Fall 2017

Send Me an Email with BIOINFORMATICS as the subject.  I will build my class email list these emails.  DO IT NOW.

TTh 9:30-10:50 Bolin Science Hall 103 on mondays and 312 on wednesdays

Instructor: Richard P. Simpson, Bolin 126E; Tel.: 397-4191; E-Mail:

Textbook and Web Sites for Study

Text:    An Introduction to Bioinformatics Algorithms,by Neil C. Jones, Pavel A. Pevzner, Pavel Pevzner (ppts)

Supplementary Text:Algorithms in Bioinformatics, A practical Introduction , Wing-Kin Sung (ppts)

Supplementary Online Text: Python for Informatics by Charles Severance,Charles Severance Videos etc 

 SOFTWARE Support: Biopython

General: This course is designed to utilize Python and associated libraries to address the needs of Bioinformatics.  There are many algorithms that are used to process the long strings of DNA that are commonly generated by Bio-research labs.  We will start the course with a rapid review of Python and then follow this with necessary Biological information associated with DNA. In other words this course will mainly be about DNA sequence processing and analysis.   We will using information from all of the above books as needed

Several programs will be given this semester that will require the implementation of suitable algorithms for certain DNA processing problems.  These will be written in Python 3.4 and we will use BioPython as a library support.

Additional Material:   Several USB drives will be necessary for saving lab projects to turn in.  You are also responsible for keeping backups of all projects until the end of the semester. If I ask you the end of the semester for a copy and you do not have it you will get no credit.  Keeping regular backups is one of the most important things a student of computing must learn to do.

Academic Policies:  Students should refer to the current MSU Student Handbook and Activities Calendar  and the MSU Undergraduate Bulletin for university policies on academic dishonesty, class attendance, student rights and activities. (See “MSU 2009-2010 Student Handbook”, Section VI: Code of Student Conduct, Standards of Conduct,Subsection 11, p. 71 which can be found at http: //   I consider even looking an another students program as being dishonest! Continuing by taken a section of their code and using it in your program is even worse.

Disability Policy:  In accordance with the law, MSU provides academic accommodations to students with documented disabilities.  Students with disabilities must be registered with Disability Support Services before classroom accommodations can be provided.  The DSS office is located in Clark Student Center, Room 168, phone 397-4140.

Counseling Center:  MSU offers personal, group, career, and academic counseling.  Students are encouraged to take advantage of these free services by contacting the Counseling Center: Room 108 Clark Student Center, 397-4618,

Course Content: The material includes online text reading assignments, lectures, videos, and projects.  Students are responsible for all material regardless of attendance.

Electronic Devices: ALL electronic devices must be stored in a bag or pocket, etc. and may not be on the desk or out during class. This includes cell phones, iPods, and any other device that might be a distraction to you, your classmates, or the instructor. If you wish to use a laptop for taking notes ( not browsing the web ) that will be OK if you clear it we me first.  Failure to adhere to this policy may result in being removed from the class.

Late Policy:  Projects will be accepted late up to one week after the due date with a penalty of 10%.  Homework will not be accepted late.

Exams:There will be 3 exams and a final.  The three exams will be 40 %  and the final is 20 %.  Projects, quizzes and homework will be 40%

Homework: All home work must be typed with your name in the upper left hand corner of the page and the Homework number and name in the upper right.   Turn in at the BEGINNING of class for credit.  No late homework will be accepted! Copied homework will receive a 0.  Do your own work.  If you have questions see me.

Programs: All programs need to be turned in within an envelope with your name and project number on the front.  Copied projects will receive a 0 as well.  All programs need to be carefully documented and properly formatted.

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