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a Assessment & Grading

Bioinformatics

Midterms

Journal presentation

Final

Discussion

The Great Paper Chase

a

 

THE VIROLOGY SHOW - produced by JW & ET Spring, 2004

Prerequisites: Completion
of the lower-division core in Biology or equivalent. Strongly recommended: at lease one semester of Organic Chemistry. Open to non-majors with consent of instructor.

Approach: A balanced broad introduction to the general field of molecular virology is my aim. Bacteria phage, plant viruses, and insect viruses will be discussed in addition to animal and human pathogens. Based on the surveys, lectures will be tailored to fit the class as much as possible. (Some restrictions do apply. J)

Structure: Lecture plus discussion. Discussion is more than simple discussion- it includes demonstrations, computer lab and wet lab exercises. [Please see discussion schedule following the lecture schedule.] Web-accessible course materials include schedule & syllabus, study aids, links to resources, assignments, and interactive exercises.

1. Lectures will be based on material drawn from the texts, from other reference sources including current literature, and from Web sources.

2. Discussion sections will include a variety of activities, including "hands-on" exercises with modeling, computers, and lab methods; focused discussion topics; short presentations; and reviews.

3. To insure everyone stays on his/her toes and doesn't wait until a midterm to read several chapters, six short self-quizzes are available for copying and will be reviewed in discussion sections during the term. [These will not count in your grade.] In addition, there will be short problem discussions throughout the term to help with and expand upon the study guide problem sets. Study guide problems are posted on-line.

4. The two midterms will be essay and will require synthesis of information and thought. A sample exam will be posted and will be available for copying.

5. There will be a series of exercises designed to expose you to Web-based resources and database searches, especially involving "bioinformatics" [translation: protein and genomic sequence searches and analysis]. For more information, check out "Computing" from the menu bar.

6. Each student will present a journal paper in their discussion group based on a designated topic. See "Journal Presentation" below for more information.

7. "The Great Paper Chase" is a literature search and information gathering exercise, with six weeks allowed for completion. [The assignment will be posted on-line by 3/2.]

8. The final will be one-half "midterm" covering the last lectures, and one-half comprehensive. The lowest score from the midterms and the final will be dropped. [For the brave and the industrious, this makes the final optional.]

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Assessment & Grading

Bioinformatics

40

Journal presentation

20

Discussion

40

2 midterms (100 pt each)*

200

1 final(100 pt)*

1 paper chase**

100

Total

400


* One midterm or the final may be dropped. [This makes the final "optional".] No make-ups on exams. If you have a problem, see me well in advance.

** See below for description. Do pay attention to the deadline schedule.


Note on final grade calculation: Grades will be assigned based on an adjusted percentage. An adjustment factor will be calculated for the highest undergraduate points received. [If the total points possible is the highest score, the factor = 1.000]. This factor will be averaged with the adjustment factors from past years. Each student's raw score will be adjusted by the averaged factor and grades assigned as follows:

A
B
C
D
F

100-90%
89 - 80%
79 - 70%
69 - 60%
59-0%

Cheating and plagiarism: This will result in dismissal from class and a failing grade.

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Course Requirements

Bioinformatics:

Bioinformatics is the descriptive term now used for web-based computer searches and analysis of protein, nucleic acid, and genomic databases. Powerful search engines and analysis software are now available which allow us to consider questions which once, not very long ago, were beyond our reach to answer. The exercises will allow you to explore what has been discovered about viruses at the gene and protein level. Perhaps you will make some discoveries of your own!

These exercises are being updated and will be reposted prior to lab sessions. Check the "Announcements" box on the Home Page periodically for updates. Points will be earned for completing the exercises.

  • 10 pt- Computer exercise 1: Introduction & molecular modeling of viral proteins
  • 15 pt- Computer exercise 2: Sequence databases and tools
  • 10 pt- Computer exercise 3: Class projects
  • a5 pt- Bioinformatics survey

Grading on these is lenient; the key point is to learn something in the process of doing them. You will be able to explore while you gain some familiarity of how to find sequences, to make comparisons of sequences, and to locate original literature related to the sequences. You will be shown where and how to continue learning more about bioinformatics beyond the brief introduction given during this course. You will also gain experience which should help you in completing the Great Paper Chase. You may find that learning virology just got a lot more interesting!

Journal Presentation:

Each student will select one paper on a topic related to immunology. This paper will be discussed in your discussion section. Check the Journal topics schedule and the description for details. Full points are earned, provided that the presentation is given and that the paper presented was both reasonably current and relevant to the topic.

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Discussion Sections:

To facilitate information flow and to establish two-way communication, there will be short forms to return in each section meeting. These will have space for input and questions. Although I won't be taking attendance per se, do see me if you have missed a meeting or if you would like to sit in on the other section as a substitute. The activities planned for discussion sections are integral to the course and are expected to add interest as well as enhance the learning process.

In addition to the discussion meetings, there will be a variety of opportunities to participate in on-line discussions. I will throw out some topics to get things started. You are invited to add others as we progress through the course.

Grading for discussion will be based on participation, both in discussion section and on-line. It is a fairly easy way to earn points while doing some things which will make learning virology easier, and maybe even fun.

Midterms:

Two one hour exams will be primarily short essay format, covering major principles and concepts. Thought and analysis will be stressed. Memorized material will be restricted as much as possible to short questions and diagrams. A representative example of a midterm will be posted in the case outside D234. Use of Study Guide 1, Study Guide 2, and the timely use of the on-line self-quizzes will help in keeping up with the material and reviewing for the exams.

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Final:

A choice of questions will be offered. The focus of one-half of the exam will be on material covered after the last midterm. The balance of the exam will be questions requiring synthesis of material covered throughout the semester. See Study Guide 3 for aid in preparation.

The Great Paper Chase:

This exercise carries the value of one midterm or the final. However, two points should be made clear. One, you have control over the quality and content of this effort, and I have control over the exams. Second, past students consider this to be the most significant learning experience of the course. The Paper Chase is a computer and library literature search exercise and is in 3 parts. All but the last part total 70 points. The first part is worth 30 points; the second part is worth 40 points and may or may not cover a summary essay question. Some questions are general enough to allow you latitude in your searches; others are specific and allow fewer options in obtaining your information. The last part is worth 30 points and is based on a question you write, submit for approval, and then answer. All tools for doing literature searches are open to you. The questions for the Paper Chase will be posted by 3/5 and are due 4/18. For papers returned by the deadline, feedback will be given by the last class, perhaps sooner. 10 points per day, including Saturday & Sunday, will be lost for lateness.

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  Updated 1/24/04 by thatcher@sonoma.edu