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Topics in Computational Science: Bioinformatics

Course Details

Course Number
Section Number
Fall 2017
Bolin Hall
Classroom Number
Days & Times

MW 1:00 pm - 2:20 pm

Richard P. Simpson (view Profile)

Course Attachments


Course Objectives

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

Course Expectations

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.

Grading Standards

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%

Final Exam 12/11/2017 3:30 pm- 5:30 pm
Submission Format Policy Note: You may not submit a paper for a grade in this class that already has been (or will be) submitted for a grade in another course, unless you obtain the explicit written permission of me and the other instructor involved in advance.
Late Paper 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.

Plagiarism Policy

Plagiarism is the use of someone else's thoughts, words, ideas, or lines of argument in your own work without appropriate documentation (a parenthetical citation at the end and a listing in "Works Cited")-whether you use that material in a quote, paraphrase, or summary. It is a theft of intellectual property and will not be tolerated, whether intentional or not.

Student Honor Creed

As an MSU Student, I pledge not to lie, cheat, steal, or help anyone else do so."

As students at MSU, we recognize that any great society must be composed of empowered, responsible citizens. We also recognize universities play an important role in helping mold these responsible citizens. We believe students themselves play an important part in developing responsible citizenship by maintaining a community where integrity and honorable character are the norm, not the exception.

Thus, We, the Students of Midwestern State University, resolve to uphold the honor of the University by affirming our commitment to complete academic honesty. We resolve not only to be honest but also to hold our peers accountable for complete honesty in all university matters.

We consider it dishonest to ask for, give, or receive help in examinations or quizzes, to use any unauthorized material in examinations, or to present, as one's own, work or ideas which are not entirely one's own. We recognize that any instructor has the right to expect that all student work is honest, original work. We accept and acknowledge that responsibility for lying, cheating, stealing, plagiarism, and other forms of academic dishonesty fundamentally rests within each individual student.

We expect of ourselves academic integrity, personal professionalism, and ethical character. We appreciate steps taken by University officials to protect the honor of the University against any who would disgrace the MSU student body by violating the spirit of this creed.

Written and adopted by the 2002-2003 MSU Student Senate.

Students with Disabilities

The Americans with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Disability Support Services in Room 168 of the Clark Student Center, (940) 397-4140.

Safe Zones Statement

The professor considers this classroom to be a place where you will be treated with respect as a human being - regardless of gender, race, ethnicity, national origin, religious affiliation, sexual orientation, political beliefs, age, or ability. Additionally, diversity of thought is appreciated and encouraged, provided you can agree to disagree. It is the professor's expectation that ALL students consider the classroom a safe environment.

Contacting your Instructor

All instructors in the Department have voicemail in their offices and MWSU e-mail addresses. Make sure you add your instructor's phone number and e-mail address to both email and cell phone lists of contacts.

Attendance Requirements

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.

Writing Proficiency Requirement

All students seeking a Bachelor's degree from Midwestern State University must satisfy a writing proficiency requirement once they've 1) passed the 6 hours of Communication Core and and 2) earned 60 hours. You may meet this requirement by passing either the Writing Proficiency Exam or English 2113. Please keep in mind that, once you've earned over 90 hours, you lose the opportunity to take the $25 exam and have no option but to enroll in the three-credit hour course. If you have any questions about the exam, visit the Writing Proficiency Office website at, or call 397-4131.

Campus Carry

Senate Bill 11 passed by the 84th Texas Legislature allows licensed handgun holders to carry concealed handguns on campus, effective August 1, 2016. Areas excluded from concealed carry are appropriately marked, in accordance with state law. For more information regarding campus carry, please refer to the University’s webpage at

If you have questions or concerns, please contact MSU Chief of Police Patrick Coggins at