A. Malcolm Campbell's Genomics Syllabus: Fall 2009

Bio309 Genomics, Proteomics and Systems Biology <www.bio.davidson.edu/genomics>

Class Meets: MWF 11:30 Chambers 3146 (GAMCo Lab)	Lab: offered as a separate course fall semester
Office Hours: M & Tu: 3-4; Thurs: 8:30 - 9:30; or anytime by appointment	.
Office: Dana 221A (through my lab, door on left)	macampbell@davidson.edu_ Phone: 704-894-2692

Note: Prior to taking this genomics lecture course, you should have taken one of these courses: Microbiology, Genetics, Cell, Developmental, Biochemistry, Immunology, or Molecular Biology. A thorough understanding of Bio111 is the bare minimum required for non-biology majors (talk to me if you have had only Bio111). Genomics builds upon the foundation provided by other courses. You do not have to own a computer to take this course, but you may find it beneficial. The GAMCo computer lab is optimized for genomics and you have access to GAMCo from 6 am - 1 am, 7 days a week, except when other classes are meeting:

Educational Goals for the Course

Grades: (see Exams and Answer Keys)

Source of Grade	Percentage of Final Grade
2 exams during semester; 1 during finals	60%
3 web pages pilot page - gene and trait of your choosing Review Paper #1 Review Paper #2	25% 5% 10% 10%
Daily Discovery Question Answers Orally in Class	15%

Grading Scale:

Conversion of Percentage to Letter Grade

	A = 100 - 95	A- = 94 - 92
B+ = 91 - 89	B = 88 - 86	B- = 85 - 83
C+ = 82 - 80	C = 79 - 77	C - = 76 - 74
D+ = 73 - 71	D = 70 - 68
	F = < 67

Attendance policy:

I will take attendance to facilitate a more objective means for assigning the class participation grade. In order to receive a passing grade in this course, you cannot miss more than 5 classes without a legitimate reason. Legitimate reasons include illness requiring physician’s care, family emergency, etc. Unacceptable reasons include social function, sleeping, exam in another class, etc.

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General Information:

You are among the very few students in the world who will take a comprehensive course in genomics. The term "genomics" does not mean the same thing to everyone. There are a growing number of genomics classes around the country, but they are often limited in scope. This course is comprehensive and intensive.

Laurie Heyer and I have written the only true genomics textbook in the world (called Discovering Genomics, Proteomics & Bioinformatics; GPB) in order to teach this course. We have worked hard on the text, but I expect there are areas that could be improved. I would appreciate your feedback on all aspects of GPB, from typos to suggestions to improve the clarity. In addition to the text, there is a web site that contains all figures that appear in the book as well as some color figures that appear only on the web site.

I worked with Dr. Laurie Heyer in the Math Department to create a set of "Math Minutes" which illuminate the math behind the biology. Increasingly, biologists (i.e. you) will need to become more proficient in math. To address this need, Dr. Heyer and I hope to illustrate the many areas where math and biology intersect. Dr. Heyer offers a course (Bioinformatics) that addresses the math that is at the heart of genomics, proteomics and bioinformatics. You might consider her course as a sequel to this one.

The format of each class will require all of you to read each day’s assignment BEFORE you come to class. Each class will begin with a period where you can ask specific questions related to the previous day's material or specific areas you do not understand from the current day's assignment. We will stick closely to the schedule because there is so much to learn and so little time. Therefore, if we do not cover a topic in class, but it is covered in your reading, you are responsible for it. We will discuss some topics as a group, I will call on you randomly to answer a question or lead a discussion, and I will present some information in the traditional lecture format. If I call on you to answer a question, it is OK to say, "I got this part but this other section lost me." It is not OK to say, "I didn't read it." I understand that some days you might fall behind a day or two but do not make this a practice since class participation is also graded.

I will assign some Discovery Questions to be answered by you orally in class. You should answer the Discovery Questions as they appear in the text. Unlike traditional textbooks, GPB is designed to engage you in an interactive process. In order to fully understand the material, you will need to use the web links and answer the Discovery Questions.

Exams: you may have heard the exams in this course are extremely long. I am working to reduce the time required for genomic exams, but I do not want to cheat you of an educational opportunity. Therefore, we will read fewer case studies, go over them in class, and discuss your answers to the Discovery Questions. The 3 exams will be a combination of Discovery Questions from cases you have not read for class, as well as a few questions from recent papers. I want to work with you to balance the time required with the value of working with new material.

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Honor Code

All of your exams are open book, open notes, open internet, take-home exams. You do not have a time limit for these tests other than the alloted days, and you can take them any place you want. This form of testing is possible only because of the Honor Code. If you violate my trust in you and the Honor Code, we will have to take the tests during the 50 minutes of class. You are required to not cheat on these tests, and to report to me or the Dean of Students any violations you observe or hear about second hand. This means that even your lab partners or best friends must be reported if you know they are cheating. The entire system will break down when individuals make exceptions to the rule in order to spare their friends.

The content of all written assignments are also covered by the Honor Code. Each person must write his or her own web pages, Discovery Questions answers, and exam answers. The content is what I will be evaluating, not the layout. Therefore, you may work collaboratively to create the layout for your web pages but not the content. For example, it is fine to ask someone for help in creating relative links, inserting Jmol files, how to use a particular public web site for sequence analysis, etc. However, it is unacceptable for you to "borrow" text from another student or any document, or electronic source unless you explicitly cite the reference. You can consult the Biology Department's plagiarism web page for help in this area.

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Reading Schedule

The following reading assignments are from the text book called Discovering Genomics, Proteomics & Bioinformatics. You should print out this schedule so you can see the schedule by itself at this URL.

Web Assignments