Bioinformatics Course Syllabus

Professors Fetrow, Burg, Miller

www.wfu.edu/~fetrowjs/Courses/BioinformaticsSpr04/startup.html

CSC 391/691; PHY 392; BICM 715

 

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Course description: 

            A course in computational biology designed to introduce the topic, history, and current research issues in bioinformatics, as well as prepare students in the skills necessary to communicate with researchers across the disciplines of computer science and biology.  The course is designed for computer scientists who want an introduction to the language of molecular biology and to the significant computational problems in the field of biology.  The course is also designed for biophysicists, biochemists, and molecular biologists who want an introduction to the language of computer programming and algorithm development, focusing on solving computational problems in biology.  As part of the course, computer scientists and bio-scientists will work in groups to design, build, implement, and test software packages to solve particular computational problems in biology. 

 

Instructors:

Jacquelyn Fetrow, Reynolds Professor of Computational Biophysics

·         Offices:  Olin Physical Laboratory 301B (Physics); West Hall 236 (Computer Science)

·         Office hours:  Physics Thurs 2-4 pm; Computer Science Fri 10-noon

·         Web page:  http://www.wfu.edu/~fetrowjs

Jennifer Burg, Associate Professor and Chair, Computer Science

·         Office:  West Hall 237

·         Office hours:  Mon and Wed, 10-11 am; Tues 9:30-10:30 am

·         Web page:  http://www.cs.wfu.edu/~burg/

Tim Miller, Parallel Computing Systems Administrator

·         Office:  Computer Science 234; 758-3257

·         Office hours: Mon 1:30-4:30 pm

·         Web page:  http://www.wfu.edu/~millerte/

 

Course meeting time:  MWF, 9-9:50 am; generally, lectures are Mon and Wed in West 244; laboratory exercises are on Friday in West 017; please bring your laptop for Friday laboratory sessions in West 017

 

Required textbook:  Bioinformatics, Sequence and Genome Analysis, by David W. Mount; Cold Spring Harbor Laboratory Press

 

(PLEASE NOTE: course prerequisites and requirements are different, depending on which course number you signed up for.  Please sign up for the course number that is most appropriate to what you want to learn)

 

Course requirements:

  • CSC 391/691: To get credit for this course number, students will be required to actively participate in the software engineering and programming aspects of the course.  All students will be required to understand the research issues and master the key concepts in the field of bioinformatics. 
  • BICM 715; PHY 392 (Special Topics, Bioinformatics): To get credit for this course number, students will be required to master the biotechnical details behind the programming projects and effectively communicate those details to the students who are doing the engineering and programming.  All students will be required to understand the research issues and master the key concepts in the field of bioinformatics.
  • Those students who register for the graduate course number will be required to answer additional questions on the laboratory exercises and final examination.  There will also be higher expectations for students registered for the graduate course numbers to participate more in class discussions.  

 

Course numbers and prerequisites:

  • CSC 391/691 (Selected Topics, Bioinformatics):  Prerequisite for registering for this course number is CSC 221 (or permission of the instructor).
  • BICM 715; PHY 392 (Special Topics, Bioinformatics):  Prerequisites for registering for this course number are introductory courses in biology, chemistry, and molecular biology or biochemistry (or permission of the instructor).

Grading:

  • Course Projects (30%): 
    • There will be two group projects that will be due during the semester.  These projects will be done in small groups, with BICM/PHY and CSC students in each group. 
    • You will be graded both on your contribution to your specific aspect of the project and on how well the group completes the entire project. 
  • Laboratory exercises (50%): 
    • There will be eleven laboratory exercises during the semester, so each exercise is worth approximately 4% of your entire grade. 
    • Each exercise corresponds to one of the Friday laboratory sessions.  Laboratory exercises will usually be due on the Wednesday following the laboratory (see Course Schedule for exact schedule). 
    • Time will be allotted at the beginning of Monday’s lectures to answer questions and discuss the laboratory exercises. 
    • Several exercises represent the output to steps involved in the evolution of the Course Projects.  Some of these exercises will be developed within the groups and other project exercises must be completed individually.  In these instances, we will be specific about how the exercises should be completed, whether individually or as a group. 
    • While the laboratory sessions and lecture discussions are interactive, these exercises should be done individually.  Copying another student’s answers is considered cheating and will result in a failure for the exercise. 
  • Class participation (10%):  Laboratory sessions and discussions are designed to be interactive.  Your active participation will be considered as part of your final grade.  Active participation includes asking questions in lecture, contributing to lecture discussions, assisting fellow students during the laboratory session (but not in writing answers to the exercises for another student), and interacting effectively with others during the group projects. 
  • There will be a take home final examination for this course which is worth 10% of your grade.