclass quiz (25 minutes)
9. Thursday, November 8th
 Continue to cover images and 2D plots
 homework7 is now due next Tuesday (Nov 13th)
 An inclass quize will be given next Tuesday to cover iterations, images and plots
10. Tuesday, November 6th
 Matrices as images
 Announcement: An inclass quiz (20 min) will be given next Tuesday to test iterations and images.
11. Thursday, November 1st
12. Tuesday, October 30th
 Class cancelled due to weather
 Homework 6 is now due on this Thursday
13. Thursday, October 25th
 Matrices as images
 The due date for Homework6 is postponed to Oct. 30.
14. Tuesday, October 23rd
 Continue to cover Iteration
 A makeup exam will be given after class (12:00 PM  1:15PM). The place will be announced in class.
15. Thursday, October 18th
 Matrices as images
 Load data to Matlab
 Assign Homework6 (due on Oct 25th)
16. Tuesday, October 16th

Matrices as images

Load data to Matlab
 Review midterm exam problems.
17. Tuesday, October 9th
A help session will be held today (13 PM). Location: IN 317 (Innovation hall)
A short notice I just received: IN 317 is actually booked for a class until 1:15pm on 10/9/12. Therefore, we cannot access IN 317 until 1;30pm tomorrow. In light of this, the help session will be postponed to 1:30 PM till 3:30 PM.
18. Thursday, October 4th
 Finish up Logic Gates
 Midterm exam review.
 A study guide and midterm exam sample will be distributed.
 A help session will be held next Tuesday afternoon. (Place: TBD; Time: 1~3PM)
 The midterm examination will be held on Oct. 9th (next Thursday).
19. Tuesday, October 2nd
20. Thursday, September 25th
 Logic Gates
 Matrices in Matlab
 Assign Homework5 (due on Oct 4th)
 Announcement: Midterm exam is arranged on Oct 11th. Help seesions will be available. More info will be announced in class.
21. Tuesday, September 25th
 Data Storage, Memory, and Digitization

Matrices in Matlab
22. Thursday, September 20th
 Arrays in Matlab
 Homework 3 due before class.
 Assign Homework 4 (due on next Thursday before class)
23. Tuesday, September 17th
 Review Quiz #1 (The scores have been uploaded to Blackboard)
 Encoding
 Arrays in Matlab
24. Thursday, September 13th
 Binary Arithmetic (Binary representation of negative numbers)
 Inclass quiz to test (1) binary data conversion, (2) binary arithmetic and (3) the signandmagnitude method to represent negative numbers.
 Homework 2 due before class.
 Assign Homework 3 (due on next Thursday before class)
 The tutorial on "Assignment and builtin functions in Matlab" has been uploaded to Blackboard .
25. Tuesday, September 11th
 Binary Arithmetic
 Matlab: Assignment and mathematical functions
26. Thursday, September 6th
 Binary Arithmetic
 Matlab: Variable and Assignment
 Assign Homework 2 (due on next Thursday before class)
 Announcement: A 15minute quiz will be given next Thursday to test binary arithmetic.
27. Tuesday, September 4th
 Binary representation of numbers
 Binary addition
 Access the virtual computing lab at mason
 Introduction to Matlab
 Distribute problem set 1 for exercises (available upon request)
28. Thursday, August 30th
 Overview of Computational Science (Introduction).
 Binary representation of numbers
 Binary number questions
 Introduce Matlab
29. Tuesday, August 28th
 I will go over the Syllabus.
 Introduce MediaWiki.
 Give a broad overview of Computational Science (Introduction).
 Assign Homework #1. Due on August 30th, This Thursday.
30. Syllabus
My syllabus is everything stated at Syllabus along with the following additions and notes.
30.1. Format
This is a threecredit course. Active learning techniques will be used during my lectures. After presenting a major concept I will pose a question which you will think about, discuss with your neighbor, and then possibly present your answers.
Be inquisitive and vocal during class.
30.2. Evaluation
Each student will be responsible to cover the material taught in class, do the assigned homework exercises. There will be midterm and final exams. Class attendance will also be counted into their final grades (see below).
30.2.1. Composition of Final Grades
35% problem sets
25% midterm exam
30% final exam
10% attendance and inclass quizzes
Two of the exams are 2 hour quizzes given during lecture sessions, the last exam will fall during finals' week. The final exam will be cumulative.
30.2.2. Final Letter Grades
Final letter grades will be determined by total weighted scores from the composition o the final grades. The approximate score breakdown will be:
90 and above  A 
8089.999  B 
7079.999  C 
5569.999  D 
Less than 55  Failing 
Note that these are the approximate score assignments: if your score falls at the border (e.g., between an A and B), your effort will decide the final grade: improvement over the course of the term; attitude in doing the problem sets; interactions with the lecturer during class etc.
30.3. Homeworks
 Are 35% of your grade!
 Weekly Homeworks. Assigned on Friday, due on next Friday before class
 Will partially work many difficult problems in class
 Most homeworks will be handwritten in the first half of the semester
 Most homeworks will be turned in electronically in the second half of the semester
 Late penalty = 20% if late by less than 7 days; 40% if more than 7 days late
31. FAQ
31.1. As a neuroscience major, what can I learn from this course?
First off, allow me to quote from Archimedes "Give me a lever long enough and a fulcrum on which to place it, and I shall move the world."
Through this course, we strive to provide a computational lever for you. With competencies in each major, I hope you eventually will be able to solve science problems such as:
 Neuronscience: Understanding the visual cortex of the brain [1].
 Biology: Solving problems of protein folding and structure [2]
 Chemistry: Designing molecules [3]
 Earth Science: Studying solid earth dynamics[4]
31.2. Exactly what kind of problems will I be able to solve?
To get a taste of it, here are two examples students worked on later in the last semester Tumor  Antialias.
31.3. Am I qualified for this course?
If you are concerned with math, most likely you are qualified for this course, provided that you understand
 Trigonometry and Transcendental Functions
 Some mathematical concepts to simplify science problems
31.4. How much programming is needed?
There is no requirement on programming languages.
In this course, a highlevel computing language Matlab will be taught. Matlab is a powerful mathematical tool that offers a computing environment for numerical computation, graphics and visualization.
Students may access and use MATLAB without charge either on campus or from any computer with an internet connection. There are three ways to use Matlab at Mason:
 Via access to the virtual computing lab at Mason
 Matlab is installed on all computers in various computer labs on campus. Simply log on, and there is Matlab.
 Install Matlab on your personal computer. A $109dollar student version of MATLAB may be purchased atPatriot Computers.
Tutorials on accessing and using Matlab will be given to students as class progresses.
31.5. What if I have a question about homeworks and am having difficulty understanding the course content?
 My office hours will be held following each class or by appointment (hsheng@gmu.edu). My office is located in Research I, Room 370. Usually I will be available after class and would like to interact with students using the whiteboard in Research I, Rm 302. Over the semester, several tutoring sections will be held to work on difficult problems.
 There are two CDS assistans available for this session. Natalia Lattanzio (nlattanz@gmu.edu) will grade your homeworks and exams, and Feredun Azari (fazari@gmu.edu) will provide inclass assistance. Both of them will be available to answer your questions either by email or by text message.
 Special announcements will be made through an email list, such as assignments, due dates, upcoming exams, tutorials, etc.
 A group page has been set up on Facebook. If you have a Facebook page, welcome to join the group.
31.6. Do we have a textbook for this course?
None. The course "Computing for Scientists" was newly approved as a general education course at GMU. It has been codeveloped by several faculty members at the CDS department. A wiki page ([5]) was created for this course in 2010 by Dr. Weigel. There are four sections in Fall 2012. All course materials covered in the current section can be obtained from http://cds130.org/2012F001.
The wiki page was designed to facilitate student interaction and to fulfill the IT requirements.
31.7. Draft Schedule
(Red links are for pages that are not complete)
 Week 1: Course Introduction, Syllabus and course logistics,Entry survey, Introduction to MediaWiki, Screenshots
 Week 2: Binary representation of numbers, Encoding and data storage, and Digitization.
 Week 3: Binary addition, Computing_Limits, Transistors, Logic_Gates,A basic computer.
 Week 4: Spreadsheets vs programming languages,Programming languages, Assignment, Matrices, Iteration
 Week 5: Matrices as images
 Week 6: If_Statement, Nested_For_Loops
 Week 7: Midterm review, midterm exam
 Week 8: Spring Break
 Week 9: Modeling introduction, Science models,Mathematical models, and Computational models
 Week 10: Difference equations and ODEs
 Week 11: Numerical_Integration
 Week 12: Science applications
 Week 13: Verification and Validation
 Week 14: Ethics and Digital notebooks
 Week 15: Security, Exit survey, Final exam review
 Week 16: Final Exam (date TBD).