The hands-on lab component of the course will consist of programming tasks centered on analysis of biological data, mainly DNA and protein sequences, consisting of tasks such as processing files with sequence data, manipulating and computing various properties of sequences (e.g. nucleotide composition), simulating population/sequence evolution, and simple motif searches. We will also play around with some next generation sequencing data.

We will use the free textbook How to Think Like a Computer Scientist: Learning with Python.

We will use the free textbook How to Think Like a Computer Scientist: Learning with Python.

Final Exam: May 15, 6:20-8:20p

• Introduction to programming and Linux

Midterm: TBD, in class.

http://registrar.colostate.edu/spring-final-exam-schedule?: May 15, 6:20-8:20p

Midterm: 3/12 9am-11am

Final Exam: 5/10 9:10am-11:10am

The course will provide the students with skills in programming and the ability to use and understand third-party programs and algorithms.

The hands-on lab component of the course will consist of programming tasks centered on analysis of biological data, mainly DNA and protein sequences, consisting of tasks such as processing files with sequence data, manipulating and computing various properties of sequences (e.g. nucleotide composition), simulating population/sequence evolution, and simple motif searches.

Midterm: TBD

Final Exam:

Office Hours: By appt. ||

Course Outline

• Introduction: steps in creating a computer program.
• Simple python programs: Variables, assignment statements, arithmetic expressions, input and output statements.
• Control flow statements: if statements, while statements, for statements.
• Functions: general concept, declaration and calls, parameters.
• Simple data structures: arrays (implemented as Python lists), strings
• Files: reading and writing text files.
• Using python objects.
• Writing python objects and object oriented programming.
• Using python packages: numpy, matplotlib and BioPython.
• Algorithms and problem solving techniques – the course presents at least one sorting algorithm in detail and introduces students to related topics such as run-time analysis.
• Program development – the process of writing longer programs by dividing tasks into methods and classes.

Bachelor's degree in the life sciences, or permission of instructor

Textbook:

Sun 3-5pm (Alex Norton)

Off hrs: Tue 3-5pm, Thu 3-5pm (in the Linux lab)

Thu 2-3pm (Alex Norton) 6:30-9:30pm (Ryan Moore)

Office: 235
Office hrs: Tue 2-3pm, Wed 1-2pm (in the Linux lab)

Office Hours: Mon 2:30-3:30pm, Tue 2-3pm, Wed 1:30-2:30pm ||

Fri 12:00-1:50pm
Fri 2:00-3:50pm ||

Course objectives

Data Abstraction and Problem Solving with Java: Walls & Mirrors, 2nd edition
Frank M. Carrano and Janet J. Prichard

Your cs160 Java book:

Course objective

A student completing this course should be able to:

• Implement object oriented programs and understand the underlying principles such as encapsulation, abstraction and reuse.
• Design and build more complex programs (multiple files and multiple objects) that solve non-trivial problems.

• Relate concepts from theory to programming and architecture, such as how recursion is implemented in the system, and when it is an appropriate programming technique.

• Arrays, lists (dynamic arrays), and binary search

• Parameter passing

• Binding and scope

• Graphical User Interfaces

CS160 or CS153 with a C or better; M124, M126 (both with a C or better).

Thu 2:00-3:40pm ||

• Objects: creating, instantiating, basic operations
• Inheritance, interfaces, exceptions, polymorphism
• Induction and recursion
• Mechanics of recursive programs; method invocation and activation records
• Assertions
• File IO
• Sorting
• Arrays, lists, and binary search
• Counting

Binding and scoping

• Parameter Passing

Graphical User Interfaces

• Linked lists

Data Abstraction and Problem Solving with Java, 2nd edition
Frank Carrano and Janet Prichard

Java: an introduction to problem wolving and programming, Fifth edition
Walter Savitch and Frank M. Carrano

There will be a programming exam as part of the final exam

Assignments will be done individually.

First Midterm: TBD

Second Midterm: TBD

Final Exam: Dec 16th 9:10am-11:10am

Course withdrawal date:

Office: 448
Office Hours: TBD ||

Office Hours: Tue 10-11, Wed 10-11:30 ||

First Midterm: 2/25/09

Second Midterm: 4/8/09

Final Exam: May 14th 7am-9am

All exams are in the same room as the lecture.

Course withdrawal date: 3/23/09

We will also use:

CS161 (Object Oriented Problem Solving) AND MATH160 or MATH141 or MATH155 (all with a C or better)

Note: in order to pass the class you need to have a passing grade for the average of the exams.

Prerequisites:

• Prerequisites:**
  

Textbooks:

Who, Where, When

Course Description

CS200 revisits and extends the principles of programming and discrete math that are introduced in CS161 and applies them to the development, analysis and implementation of data structures and efficient software. The course is taught using the Java language and emphasizes an object oriented approach to data structures. Specific topics in data structures/algorithms include advanced sorting, queues, stacks, hashing, trees, and graphs. Complementary topics from theory include recurrence relations, trees, and graphs. The course requires larger programs and team programming.

Topics

• Linear Data Structures: Stacks and Queues
• Advanced Sorting
• Trees
• Graphs
• Hash Tables
• Computational Complexity

Grading:

Assignments will be done individually, except selected programming assignments

Quizzes will typically be given during one lecture class each week, except those weeks in which a midterm exam is being given. No makeups will be given for quizzes, but two quiz grades will be dropped.

Class participation is strongly encouraged. Students who ask or answer a question during lecture will be given a chit (maximum of one per student per class session). Three chits earned translate into 10 additional points on the next quiz.

The assignment of letter grades will be made as follows:

NOTE: We will NOT cut higher than these points (but may cut lower).

Late and Makeup Policy

Midterm and Finals: Make-up exams are only given in extraordinary circumstances (e.g., illness, death of family member). Students must consult with the instructor as soon as possible, preferably before the start of the exam. Course examination dates are listed in the syllabus; be aware of them and plan accordingly.

No make-ups will be given for missed quizzes.

Programming assignments are to be submitted electronically using the checkin program. Always check the assignment page for due dates. Late assignments submitted within 48 hours of the time required (or otherwise specified) will receive a 20% late penalty. Electronic submission is closed 48 hours after assignments are due (or as otherwise specified); students not having submitted programs receive an automatic zero on the assignment.

Written assignments are to be submitted in class. These may be handwritten, but must be legible. The instructors and TAs reserve the right to decide whether or not a paper is legible. Late assignments are accepted in class on the first MWF after the original due date, and will receive a 20% late penalty.

Assignment will be returned within 5 working days of the end of the late period.

Important Dates

First Midterm: TBA

Second Midterm: TBA

Final Exam: TBA

All midterm exams are in the same room as the lecture.

Course withdrawal date:

Professional Conduct

All students are expected to conduct themselves professionally. We assume you are familiar with the policies in the student information sheet.

Additionally, you are (beginning) computing professionals, so you should be familiar with the code of conduct for the primary professional society, the Association for Computing Machinery (ACM).

We work to maintain an environment supportive of learning in the classroom and laboratory. Towards this end, we require that you be courteous to and respectful of your fellow participants (i.e., classmates, instructors, TAs and tutors). In particular:

• Please turn off the ring on your cell phone. If you are expecting an emergency call, sit near the door and slide out discretely to take it.
• If you plan to use a laptop during class, please sit at the back of the classroom and turn off any sound from the machine. The tap-tap of the keyboard and the images showing on a screen can be distracting to those sitting around you. Also, be aware if you IM during class, that giggles, snorts or other reactions to what you are reading can be heard by the class and instructors and may be completely inappropriate with what is going on in the classroom.
• Laptops and other personal computing devices must be shut during exams and quizzes.