BIOL/CHEM 3100 - Biocomputing
Course Syllabus - Spring 2008

Course Schedule

Individuals with disabilities who need to request accommodations should contact the 
Disability Services Coordinator, Student Center 255, 678-466-5445, disabilityservices@clayton.edu.

Course Description:

        Number and Title

        BIOL 3100 (CRN 26001)
        Biocomputing

        Credit Hours:

        3.0 semester credit hours

        Course Description:

The human genome project and the web revolution present new challenges and opportunities for biologists. The only way to deal effectively with the information explosion in biology is to use computers.  Students in this course will use computer applications to search databases, perform calculations and develop models concerning biological problems.

        Course Prerequisites:

        Prerequisites: BIOL 3250, BIOL 4201 and  MATH 1231

        Computer Requirement:

Each CSU student is required to have ready access throughout the semester to a notebook computer that meets faculty-approved hardware and software requirements for the student's academic program. Students will sign a statement attesting to such access.  For further information on CSU's Official Notebook Computer Policy, please go to http://itpchoice.clayton.edu/policy.htm.

        Computer Skill Prerequisites:

• Able to use the computer’s operation system (Windows®)
• Able to send and receive e-mail (Outlook® or Outlook Express®)
• Able to attach and retrieve attached files via email
• Able to use a Web browser (Internet Explorer®)
• Able to download files from a web site to your computer
• Able to use a word processor system (Word®)
• Able to use Microsoft PowerPoint®

In-class Use of Student Notebook Computers:

Student notebook computers will be used during EVERY class meeting in this course. Computers will also be required to access course materials and to communicate with your instructor. Students who are found using their computer for activities not related to the course (including, but not limited to checking email, web surfing, instant messaging, etc.) will have their computer confiscated for the remainder of the class period and will lose attendance points.  This same limitation applies to the use of any other electronic devices in class (including, but not limited to cell phones, personal digital assistants, etc.).

Course Objectives:

• To learn the concepts behind bioinformatics tools and to learn how to use tools in bioinformatics to study the phylogeny, expression, structure, and function of genes and proteins.

Student Learning Outcomes:

Biology Outcomes: BIOL3100 supports outcomes 1, 3, 4, 5, 6 and 7 of the biology major:

• Outcome 1:  Knowledge of the basic principles of major fields of biology.
• Outcome 3:  Knowledge of physical science, mathematics, and statistics required to support an understanding of biology. 
• Outcome 4: Ability to communicate orally and in writing in a clear, concise manner.  
• Outcome 5:  Ability to collect, evaluate and interpret scientific data, and employ critical thinking to solve problems in biological science and supporting fields.
• Outcome 6:  Ability to function effectively on team-oriented projects.
• Outcome 7:  Appreciation for the impact of biological and physical science on the environment and society. 
  

Term:

Spring, 2008

Instructor Information:

Dr. Caroline Clower
Office phone: (678) 466-4777
Fax: (678) 466-4899
Office: Arts and Sciences Building, Room G105-C
E-mail: CarolineClower@clayton.edu
Internet address: http://a-s.clayton.edu/cclower/
Office hours: M, W: 2:00 pm - 4:00 pm, A&S G105-C
                       Thursday, 1:30 - 4:30 pm, A&S G105-C
                                              or by appointment

Dr. Michelle Furlong
Office phone: (678) 466-4778
Fax: 678-466-4899
Office: Arts and Sciences Building, room G210A
E-mail: mfurlong@clayton.edu
Internet address: http://a-s.clayton.edu/furlong/FurlongHome1.htm
Office hours: M,T,W,R 10:30 a.m. - 12:00 p.m.

During office hours, Dr. Furlong will be in one of three locations:  G210A (her office), the biology lab (C21) or the research lab (C32). 

Class Meetings:

Textbook Information:

Fundamental Concepts of Bioinformatics by Krane and Raymer.  Pearson Education, 2003.  ISBN:  0-8053-4633-3

Evaluation:

Your evaluation in BIOL 3100 will be based upon the following components:  

Grading:

The grade you receive in BIOL 3100 will be based upon the following distribution:

The mid-term grade in this course which will be issued on Feb. 22, reflects approximately 30% of the entire course grade.  Based on this grade, students may choose to withdraw from the course and receive a grade of "W."  Students pursuing this option must fill out an official withdrawal form, available in the Office of the Registrar, by mid-term, which occurs on February 29, 2008.

Tentative Course Schedule

The course schedule is listed on a separate page.  Be sure to check it often to keep track of any changes in the due dates of assignments and exams during the semester.  Due dates for assignments may be changed at the instructor's discretion.  You are responsible for keeping track of due dates and turning in your work when it is required. The instructors reserve the right to change the schedule as necessary and will communicate any changes clearly to the class. 

Course Policies:

Assignments:

Homework assignments will vary in length and format, and will be graded. Details for each assignment will be announced in class and posted on the course website. Each student must submit their own work for grading. Each homework assignment must be completed on a word processor, printed and turned in on the due date, which will be announced in class and will be on the course web site. Homework assignments will not be accepted via email. Any work that is turned in after class on the due date will be considered late and penalized 10%.  Assignments will be penalized an additional 10% for each extra day late.  Under no circumstances can an assignment be turned in more than 9 days late.

Attendance:

Attendance is required, and is a component of your grade in the course. If you are more than 10 minutes late to class you will be marked as absent. If you are absent from more than 50% of the classes this semester (excused or unexcused) you will be automatically withdrawn from the class. Come to class prepared. If you do not have your computer with you in class, you are unprepared and will lose attendance points for that day. Absences may be excused if you provide the instructors with a note from a competent authority (doctor, judge, etc.). The excuse must specifically indicate the dates that are to be excused, and must be presented upon the first class day that the student returns to school.

Academic Irregularity:

Cheating in any form will not be tolerated; all work that you turn in must be in your own words and must be your own work.  If your brainpower did not generate what you turn in, it is considered cheating.  The following are examples of cheating:  falsifying any information submitted on course assignments, copying the work of another person, allowing another person to do your assignment,  working in a group on a graded item that is not intended as group work, copying or closely paraphrasing referenced sources, using anything but your brainpower on an exam, etc.  Cheating in any form will result in a zero on the assignment and academic misconduct forms will be filed with the Office of Judicial Affairs for any violation.  Judicial procedures are described on the webpage of the Office of Judicial Affairs.

Exams:

There will be one in-class midterm examination and one 2-hour final (comprehensive). All examinations are closed book. Attendance is mandatory.  If a student has an excused absence on an exam day, the student's final exam percentage score will be used in place of the missed exam score.  No make-up exams will be given. Without a valid excuse, a grade of zero points will be assigned for any missed work. Exams will be given at the beginning of the class; if you arrive late, you may be permitted to take the exam as long as the materials have not been collected from the class.  However, you will be required to turn in the assignment at the same time as the rest of the class - NO extra time will be given. 

Disruption of the Learning Environment

Behavior which disrupts the teaching–learning process during class activities will not tolerated.  While a variety of behaviors can be disruptive in a classroom setting, more serious examples include belligerent, abusive, profane, and/or threatening behavior.  A student who fails to respond to reasonable faculty direction regarding classroom behavior and/or behavior while participating in classroom activities may be dismissed from class.  A student who is dismissed is entitled to due process and will be afforded such rights as soon as possible following dismissal.  If found in violation, a student may be administratively withdrawn and may receive a grade of WF.  A more detailed description of examples of disruptive behavior and appeal procedures is provided at: http://a-s.clayton.edu/science/Biocomputing/Disruptive Classroom Behavior.doc

Other Class Policies:

• Grades will not be communicated via email or telephone.  
• Students must abide by policies in the Clayton State University Student Handbook, and the Basic Undergraduate Student Responsibilities. Of particular concern is any sort of disruptive behavior where a student is not showing proper respect to the instructor or other students in the class.  Such behavior will not be tolerated and a student engaged in such behavior will be required to leave the class, forfeiting any points that are associated with that day's activity.  The ability of the student to return to class is determined by the instructor, based on the severity of the disruption, and can range from missing the current class period up to administrative withdrawal from the course.  In addition, charges may be filed with the Office of Judicial Affairs.
• Turn off all electronic devices during class. All electronic devices including cell phones, palm pilots, pagers, calculators, MP3 players, etc. are not allowed during exams or quizzes.  During such activities, these devices are not permitted to be in your possession at all (which means they cannot be clipped to your belt, in your pocket, etc.).  Possession and/or use of these items during an exam or quiz will result in an automatic zero on the graded activity.
• No eating, smoking or drinking in the classrooms.
• Visitors (friends, children, etc.) are strictly prohibited from attending class without the permission of the instructor.

Last update: May 06, 2010