CSC 209 / BIO 209 Introduction to Bioinformatics Programming Fall 2016

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1 CSC 209 / BIO 209 Introduction to Bioinformatics Programming Fall 2016 Instructor: Dr. Laurie Heyer Chambers 3027 Phone: (office) Course home page: We will use the Moodle course management system for announcements, links, and posting assignments and examples. Course description: Bioinformatics is an interdisciplinary course that explores computational techniques useful in the study of genomes, proteomes, and other biological data. It is also a first course in computer programming that will prepare you for further study in computer science. No previous experience in programming is required, assumed, or even desired. This course counts toward the genomics and computer science concentrations, the biology major and the mathematics major. Prerequisites: There are no prerequisites for this course. In particular, I will assume no previous experience with computer programming. Please note that you may not receive credit for both BIO/CSC 209 and CSC 121. Both of these courses are introductions to computer science and include programming in Python, and both will prepare you adequately for CSC 221. Textbook: Programming in Python 2.7 at zybooks.com. Instructions for subscribing to the textbook: 1. Sign up at zybooks.com 2. Enter zybook code DAVIDSONCSC209HeyerFall Click Subscribe Subscription expires after the semester ends. You may choose to print any part of the text to PDF if you wish to save it for future use. You can print an entire chapter at a time. Learning outcomes: (adapted from the ACM 2013 Curricular Guidelines) Create algorithms for solving simple problems and express them in English or pseudocode Implement, test and debug algorithms for solving bioinformatics problems in the Python language Analyze and explain the behavior of simple programs involving the fundamental programming constructs: variables, expressions, assignments, I/O, control constructs, functions, parameter passing and recursion Design, implement, test and debug a program that uses each of the following fundamental programming constructs: basic computation, simple I/O, standard conditional and iterative structures, the definition of functions, and parameter passing Choose appropriate conditional and iteration constructs for a given programming task Apply the techniques of decomposition to break a problem into smaller pieces Identify the base case and the general case of a recursively-defined problem, and

2 implement a solution in Python Implement a class in Python Apply consistent documentation and program style standards that contribute to the readability and maintainability of software Access and accommodation: Together, we will strive for your success in meeting the above learning goals. The components of the course, including the modes of assessing your progress toward these goals, require a range of skills and abilities. Every student s success is important to me. If there are any circumstances that may affect your performance in the class, please let me know as soon as possible so that we can work together to develop strategies that will meet your needs while fulfilling the requirements of the course. In particular, if you have a documented disability (or believe you may have a disability) and need a reasonable accommodation to participate fully in this class, complete course requirements, or benefit from the Colleges programs and services, please contact the Academic Access and Disability Resources Office (Nance Longworth, as soon as possible. You are welcome to speak with me as well so that we can devise a plan that maximizes your chances of success in the course. All such discussions will be fully confidential. Please look carefully at the course schedule during the first week of class. If any of the assignments conflict with a major religious holiday for your faith, please let me know. I will make every effort to make the necessary accommodations. If you must miss class for any reason, excused or otherwise, you are responsible for getting notes from a classmate and making up the work you miss. Anticipated absences, e.g., for athletic or family events, should be communicated to me in advance, and any work due those days should be turned in before you leave. Attendance: Missing class will adversely affect your grade in many ways. In addition, the college attendance policy will be enforced: missing more than 25% of class meetings makes you eligible for a failing grade. Course components: The following will help you achieve and measure your progress toward these outcomes: Reading. The textbook is an interactive workbook, and you should do (most of) the exercises as you read. I will monitor your reading activity regularly, and consider your engagement in the reading when assigning your participation grade. It is crucial to your success that you take the reading assignments seriously. Otherwise, you will find yourself lost in class, unable to do the in-class activities or homework, and poorly prepared for quizzes. In-class activities. Each class day will involve a significant amount of hands-on work with Python and biological data. I will expect you to have completed the assigned reading before you come to class, and be prepared to ask (and answer) questions about the reading. Attendance and engagement in in-class activities is an important part of your reading and participation grade. This is not a lecture class; it is more like a lab.

3 Homework. Weekly assignments (due most Thursdays) will provide you with regular practice with Python programming and bioinformatics procedures and algorithms. You will be assigned a partner, and you must adhere to the following guidelines for completing homework assignments: One partner is the "driver," and the other is the "navigator." Much like on a road trip, both roles are essential to the success of the team, and the navigator is also a "back seat driver." The driver is the one typing, but the navigator is watching every word and making suggestions about the next thing to type. Switch roles approximately every 20 minutes. Strive to do ALL work on the assignment in this paired configuration. Never spend more than 20 minutes working on an assignment by yourself. All code must be the work of the team. The only authorized help on homework is from Math and Science Center tutors or me, and all requests for help must come from you and your partner jointly. Other than reading help on particular commands that you have already learned in class, you may not seek help from the Internet. You may not get help from friends, family, etc. Each assignment will include detailed instructions for formatting and turning in your program(s). Your code will be tested by an automated script, and scored for correctness and appropriate coding style by a grading assistant. Significant penalties will be assessed if your code does not run as specified by the assignment. Sometimes programming assignments take longer than expected for a variety of reasons. Therefore, you can be up to 24 hours late on an assignment with no penalty, but no more than four times during the semester. Because of the system required to grade assignments, work will not be accepted more than 24 hours late. Project. You will work with a partner to implement a program of your own choosing, approved by me. Options include interactive games, teaching demonstrations, and online tools (bioinformatics or otherwise). You will have at least three weeks to complete your work. In addition to giving a brief demo of your project on the last day of class, you will be asked to present your project at the Digital Project Showcase on December 7, the last day of optional classes, 3:30-5:30 pm. You must inform me of any conflicts with this presentation at least two weeks in advance, so we can make other arrangements for you to present your work. Quizzes. The Python programming language is like any other language in the sense that you must master the vocabulary to be an effective "speaker." Quizzes will be given on most Tuesdays. In-class portions of quizzes are closed-book, handwritten, and timed exercises in which you will be asked to explain or specify the output of code that I provide and/or write very short code segments. Some quizzes will have a take-home programming portion that is closed book, but allows you to check your code as you write it. The material you are expected to know for each quiz is all material covered in the reading and in class up to that point, but with a focus on the previous week's material. Final Exam. The final is a comprehensive take home exam. You will have a limited number of hours of active work time on these programming exercises. The exam will be released on the first day of final exams, and will be due at the end of final exams.

4 Software and computing resources: Python is built into Mac OS X and is freely available on Windows computers (but I m sorry, I cannot help you set it up on a Windows machine). WingIDE is also available on all lab Macs on campus, and may be installed on your own computer. You will all have access to the GAMCo (Genomics, Applied Mathematics and Computer Science) computer lab (Chambers 3146) during building hours, whenever class is not in session. The class schedule for GAMCo will be posted on the door and on the course home page. Getting help: It is normal and expected that all students will need help outside of class with the material in this course. Because programming is only learned with practice, an important source of help is additional exercises, in the required textbook or online resources that I will provide. The following additional resources are also available. Math and Science Center: The Math & Science Center (MSC) offers free assistance to students in all areas of math and science, with a focus on the introductory courses. Trained and highly qualified peers hold one-on-one and small-group tutoring sessions on a drop-in basis or by appointment, as well as timely recap sessions ahead of scheduled reviews. Emphasis is placed on thinking critically, understanding concepts, making connections, and communicating effectively, not just getting correct answers. In addition, students can start or join a study group and use the MSC as a group or individual study space. Located in the Center for Teaching & Learning (CTL) on the first floor of the College Library, drop-in hours are Sunday through Thursday, 8-11 PM, and Sunday, Tuesday, Thursday, 4-6 PM, beginning Sunday, August 28. Appointments are available at other times. For more information, visit or contact Dr. Mark Barsoum (mabarsoum or ext. 2796). AT Sessions: Erica Shook is an experienced programmer who took this class two years ago, and has extensive coding experience in several languages. She will attend class and help me answer your questions as they arise. She will also meet with students at two different times in the week. The focus of AT sessions is on preparing for quizzes. AT sessions are not required, but are strongly encouraged. Office Hours: Office hours, Monday and Wednesday 2:00-3:30 and Tuesday and Thursday 2:30-4:00, are specifically dedicated to meeting with students in my office, Chambers Please feel free to drop by at other times; I am in the office more than just these hours. Or, I welcome you to make an appointment for a specific time other than those I have listed. is a great way to reach me, day and night. Grading: Course grades will be computed as follows: Reading & Participation 10% Assignments 40% Project 10% Quizzes 20% Final exam 20% Approximate class schedule:

5 Date Topic Reading Due Work Assigned Work Due Preparing for Programming and 23-Aug Python Writing Simple Programs ; HW1: 25-Aug Picobot Computing with Numbers ; 30-Aug 3.8 String basics 2.8, 3.1, 3.7, 7.3 HW2: Melting HW1: Picobot 1-Sep temp 6-Sep Branching Quiz 1 While loops; Debugging 8-Sep HW3: ORFs HW2: Melting temp More with strings 7.1, 7.2, Quiz 2 13-Sep 15-Sep 7.4 Reading and writing files , HW4: Restriction sites HW3: ORFs Lists 3.2; 4.5; Quiz 3 20-Sep Graphs Links HW 5 HW 4: Restriction 22-Sep sites 27-Sep Biological Sequence Analysis Links Quiz 4 HW 5 Biological Sequence Analysis Links HW 6: Sequence 29-Sep comparison 4-Oct For loops Quiz 5 6-Oct More on lists HW 6: Sequence comparison FALL BREAK Nested loops and other loop structures , 5.12 HW 7: Longest 13-Oct repeat 18-Oct Functions; Simulation Quiz 6 More about functions , HW 8: Alignment HW 7: Longest 20-Oct repeat 25-Oct Object oriented programming Quiz 7 Object oriented programming HW9: HW8: 27-Oct Regression Alignment 1-Nov Turtle graphics Links Quiz 8 Graphics package Links HW9: 3-Nov Regression 8-Nov More graphics Links Quiz 9

6 10-Nov Projects --- Project 15-Nov Recursion Quiz Nov Recursion Nov More bioinformatics algorithms Links THANKSGIVING BREAK 29-Nov Projects Course evaluations 1-Dec Prepare for final exam 6-Dec Project demos Project 7-Dec Digital project fair 3:30-5:00

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