BIO 309 - Genomics, Proteomics and Systems Biology
Dr. Haynes - Fall 2007


Instructor: Dr. Karmella A. Haynes
Office Hours: Tues. 4 pm - 5 pm; Wed. 1 pm - 3 pm; Thurs. 10 am - 12 pm
Office Location: Watson Science Building, Room 275
Office Phone: 704-894-2603
Lecture: Chambers Hall, Room 3146 (Mac Lab)
Class meets every Monday, Wednesday and Friday, 11:30 AM - 12:20 PM
Reading Schedule -
Lab: Watson Science Building, Room 247 (Mac Lab)
Section A meets every Monday, 1:30 - 4:20 PM
Section B meets every Tuesday, 1:00 - 3:45 PM
Lab Schedule -


BIO 309: Genomics, Proteomics and Systems Biology is group A course designed to help you develop your critical thinking skills towards an advanced (professional scientist's) level. You will benefit if you have taken one or more of these courses: Microbiology, Genetics, Cell, Developmental, or Molecular Biology. A thorough understanding of Bio111 is the bare minimum required for non-biology majors. The course will begin with a case study of a genetic disease. This case study will give you an overview of the state-of-the-art in genetic disease diagnosis and the strengths and weaknesses of genetic/ genomic technologies. The remainder of the course will guide you in performing original investigations to make discoveries relevant to genomics and systems biology. Your comprehension of the material and your ability to logically interpret research data will be assessed by written assignments, take-home reviews (exams) and oral presentations (see "Grading").

Professor A. Malcolm Campbell, who introduced this course in 2001, has has invited me to teach it this semester with a modified format. You are the first class to take this course as a lecture/ lab combination. The previous format was designed to give students bioinformatics research experience in the form of homework and exams. This semester's course now allows student to carry out their research in a computer lab setting. As a result, the homework assignments are shorter and the reviews are less intensive. However, the overall content and challenge level are maintained.



Lecture Homework (Discovery Questions)
Daily homework assignments are designed to keep you on track with the dense and challenging subject matter presented in this course. You are required to read the assigned pages and complete the assigned exercises before class. Submit typed answers (i.e. Microsoft Word) to the assigned exercises to me via e-mail before 11 am, the day of class. You are allowed to drop two assignments (per unit) from the final grade. Use these allowances responsibly.
5% Unit 1 assignments (8/10)
5% Unit 2 assignments (9/11)
5% Unit 3 assignments (8/10)
15% final grade
Lecture Take-home Reviews (Exams) 1 & 2
These are open book, open notes, open internet, take-home reviews based on a selected original research article. You do not have a time limit for these tests other than the allotted days, and you can take them any place you want.

15% each
30% final grade
Lecture Final Review (Exam)
Same as semester take-home exams (in nature and length), but more comprehensive.
15% final grade
Lab Research Abstracts 1 & 2
You will submit an abstract of your lab work prior to giving your oral presentation.
5% each
10% final grade
Lab Research Presentations 1 & 2, and Notes
You are required to carefully document your bioinformatics research to help compose your final report. Submit your research notes (2% of your final grade) the day of your oral Power Point presentation (3% of your final grade).
9% each talk
1% each research notes submission
20% final grade
Lab Research Final Report (Web Site)
Your research will follow a specific gene product and place it into a whole genome/ proteome context. The final report (web site) will tie together the research completed during the semester. You will present
10% final grade
Class Participation
Based on attendance and participation in class discussions.
+ or - one grade level
Grading Scale:
A A- B+ B B- C+ C C- D+ D F
100 - 95 94 - 92 91 - 89 88 - 86 85 - 83 82 - 80 79 - 77 76 - 74 73 - 71 70 - 68 67 - 0

For details on assignments, see the Assignment Help Guide (


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.


The open-resource, open venue exam format is a priveledge made possible by 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 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. Team work in using resources/ software is strongly encouraged, but each person must author his or her own oral presentations, lab reports, Discovery Question answers, abstracts and review answers. For instance, it is fine to ask someone for help how to use a particular public web site or how to use Power Point, etc. but it is unacceptable for you to "borrow" text from another student or any document, or electronic source unless you explicitly cite the reference. Consult the Davidson College Department of Biology Statement on Plagiarism ( for details.