CS-327: Computational Methods in Biology

CS-327-1: Computational Methods in Biology
College of Arts & Sciences Syllabus
Spring 2020
Course Information
Credit Hours:
3.0
Course Description:
Bioinformatics is the discipline that applies mathematics, statistics, computer science, chemistry, and biology to solving problems in biology using biological data sets. The problems investigated are usually at the molecular level. These problems include sequence alignment, genome assembly, models of evolution and phylogenetic trees, analyzing gene expression data, and gene linkage analysis. One of the most important statistical tools used in bioinformatics is the Bayesian network. This course introduces the techniques used in bioinformatics, in particular Bayesian networks, and provides solutions to several bioinformatics problems.
Prerequisites:
CS-201 or MATH-251 (A grade of C or higher is required), BIO-100 or BIO-201 (A grade of C or higher is required), CS-200 (A grade of C or higher is required)
Class Time:
Monday/Wednesday 4:15 p.m. - 5:30 p.m.
Class Location:
LWH 2054

Faculty Information
Instructor:
Rachel Trana
Office Location:
LWH 3036
Office Hours:
Mondays/Wednesdays: 5:45 p.m. - 6:45 p.m.
Thursdays: 1:00 p.m. - 3:00 p.m.
Phone Extension:
773.442.4723
Email:
r-trana@neiu.edu
Per university policy, grades may not be discussed via email.
All course related questions should be posted on the Piazza discussion forum.

Course Materials
Required Text:
Introduction to Bioinformatics (5e Edition) by Arthur Lesk, Oxford University Press, ISBN-13: 9780198794141
Supplemental Materials:
As this is an interdisciplinary course, materials will be taken from a variety of sources. Students can reference the additional resource below.

Python 3 Object-Oriented Programming by Dusty Phillips. Packt Publishing, 2018. ISBN-13: 978-1789615852
Websites:
Grades, Homework Submissions: D2L
Discussion Forum: Piazza
Course Lectures, Study Guides, Homework Assignments, Schedule: http://racheltrana.com/includes/classes/327.php

Course Objectives / Student Learning Outcomes
Upon completing CS-327: Computational Methods in Biology, students will be able to do the following:
  • Apply computer science principles to solving problems in biology.
  • Investigate some of the algorithmic ideas, such as dynamic programming and graph theory, that are fundamental to an understanding of modern biology.
  • Prepare students to work in the interdisciplinary area of recent advances in high-performance computing and biology, especially with the massive information resources of the human genome.
  • Increase computational literacy.
  • Understand the principles and some methods of genomics, gene expression and proteomics that aid precision medicine, modern plant and animal breeding.
  • Work with large, complicated datasets that once took researchers years to manually analyze.

Major Topics
  • Introduction to Molecular Biology
  • Introduction to Python
  • Genome Replication: Transcription, Translation • Sequencing Antibiotics
  • Genome Alignment
  • Genomic Data: Genome databases
  • Genome Rearrangements
  • Climate Change

Student Tasks / Assignments / Requirements
Attendance:
Attendance is mandatory. More than six (6) absences will result in an automatic F in the course.
Assignments:
Homework will be assigned weekly, posted online. While working on homework assignments with other students is encouraged, plagiarism is not tolerated. All work should be unique. Students that submit duplicate/identical work will receive an F for that homework assignment. All assignments must be submitted to D2L by the specified due date and time.
Quizzes:
There will be multiple online (D2L) open-book quizzes throughout the semester, designed to reinforce core concepts. These quizzes must be completed by the specified due date and time.
Exams:
There will be two in-class exams, each worth 25% of the final grade. If you are unable to attend an exam due to a religious observance or significant major event, you must notify your professor at least 3 weeks in advance of the exam in order to schedule a make-up exam (approval of a make-up exam is at the discretion of the course instructor). Failure to do so will result in an F for that exam. Exams are closed-book and closed-notes. Access to any digital devices is prohibited.
Requirements for graduate students:
In addition to completing homework assignments, taking the exams and completing the final project, graduate students will be required to turn in a term paper along with their final project (in addition to the write-up). All work must be unique. Students that plagiarize on their term paper will receive an F for the project. The term paper will be worth 5% of the final project grade.
Final Project:
A final project will be assigned and is worth 15% of the final grade. This final project will incorporate at least one of the topics presented in class.
Grading Policies and Formulae:
Item Weight
Homework 20%
Quizzes 15%
Exams 50%
Final Project 15%
Percentage Letter Grade
90 - 100 % A
80 - 89.99999999 % B
70 - 79.99999999 % C
50 - 69.99999999 % D
< 50 % F

Course Policies and Statements
Absence Policy:
Attendance is mandatory. More than six (6) absences will result in an automatic F in the course.
Cheating:
Cheating is a serious academic offense and violates the NEIU Student Code of Conduct (see University Policies below). All students will be required to turn off their electronic devices (phone, smart watches, etc) at the beginning of each exam. Failure to do so and/or any involvement in or suspicion of cheating will result in a failing grade for the final exam (and the course). Additionally, students involved in cheating will be reported for academic misconduct to the Dean of Students (two reports can result in expulsion from the university).
General Policies:
  • Because quizzes are online and open-book/note, no make-up quizzes will be given.
  • You must bring your NEIU ID to each exam, including the final exam.
  • The use of cell phones during class time for non-class or non-emergency purposes is not allowed.
  • There will be NO extra credit projects given to improve individual grades.
  • Cheating and/or plagiarism will not be tolerated. Students that violate the NEIU academic conduct policy may be subject to an F for that assignment, quiz, exam, project or any portion (or all) of the final course grade
  • Policies may be modified or added as I deem appropriate/necessary.
Important Dates:
  • Monday, January 20th, 2020 - Martin Luther King, Jr. Birthday - No Classes
  • Wednesday, February 12th, 2020 - Lincoln's Birthday - No Classes
  • Monday, March 16th - Sunday, March 22nd, 2020 - Spring Recess - No Classes
  • Friday, March 27th - Last day to drop with a W

University Policies and Statements
Academic Integrity Policy:
By enrolling in this course, you are bound by the NEIU Student Code of Conduct. You will be informed by your instructor of any additional policy specific to your course regarding plagiarism, class disruptions, etc.
ADA Statement:
Northeastern Illinois University (NEIU) complies with the Americans with Disabilities Act (ADA) in making reasonable accommodations for qualified students with disabilities. To request accommodations, students with special needs should make arrangements with the Student Disability Services (SDS) office, located on the main campus in room D104. Contact SDS via (773) 442-4595 or email sds@neiu.edu. It is your responsibility to have the Accessibility Center send me this information by the 3rd week of the semester.
Campus Safety:
Web links to Campus Safety: Emergency Procedures and Safety Information can be found on NEIUport on the MyNEIU tab or as follows: https://www.neiu.edu/university-life/university-police.