Olga Kopp - Utah Valley State College

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Brief Description/Overview:

Genomics and bioinformatics principles. Students get the basics of bioinformatics and at part of the course was used for genome annotation


We used the Campbell and Heyer book for the basics of bioinformatics. Then, approximately in the middle of the semester we initiated the genome annotation project.

Lessons Learned:

Things went well. The basics of bioinformatics were useful for the students. We only had 3 hours per week in the course, so we didn’t have as much time as we wanted to go through what we wanted to cover. Students were enthusiastic about the annotation. It was a learning process for all of us. Since we were short of time, a modification was sent to the curriculum office to increase the class two hours more. It is hard to recruit students for classes like this at UVSC because many of them only want the minimal requirements to get into medical school. I guess more advertisement of the class will be needed to get the enrollment up.

Future Plans:

We will plan to teach the class every other year and also to have students getting research credit for annotating the genes. This semester we have two students annotating and we were expecting to get additional students recruited but we have not been that successful. Unfortunately some students think that research is only at the bench. We need to work more on changing this thinking and allowing them to see the bigger picture.

Syllabus for Biology 4300 Introduction to Genomics and Bioinformatics

Fall Semester 2006

Instructor: Dr. Olga Kopp Office: SB202

e-mail: Please use the WebCT e-mail.

Schedule: Tuesdays and Thursdays 11:30-12:45 A.M.- PS 203A

Office hours: Monday, Tuesday and Wednesday 9-9:50 A.M. or by appointment any other time.


Genomics, Proteomics and Bioinformatics – Campbell, A.M. and Heyer, L.J. ISBN-0-8053-8219-4

Find the courses you are taking. Here you will find your syllabus, presentations, assignments, grades, announcements. The following web page contains the figures of your textbook: http://wps.aw.com/bc_campbell_genomics_2/0,11571,2875502-,00.html


Biology 1610 and BIO 3500

Students completing this class should be able to

  • Understand the basis for genome analysis
  • Access, retrieve, and analyze bioinformatics data available from several databases
  • Evaluate the quality of the data available from the internet
  • Use standard bioinformatics tools in order to answer biological questions

This course will survey a series of databases useful for analysis of genes and genomes. At the end of this course you should be able to use a set of different tools to analyze a particular gene, nucleotide sequence or protein and gather important biological information from this analysis. This course will enable you to use these tools. Students completing this class are not expected to develop new bioinformatics tools or construct databases to store biological data.

Attention students with disabilities

If you have any disability which may impair your ability to successfully complete this course, please contact the Accessibility Services Office, 863-8747, BU 146. Academic Accommodations are granted for all students who have qualified documented disabilities. Services are coordinated with the student and instructor by the Accessibility Services Office.

Suggestion for successfully completing this course

  1. Attend class and bring the textbook with you. Read the assigned material before class. The quizzes will include also your assigned reading. Work carefully in class. NO E-MAIL READING OR COMPUTER GAMES IN CLASS.
  2. Take responsibility! Learning does not take place primarily in the classroom. You are responsible for what you learn; all of you have the capability to do well in your classes, but talent alone cannot produce success. Higher education means taking responsibility for your own learning. You should program 2 hours per week outside of class for each hour of lecture in order to review the material.
  3. Use the resources provided: me, materials on the web page, reading assignments, study groups, library
  4. Complete all assignments and exams on time.
  5. Read the assigned sections in advance of coming to lecture. This way I can answer any question you may have during the course of the lecture and the material we discuss will make much more sense.
  6. Know the basics of Biology, specially DNA, RNA, proteins

Attendance is very important. Good attendance also means being to class on time. Entering class after it has started or leaving before finishing is disruptive for everybody. No playing games at the computer or using e-mail during class time. If you think you have time left over, work in your projects.

UVSC Policy: If you stop attending class without dropping, a grade of "UW" (which counts as a failing grade on your grade point average) is assigned only if you have a passing grade at the time you stop attending. Otherwise, an E will be assigned regardless the date you stop attending. “I” and “UW” are NOT used to avoid a low grade. (p 22 UVSC catalog). A grade of “I” (Incomplete) is the instructor’s option and is not given except only under the most extenuating circumstances for which there is verifiable written documentation and all course work is complete except for the final exam.

Policies from the “Student Rights and Responsibilities code

  1. Each student is expected to take an active role in the learning process by meeting course requirements as specified in written syllabi.
  2. Each student is expected to display appropriate conduct in classroom situations, which will enhance the learning environment.
  3. Faculty members have the right to establish classroom standards of behavior and attendance requirements. Students will be expected to meet these requirements and make contact with faculty members when unable to do so.
  4. Each student is expected to maintain academic ethics and honesty in all its forms, including but not limited to, cheating and plagiarism as defined hereafter:
    1. Cheating is the act of using or attempting to use or providing others with unauthorized information, materials or study aids in academic work. Cheating includes, but is not limited to passing examination answers to or taking examinations for someone else, or preparing or copying other’s academic work.
    2. Plagiarism is the act of appropriating any other person’s or group’s ideas or work (written, computerized, artistic, etc) or portions thereof and passing them off as a product of one’s own work in any academic exercise or activity.

I will apply ZERO TOLERANCE for lapses of academic integrity. Any student found to be guilty of lying, falsifying, cheating, plagiarism or any other form of academic dishonesty will be given a failing grade. Copying material from the Internet without citing the sources is plagiarism. You will get zero credit for your submitted material. Copying and pasting more than one sentence without using quotation marks and citing the author is plagiarism.

Cell phones and pagers: Please turn off cell phones and pagers while in class.


  • In class assignments: 340 points (20 points each)
  • Flow charts - chapters: 80 points (5 points each) - individual work
  • Handout and presentation one database: 50 points - in groups of 2 or individually
  • WebCT homepage: 20 points
  • Annotation project: 100 points (in groups of 2)
  • Final Disease project: (write up and presentation) 150 points (in groups of 2 or individually)
  • Total: 740 points

In class work cannot be made up and will count as zero points if you are absent. NO EXCUSES WILL BE ACCEPTED AFTER THE FACT.

Grading Scale:

A = 94% & above A- = 90-93.95% B+ = 87-89.95%
B = 83-86.95% B- = 80-82.95% C+ = 77-79.95%
C = 73-76.95% C- = 70-73.95% D+ = 67-69.95%
D = 63-66.95% D- = 60-62.95% E (failing) = Below 60

Course schedule

Note: Schedule is tentative. Schedule changes announced in class and in the web page take precedence over this schedule.

chapter Read before class - pages Discovery questions
Thr Aug 24 Introduction
Tue Aug 29 1-What’s wrong with my child? Pages 1-12 8, 10,12,13,14,15,16,17,19,20
Thu Aug 31 1-What’s wrong with my child? 13-29 26,27,29,32,35,36,38,40,44,45,46
Tues Sep 5 2-How are Genomes sequenced? 34-46

Cancer gene exercise || 8,9 (MM2.1:1,2), 12,13,14,15

Thur Sep 7 2-How are Genomes sequenced? 47-58 20,22,23,24,25,26,27,28,30,32,38
Tues Sep 12 2.2.What have we learned from prokaryotes 59-74 40,48,49,52,53,57,62
Thur sep 14 2.3.What have we learned from eukaryotes 83-109 80,81,82,87,88,93,94,96
Tue Sep 19 3.1-3.2-Comparative genomics-evolution 114-145- MM3.3 13,15,16,22,23,35,36,37,38,43
Thur Sep 21 3.3-3.4:genome identification-biomedical 145-172 50,53,55,56,57,62,63,67,72
Tue Sep 26 4.1-4.2:Case study-Human genetic var… 178-198 3,8,10,16,17,18,28,36,37
Thur Sep 28 4.3-4.4:. Is death a genetically determined trait?- Ethics of genomic variation 198-214 – MM4.4 40,42,48,52,58,61,70,72
Tue Oct 3 5. Why can’t I just take a pill to lose weight? 219-231 2,3,6,7,9,19,20,22,23,26
Thur Oct 5 6.1- Introduction to Microarrays - MM 6.1 234-254 MM 6.1 2,3,9,17,18,19,20,21,32
Tues Oct 10 6.2-Alternative uses of microarrays 254-261 45,46,48,63,64,67,77
Thu Oct 12 FALL BREAK No class
Tue Oct 17 7.1-cancer and microarrays 264-272 MM7.1 1,2,4,5,6,8,9,10,12,15,21,23,30,31
Thur Oct 19 7.2-Improving health care with microarrays 273-282 41,42,52,54,56,63,67
Tue Oct 24 Presentations – Internet tool Exercises of classmates
Thur Oct 26 Presentations – Internet tool Exercises of classmates
Tue Oct 31 9-Why can’t we cure more diseases? 331-340 MM9.1 7,9,14,17,18,19,20
Thur Nov 2 Genome annotation Practice example
Tue Nov 7 Genome Annotation Practice example
Thur Nov 9 Finish Disease project
Tue Nov 14 Genome annotation
Thur Nov16 Genome annotation
Tue Nov 21 Genome annotation
Thu Nov 23 Thanksgiving No class
Tue Nov 28 Genome annotation
Thu Nov 30 Genome annotation
Tue Dec 5 Discussion of projects
Thur Dec 7 Discussion of projects

The discovery questions will be answered by you in the classroom, using the web resources provided. They will have to be hand in at the end of the class. Late work will not be accepted except under documented extenuating circumstances.

Useful Web Sites

Web site

Post 3 links related to bioinformatics with a short commentary about each link. (10 points). Find 2 papers related to bioinformatics. Write the citation and a short commentary about each paper. If possible, insert a link to the paper (if found on the Internet (10 points)

Tutorial development, handout and presentation

Chose a database and check with me whether would it be o.k. to work with that one. For guidance, check the links given in the “Links” file and either choose one of those or any other one of interest. Do not choose BLAST because we are going to be working with that database extensively.

Once you have selected your database, create a tutorial that will allow people to learn how to use that database (see example in handout #1, given the first day of class). Do not just say, somebody already have a tutorial. Create your own. Your work will be evaluated by your classmates also because once you have your tutorial ready, you will prepare a short presentation discussing the tutorial you have developed and then you will guide the entire classroom through the exercise you have developed. The file with the tutorial handout should be sent to me one week before you are giving the presentation.

Flow charts

At the beginning of each class you should hand in a flow chart about your assigned reading. These will be counted as quizzes. Reading before class is essential for the success of this class. Bring your questions or mail your questions before class.

Final project

Instructions for your final projects are given in the link: Final –Disease project. These presentations will given either the last day of classes or the day of the final exam. You also need to hand in the report with the information needed. Choose a disease you are interested on learning about.

Annotation project

We will discuss the project later on. It consists in participating in a national research project for genome annotation. You will learn to annotate genes and then take a piece of DNA and annotate it. Those students that want to continue participating in this research could either apply for 495R or apply for work study and get involved in the project. Depending on the quality of the annotation done by the groups, this semester, the final data might be sent to Washington University. A publication will eventually be produced and the students involved will be given credit for their work.