PPWS/GBCB 5314

Biological Paradigms forBioinformatics

Fall, 2006

TTH, 8AM, 1000 Torg.

Dr. Ruth Grene

435 Old Glade Road, Room 103

Take Math Emporium Shuttle to GladeRoad.

1-6761, grene@vt.edu

Office hours: T TH 3:30-5PM

Also available on Sundayafternoons, if needed.

 

Text: Genomes 3  T.A.Brown, Garland Science, 2007

 

1.      TheVT Honor code will be strictly enforced. Everything that you write must be your own.  You will be reported to the authorities for any breach ofthe Honor Code.

 

2.     Therewill be two midterm exams, and a final exam.  All the exams will be take-homes, open book.  They must be completed alone. 

 

3.     Activestudent participation is essential, since this is a graduate course.  Students will work as partners toprepare solutions to problems for presentation in class. Other problems will beassigned as homework, and are to be completed alone.

 

4.     Duringmy office hours, I will discuss the starred problems that appear at the end ofeach chapter with any student team that cares to come by.  PLEASE avail yourselves of thisopportunity!!!   It can affectyour grade!!!  The more I see ofyou, the more you learn, and the better I can evaluate your performance.

 

5.     Therewill be two field trips to VBI, covering topics in instrumentation andmethodology.  Material from the VBIlectures will be part of the final exam.

 

6.     Anoral presentation of an assigned research paper by each student team is required.   For this assignment, you mayconsult any faculty member who is available to you. The presentations, given bythe student teams, will be held on an evening during the last week of thesemester. Refreshments will be provided!

 

7.     Pleasenote that there will be extra classes during the first two weeks of thesemester, since I will be out of the country during Week 3. 

 

 

 

Distribution of Grades

 

 

2 Midterms

15% each

1 Final

15%

1 Oral Report on Research Paper (teams)

15%

4 Homework Assignments

5% each

Participation in class*

20%

Total

100%

 

*Participation includes attending every class, presenting answers to theassigned problems, and joining the informal discussions.  Any person missing three classes for nogood reason will lose the entire 20% assigned to participation.

 

** Class will be held in 1000 Torgersen at 8AM, exceptfor  the makeup classes of 8/23/06and 8/28/06, when we will meet in Torgersen3080 at 5:30 PM.

 

 

Syllabus

 

Lecture

Date

Subject

Assignment

Comments

1

08/22/06

Introduction

Chapter 1

Work on starred problems

2**

08/23/06

Introduction

Chapter 1: Starred problems

Class discussion of problems

3

08/24/06

DNA 1

Chapter 2: 31-44

Starred problems

Class discussion of problems

4**

08/28/06

DNA 2

Chapter 2:

44-58

Starred problems

Class discussion of problems

5

08/29/06

DNA 3

Chapter 2:

unstarred problems

Student teams present  solutions

6

08/31/06

Mapping Genomes 1

Chapter 3:

64-77

Starred problems discussed in class.

7

09/14/06

Mapping Genomes 2

Chapter 3: 78-95. 

Discuss Lander and Weinberg paper in class

8

09/19/06

Mapping Genomes 3

Chapter 3: Unstarred problems

Student teams present  solutions

9

09/21//06

Sequencing Genomes 1

Chapter 4:

104-115

Starred problems solved jointly in class

10

09/26/06

Sequencing  Genomes 2

Chapter 4:

115-124

Starred problems.

 

Homework 1assigned

11

09/28/06

Reading Genomes 1

Chapter 5:

133- 148

Starred problems

.

12

10/05/06

Reading Genomes 2

Chapter 5:

148-160

Homework 1 due. 

Review session for midterm in evening if requested:

13

10/10/06

Understanding Genomes 1

Chapter 6

 

14

10/12/06

Understanding Genomes 2

Chapter 6:  All starred problems

Midterm 1: Lectures 1-10

15

10/17/06

Eukaryotic Genome Anatomy 1

Chapter 7

Midterm 1 due Homework 2 assigned

16

10/19/06

Eukaryotic Genome Anatomy 2

Chapter 7

Unstarred problems

Student teams present  solutions in class

17

10/24/06

Accessing the Genome 1

Chapter 10

Homework 2 due

18

10/26/06

Accessing the Genome 2

Chapter 10: starred problems

Homework 3 assigned

19

10/31/06

Transcription 1

Chapter 11: 295-312

 

20

11/02/06

Transcription 2

Chapter11: 312-326, starred problems

Homework 3 due

21

11/07/06

Transcription 3

Chapter 11

 

Unstarred problems presented in class

Review session for midterm in evening if requested:

22

11/09/06

Processing RNA 1

Chapter12:

333- 348

Midterm 2 given out: Lectures 11-20

23

11/14/06

Processing RNA 2

Chapter12:

348-368

Midterm 2 due. Research papers assigned to teams

24

11/16/06

Processing RNA 3

Chapter12:

369-376.

Homework 4 assigned

Starred problems

25

11/28/06

Regulation of Genome Activity 1

Chapter 14: 423-437

Homework 4 due

Starred problems

26

11/30/06

Regulation of Genome Activity 2

Chapter 14:

438-456

Starred problems

27

12/05/06

Regulation of Genome Activity 3

Chapter 14: Unstarred problems

Unstarred problems  presented in class

Reading Day

12/07/06

 

 

Final given out: Lectures 21-27, and VBI lectures

Final Due:  5PM, 12/12/06