BCH709 Introduction to Bioinformatics: Syllabus BCH709

Course description

As contemporary biologists, we have entered an age where the use of computers in our daily work has become all but essential. The manipulation and analysis of DNA, RNA, and protein data by electronic means has become a routine task. Further, the amount of DNA, RNA and protein sequence data we are putting into databases every day is expanding at a geometric rate, and with coming advances in sequencing technology, this rate is only expected to increase. With all this new data, analysis by individual humans is simply not possible. Thus, in the past 15 years, computational biology has emerged as a field concerned with storage, manipulation, and extraction of valuable information from all this new data. However, because computational biology is an emerging field, organized courses are generally saved for higher-level study, and often are not required parts of an undergraduate curriculum. We seek to fill this void in education and create a course that will introduce students to bioinformatics at an earlier point in their education. This knowledge will prove to be not simply useful, but essential, for any student considering a degree in any area of biology and medical science.

Instructor Information

Instructor: Won C Yim
Office: Howard Medical Scicence Bd. (HMS216)
Phone: 775-682-9447
Email: wyim@unr.edu
Office Hours: Wed, 10:30-noon by appointment on Monday.

Office hours:

by appointment. Wed, 10:30-noon by appointment on Monday

Prerequisites:

BCH 400 or equivalent; two semesters of general biology; BCH 413, 613 or consent of the instructor as pre- or co-requisites. It is STRONGLY recommended that students complete an undergraduate Molecular Biology course (e.g., BCH/BIO 405) prior to enrolling in BCH 709.

Required texts, course materials:

All required text and course materials will be freely available on website.

• Introduction to Bioinformatics (3rd Edition)
• Learn Linux Shell Scripting - Fundamentals of Bash 4.4
• Effective awk Programming, 3rd Edition
• Bioinformatics with Python Cookbook - Second Edition
• Basic Applied Bioinformatics
• Ubuntu Unleashed 2019 Edition: Covering 18.04, 18.10, 19.04, 13/e
• Unix and Perl: Keith Bradnam & Ian Korf
• Other bioinformatics books from knovel
• Other bioinformatics books from Oreilly Note: all reading material can be freely accessed and downloaded from the UNR internet.

Tentative Course Schedules

Unique class procedures /structures:

This course will be taught with the extensive use of terminal, investigation and problem-solving. Students will be using computers in most sessions to analyze data, write/run code, troubleshoot, and discuss.

Student Learning Outcomes:

SLO 1: Through terminal, students will demonstrate the ability to design experimental strategies using state-of-the-art methods/approaches to address biological questions. SLO 2: Through computational work and in-class discussions, students will demonstrate a working understanding of advanced topics in bioinformatics. SLO 3: Through written and oral summaries, students will demonstrate the ability to evaluate the salient points of primary research articles critically. ? SLO 4: Students will demonstrate the ability to summarize and effectively lead discussions of primary research literature.

Grading Criteria, Scale, and Standards:

You will be graded on your participation in class, the leadership of class discussions, and quality of your written assignment and midterm and final exams. Final grades may be adjusted on a sliding scale to ranges lower than those indicated below if appropriate. Students consistently receiving 70% or lower on exams should realize they are in serious difficulty and should seek help from the instructor.

Class Participation:

You are required to attend all scheduled classes (both Tuesdays and Thursdays) regardless of material scheduled. It is your responsibility to notify the instructor if circumstances beyond your control prevent your attendance in any class. Reasonable excuses include family or medical emergencies, legal summons, religious holidays, travel to academic/scientific conferences, etc. Unacceptable excuses include sleeping in, birthdays or anniversaries, leisure activities including travel, conflicts with work, etc. For university policy regarding class absence, see UAM 3,020. Your participation is required for the success of the course and will be graded.

Term Paper:

You will prepare a 4 – 5 pages written “mini-review” of bioinformatics from a list provided by the instructor. Your review will summarize the state-of-the-art in a particular topic area while citing both seminal historical and modern, cutting edge references that have defined major advances in the field. This review should demonstrate your ability to understand and critically review primary literature dealing with advanced topics in bioinformatics.

Exams:

There will be one midterm and one final exam. Both will be written and will use the computer. Each will test your knowledge of material for one half of the course (i.e., the midterm will test the first half of the semester, and the final will test the second half). In addition, the final exam will include a written analysis of bioinformatics.

Course Component Points

• Exams, projects, papers, and the proportion each counts toward the final grade are as follows:

* Attendance and participation in lectures and discussions

Grading policy will be whole letter grade, as follows:

University Policies

Academic dishonesty policy:

Academic dishonesty is against university as well as the system community standards. Academic dishonesty is defined as: cheating, plagiarism or otherwise obtaining grades under false pretenses. Plagiarism is defined as submitting the language, ideas, thoughts or work of another as one’s own; or assisting in the act of plagiarism by allowing one’s work to be used in this fashion. Cheating is defined as l) copying homework assignments, 2) cheating on quizzes or exams including sharing answers with students in other sections of the course, 3) obtaining or providing unauthorized information during an examination through verbal, visual or unauthorized use of books, notes, text and other materials; 4) obtaining or providing information concerning all or part of an examination prior to that examination; 5) taking an examination for another student, or arranging for another person to take an exam in one’s place; 6) altering or changing test answers after submittal for grading, grades after grades have been awarded, or other academic records once these are official, 7) including information in written assignments without proper citations.
Disciplinary procedures for incidents of academic dishonesty may involve both academic action and administrative action for behavior against the campus regulations for student conduct. The procedures involve the determination by the faculty member pursuing concerns over alleged cheating or plagiarism as to whether administrative action is warranted, in addition to making a determination as to any academic consequence. Academic dishonesty will not be tolerated and penalties can include: (1) canceling the student’s enrollment in the class without a grade; (2) filing a final grade of “F”; (3) awarding a failing mark on the test or paper in question; (4) requiring the student to retake the test or resubmit the paper. See the “Student Conduct Information” section of the UNR General Catalog for specific University policies and procedures regarding academic dishonesty. For more details, see http://www.cis.unr.edu/ecatalog/Default.aspx?article_list_id=11076 UNR General Catalog.

Note: all assignments need to be independent work. File sharing, command line sharing will be considered as cheating.

Attendance Policy:

You are required to attend lecture/oral presentation/discussion sessions. If you cannot attend due to circumstances beyond your control, the instructor kindly requests the professional courtesy of being notified of your absence ahead of time. Class participation points will be deducted for each unexcused absence (5 points per class missed without informing the instructor before the class meets). For a full description of UNR’s class attendance policies, please see: “https://www.unr.edu/administrative-manual/3000-3999-students/3020-class-absence-policy.

Plagiarism Policy:

Plagiarism (copying all or part of someone else’s work and passing it off as your own) is a serious form of academic misconduct and will not be tolerated in this class. Plagiarism is defined as submitting the language, ideas, thoughts or work of another as one’s own; or assisting in the act of plagiarism by allowing one’s work to be used in this fashion. “The work of another” does not just mean whole papers or articles copied from another source. It includes any information, ideas, sentences, or phrases that came from somewhere other than your own head (i.e. books, articles, internet sites, videos, documents, lecture notes or handouts from other courses, and any other sources used in your paper). These must be properly acknowledged by providing references either in the text or in a footnote, along with a bibliography giving the complete publication information for all sources used in your paper. Even if you paraphrase someone else’s ideas and do not quote them directly, you still must acknowledge your source. Citations should also be given for little known facts and statistics. Ignorance is not an excuse for plagiarism. If you are not sure whether you need to provide a source for a piece of information or how to cite a source, ask the course instructor.

Students with disabilities statement:

“Any student with a disability needing academic adjustments or accommodations is requested to speak with me or the Disability Resource Center (Pennington Achievement Center Suite 230) as soon as possible to arrange for appropriate accommodations.” This course may leverage 3rd party web/multimedia content, if you experience any issues accessing this content, please notify your instructor.

Academic success services:

The University of Nevada, Reno is committed to providing a safe learning and work environment for all. If you believe you have experienced discrimination, sexual harassment, sexual assault, domestic/dating violence, or stalking, whether on or off campus or need information related to immigration concerns, please contact the University’s Equal Opportunity & Title IX office at 775-784-1547. Resources and interim measures are available to assist you. For more information, please visit: https://www.unr.edu/equal-opportunity-title-ix Your student fees cover the usage of the University Math Center (http://www.unr.edu/math-center) (775) 784-4433, University Tutoring Center (http://www.unr.edu/tutoring-center) (775) 784-6801, and University University Writing Center (http://www.unr.edu/writing-center) (775) 784-6030. These centers support your classroom learning; it is your responsibility to take advantage of their services. Keep in mind that seeking help outside of class is the sign of a responsible and successful student.

Statement on audio and video recording:

Surreptitious or covert videotaping of class or unauthorized audio recording of class is prohibited by law and by Board of Regents policy. This class may be videotaped or audio recorded only with the written permission of the instructor. In order to accommodate students with disabilities, some students may have been given permission to record class lectures and discussions. Therefore, students should understand that their comments during class might be recorded.

Statement on Equal Opportunity (Title IX) and Sexual Harassment:

“The University of Nevada, Reno is committed to providing a safe learning and work environment for all. If you believe you have experienced discrimination, sexual harassment, sexual assault, domestic/dating violence, or stalking, whether on or off campus or need information related to immigration concerns, please contact the University’s Equal Opportunity & Title IX office at 775-784-1547. Resources and interim measures are available to assist you. For more information, please visit the Equal Opportunity and Title IX page.”

Statement on Cultural Diversity:

The University of Nevada, Reno is committed to providing a safe learning and work environment for all. If you are an individual person from an underprivileged or culturally diverse background and you believe you have experienced discrimination, whether on or off campus, please contact please contact Title IX Coordinator at 784-1547. Resources and interim measures involving classes and/or residential life are available to assist you. For more information, please visit: http://www.unr.edu/equal-opportunity-title-ix. Students, staff, and faculty members should be aware that there can often be obstacles associated with cultural diversity. To counteract or overcome these obstacles, all should become self-aware of your personal cultural biases.

The website theme was adapted from the original by Data Carpentry. The infrastructure, including adventure-time and docker-browser-server, was built by @maxogden and @mafintosh. The setup of this app was based on the get-data adventure. This adventure app was made by Richard Smith-Unna. The lecture materials were crafted by Won Yim. This work is licensed under a Creative Commons 4.0 International License.