BCH709 Introduction to Bioinformatics: 1_Orientation

The philosophy of ‘BCH709 Introduction to Bioinformatics’ is to teach researchers basic concepts, skills, and tools for working with data so that student can get their own bioinformatics work done without pain. This illustrates the concept of bioinformatics analysis and Next Generation Sequencing for genomics including hands-on bioinformatics, understanding genomics through bioinformatics, use of command-line in multiple platforms, use of command-line tools to analyze sequencing data, and connecting to and using cloud computing.

Class Schedule

MonWed 9:00AM - 10:15AM
Aug 24, 2020 - Dec 18 2020

Modes of Instruction

Response to COVID-19, BCH709 will offer Alternative HyFlex course model.

Alternative HyFlex: Course originally scheduled to be delivered in-person, but will have attendance adjustments so students will alternate in-person and remote participation. Students will receive communication directly from their instructors with specifics. Fully remotely participation by students can be accommodated for those with extenuating circumstances.

In addition, we will provide recorded video for everyone.

Class Room location

Classroom is located at Fleischmann Agriculture Building room 234 (FA234)

FA234

Class Room location

Alternative participate via Zoom Join Zoom Meeting Zoom link Meeting ID: 631 461 1123 Passcode: 709 One tap mobile +16699006833,,6314611123# US (San Jose) +12532158782,,6314611123# US (Tacoma)

Prerequisites

• Computer with ethernet port or wifi (If in case you bring your desktop, please do not bring your monitor. we have a monitor in our classroom) Online introduction to Linux. Students must complete one of the following online tutorials (or both) before class begins.
• UNR affilated email <ID>@unr.edu or <ID>@nevada.unr.edu - How to Activate
• Please fill this form
• Please apply your Pronghorn account here ; Please follow this instrunction
• Setup your computer
• Setup Slack ID
• Please register datacamp

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.

Tentative Course Schedules

Optional Additional Meeting

Research Computing Hackathon (Hosted by HPC team)

Every Friday at 2:00pm to 4:00pm through SLACK

Hackathons provide a space for hands-on training and solution development within a Research Computing environment at the University. This is also a place to get clarification on questions/concerns regarding the HPC environment. Please bring problems to challenge the HPC team, the Office of Information Technology, and research colleagues. If you don’t need help, we still encourage you to attend and share your time and expertise with those in need of assistance. You don’t need to be an expert to attend a hackathon. Individuals at all computing skill levels are welcome! Won Yim will attend this hackathon.

Meeting

Office Howard Medical Science 216
I prefer to have online meeting through SLACK.

Optional Reading materials

• 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.

Other Website

Command line website
Plant Genomics Lab

Frequently Asked Questions

Read our FAQ. Currently, this page is empty, but we will build it through the class.

Teaching Platform

This workshop is designed to be run on Unix-base system such as Ubuntu, mac, etc. All the software and data used in the class will be open source. All example data will be hosted on a Google Cloud Service. If you want to know how to use Unix-base system on your computer, please follow the directions in the Setup tab.

Course Requirements

1.	Students are required to attend all scheduled classes (both Monday and Wednesday) or required to watch online recorded material until class scheduled Friday noon.

2.	Complete assignments (including in bioinformatics exercises) associated with course objectives.

3.	Prepare a Term paper, 4 – 5 pages written “mini-review” of bioinformatics from a list provided by the instructor. Our 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.

4.	Participate in the exam. 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. Both exams will have three days period to complete. More information can be found in the WebCampus course section

Grading and grading policy

Points will be distributed as follows:

Within each category above, the grading scale will be:

Late Work / Make-up Exams / Participation Policies

A penalty of 10 % per day will be imposed on a pro rata basis for any late work or attendance. You will be graded on the quality of the assignments listed below and the quality and quantity of your participation in class discussions. Final grades may be adjusted at the discretion of the instructor.

No make-up exams allowed. If you cannot finish exam due to circumstances beyond your control, the instructor kindly requests the professional courtesy of being notified of your absence ahead of time. Email only

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.” Email only

Attendance

You are required to attend lecture/online 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. (Dr’s notes etcs). Email only.

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.