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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Spring 2020

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Announcements

  • Biology Department Senior Party: Friday, February 21, 5:00-7:00pm, the Bird's Nest

Upcoming Seminars

  • Environmental Lecture Series: Tuesday, January 28, 4:30-5:30pm, McIntosh Center (UH 3999), Dr. Bemmy Maharramli, UCI, Your Ecosystem Disservice is My Ecosystem Service: Narratives of Nature in Cities
  • Biology Department Seminar: Friday, January 31, 2:00pm, LSB Auditorium, Mary Everette, Gulls of Appledore Research Group, Trash Birds": How and Why Gulls Thrive (or Die)
  • Biology Department Seminar: Friday, February 7, 2:00pm, LSB Auditorium, Dr. Eric Strauss, LMU Biology and Center for Urban Resilience, Coyotes in Your Back Yard: Understanding the Ecology of an Urbanized Predator
    • Darwin's Birthday Chili Cook-off immediately following the seminar from 3:00-5:00pm in the LSB kitchen and terrace!
      • Prizes awarded for best chili for carnivores (best meat chili), best chili for herbivores (best veggie chili), and best chili for omnivores (best overall chili). Make some chili or just come taste and vote for the winners.
  • Bioethics Lecture: Tuesday, February 11, 7:00pm, LSB Auditorium, Three 20-minute lectures by Dr. Roberto Dell'Oro (LMU Bioethics), Jennifer Gumer (Health law attorney), Cesare Romano (Legal expert), moderated by Dr. Nicholas Brown (LMU Bioethics), The Ethics of Germline Modification
  • Biology Department Seminar: Friday, February 21, 2:00pm, LSB Auditorium, Dr. Melania Abrahamian, UCLA, The novel mitochondrial RNA transport pathway
  • Seaver Spotlight: Thursday, February 27, 5:30-7:30pm, LSB Auditorium, Steve Isakowitz, President and CEO, The Aerospace Corporation
  • Biology Department Seminar: Friday, March 20, 2:00pm, LSB Auditorium, Dr. Deepa Dabir, LMU Biology, Aim32 is a new [2Fe-2S] protein that facilitates mitochondrial redox quality control
  • LMU Undergraduate Research Symposium: Saturday, March 21, all day, various locations in University Hall
    • You may earn up to two seminars worth of extra credit by doing the following:
    • Attending one Biology-themed oral session (minimum 1 hour)
    • Attending the Biology poster session and talking to the students at 5 different posters
    • You could attend two oral sessions, one poster session and one oral session, or two posters sessions (i.e., talking to students at 10 posters).
    • If you are presenting in a session, you cannot use your own session as extra credit.
  • Biology Department Seminar: Friday, March 27, 2:00pm, LSB Auditorium, Prashant Bhat, California Institute of Technology, Determining the function and mechanism of the MALAT1 long non-coding RNA in co-transcriptional splicing
  • Biology Department Seminar: Friday, April 3, 2:00pm, LSB Auditorium, Dr. Graciel Diamante, UCLA, Assessing the developmental effects of endocrine disrupting compounds
  • Biology Department Seminar: Friday, April 17, 2:00pm, LSB Auditorium, Dr. Shayna Sura, UCLA, Anthropogenic impacts on top down and bottom up processes affect coral reef resilience

Schedule

Updates to the schedule will be posted here. Readings need to be completed in preparation for class. Readings or slides that cannot be posted here due to copyright restrictions will be posted on Brightspace.

Week Date Reading Topic Assignment
1 Jan 16 Peter Denning Voices of Computing and Computing is a Natural Science, Chapter 1 of On Becoming a Biologist by John Janovy, Jr. on Brightspace
  • Syllabus & Academic Honesty discussion
  • Introduction to Bioinformatics
  • Introduction to the OpenWetWare Wiki
  • Jan. 17: Last day to add or drop a class without a grade of W
Week 1 Assignment

Due 12:01 AM 1/23

Class Journal Week 1

2 Jan 23 Molecular Genetics Explorer Protocols listed on the Week 2 Assignment page, Schnell (2015)
  • What is a model? Activity and discussion
  • Molecular Genetics Explorer (Aipotu)
Week 2 Assignment

Due 12:01 AM 1/30

Class Journal Week 2

3 Jan 30 Cohen et al. (2008) review; Exploring HIV Evolution Handout;
  • Begin HIV Evolution Project
Week 3 Assignment

Due 12:01 AM 2/6

Class Journal Week 3

4 Feb 6 Markham et al. (1998)
  • Journal Club 1
  • HIV Evolution Project
Week 4 Assignment

Due 12:01 AM Feb 13

Class Journal Week 4

5 Feb 13
  • HIV Evolution Project
Week 5 Assignment

Due 12:01 AM 2/20

Class Journal Week 5

6 Feb 20
  • HIV Evolution Project
Week 6 Assignment

Due 12:01 AM 2/27

Class Journal Week 6

7 Feb 27 No Week 7 Assignment
8 Mar 5
  • Searching the scientific literature
Week 8 Assignment

Due 12:01 AM 3/19

Class Journal Week 8

Mar 12 Spring Break
9 Mar 19

Rigden & Fernández (2020) "NAR Database issue", DataONE: Why Data Management, DataONE: Data Sharing

  • Biological Databases
  • Mar. 20: Last day to withdraw or apply for credit/no credit grading
Week 9 Assignment

Due 12:01 AM 3/26

Class Journal Week 9

10 Mar 26 Week 10 Assignment

Due 12:01 AM 4/2

Class Journal Week 10

11 Apr 2 No Week 11/12 Assignment
12 Apr 9

Easter Break

No Week 11/12 Assignment


13 Apr 16
  • HIV Structure Project
Week 13 Assignment

Due 12:01 AM 4/23

Class Journal Week 13

14 Apr 23
  • HIV Structure Project
  • Course Evaluations
Week 14 Assignment

Due 12:01 AM 4/30

Class Journal Week 14

15 Apr 30

Course Information

BIOL 368-01: Bioinformatics Laboratory, 1 credit hour

Instructor

  • Kam D. Dahlquist, Ph.D.
    • Phone: (310) 338-7697
    • Email Dr. Dahlquist through OpenWetWare (Messages sent to me at night or on the weekend will be answered the next school day.)
    • Office: Life Sciences Building 289
    • Office hours: Mondays, Tuesdays, and Wednesdays, 10:00 - 11:00 AM and by appointment (send me an e-mail or sign up for a time on the sheet on my office door)

Teaching Assistant

Prerequisites/Recommended Background

Biology 111 (General Biology I Lab), Biology 112 (General Biology II Lab), Biology 202 (Genetics), Chemistry 220 (Organic Chemistry I)

Class Meetings & Attendance

Thursdays 1:00 – 4:50 PM, Seaver 120

This is a hands-on laboratory course, thus attendance at all class meetings is required. This class meets continuously between 1:00 PM and 4:50 PM and will rarely, if ever, "get out early". An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructor should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Mutual Responsibilities

This course is designed to foster your development as a scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructor is to provide the expert coaching to support and assist you on your journey. All of the laboratory exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

Classroom and Laboratory Environment

We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:

  1. As an LMU Lion, by the Lion’s code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students.
  2. You are responsible for your own learning and for being a good class citizen.
  3. Class will start promptly on time.
  4. You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.
  5. You are expected to bring the required materials to each class session.
  6. Cell phones and other ancillary electronic devices must be turned off and put away out of sight. Your own laptop and/or tablet may be used to conduct the class exercises, provided that you have confirmed with the instructor that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets are being used for other purposes and become distracting to you or others, you will be asked to put them away.
  7. After signing a Laboratory Access Authorization Form and gaining approval, students will be granted One card access to Seaver 120 so that they may use the computers to complete homework and projects when the lab is not open.
    • Students will be able to access Seaver 120 whenever the Seaver building is open.
    • Students shall not work alone in the laboratory outside of standard business hours.
  8. All students are governed by LMU Community Standards publication. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code.
  9. Students will be authorized for access to Seaver 120 outside of standard business hours (Monday through Friday, 8:00 AM - 5:00 PM, excluding University holidays) to complete assignments on the lab computers, as long as the Seaver building is open. Students may not work alone in the lab outside of standard business hours.

Course Web Site

This is the course web site. You will need to register with OpenWetWare.org to be able to edit the wiki and complete coursework. I will post updates to the course schedule and electronic copies of all handouts, assignments, and readings on this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in BIOL 368 on Brightspace. Brightspace will be used for materials that cannot be made public on the OpenWetWare.org wiki and to post grades.

E-mail Communication

At times I will communicate with the entire class using campus e-mail systems, so it is essential that you regularly check your lion.lmu.edu e-mail address or forward your lion account e-mail to your preferred e-mail address. Messages sent to the instructor at night or on the weekend will be answered the next school day.

Required Materials

Lab Fee

  • There is a $50 lab fee associated with this course.

Texts

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on this wiki or Brightspace site. Specific reading assignments are given on the course schedule and should be completed before coming to class.

  • Assorted handouts, articles, protocols, and data will be distributed throughout the semester.
  • Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

Materials (must be brought to each class meeting)

  • 3-ring binder with all course handouts
  • Pen, pencil, extra paper
  • USB flash drive to store bioinformatics data

Course Description

Bioinformatics is the application of information technology (informatics) to biological data. Informatics is the representation, organization, manipulation, distribution, maintenance, and use of digital information. When applied to biological data, informatics provides databases and analytical tools for answering biological questions. Bioinformatics is inherently interdisciplinary, involving aspects of biology, computer science, mathematics, physics, and chemistry. While computers have been used to analyze biological data since their invention, the need for computational methods has recently exploded due to the huge amounts of data produced by genome sequencing projects and other high-throughput technologies. Bioinformatics techniques are being used to move the field of biology from a “one gene at a time” approach, to the analysis of whole systems. In this course, students will learn current bioinformatics techniques to address systems-level biological questions. Topics include sequence alignment and phylogeny, protein structural biology, and the analysis of DNA microarray data.

Course Objectives and Learning Outcomes

  • To gain foundational knowledge about molecular evolution, protein structure, and gene expression.
  • To show discipline and proficiency in day-to-day science and engineering best practices that facilitate reproducible research, such as maintaining journals and notebooks, and managing your files and code.
  • To gain computer, data, and information literacy skills.
  • To find and use scholarly and discipline-specific professional information from the literature and biological databases, differentiate between source types, and evaluate resources for reliability, validity, accuracy, authority, and bias.
  • To properly cite and acknowledge sources.
  • To ask your own biological questions and answer them with the appropriate bioinformatics tools and techniques.
  • To read and critically evaluate the primary scientific literature.
  • To give effective scientific presentations.
  • To recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves.
  • To be confident in "leaving your comfort zone", flourishing outside of it, and learning more about bioinformatics on your own.

University Core Curriculum

This course fulfills the following requirements in the University Core Curriculum:

  • Upper Division Information Literacy Flag
  • Upper Division Oral Communication Flag

Course Work & Grading

Your work in this course will be assessed in these areas:

Individual electronic laboratory notebook/journal assignments          110 points
Shared journal assignments                                              33 points
Journal club and research project presentations                        157 points 
Total                                                                  300 points

Grades will be posted on Brightspace.

Final course grading scale

94.0-100%		A
90.0-93.9%		A-
86.0-89.9%		B+
82.0-85.9%		B
78.0-81.9%		B-
74.0-77.9%		C+
70.0-73.9%		C
67.0-69.9%		C-
60.0-66.9%		D
≤ 59.9%                 F

Electronic Lab Notebook/Journal Assignments

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. The bioinformatics equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice the documentation skills needed by users of bioinformatics tools by keeping an electronic lab notebook or journal. The technology we will use is this public MediaWiki site hosted by OpenWetWare.org, that we will create and edit during the semester. You will create an individual user page and make weekly individual and shared entries that the instructor will read and grade. The following guidelines apply:

  • Your weekly journal entry is typically due every week at 12:01 AM on Thursday Pacific time (Wednesday night/Thursday morning); consult the schedule for specific due dates for each assignment.
    • Late journal entries will be accepted up to one week later for up to half credit.
    • Here are instructions for what to do in the event that there is an OpenWetWare outage near a deadline.
  • Each weekly assignment has an individual component and a shared component. You will typically earn 10 points per weekly submission for the individual journal entry and 3 points per submission for the shared journal entry.
  • You will be assigned to work with other students in pairs, threes or fours, depending on the assignment or project. You will be expected to consult with your partner(s), in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).
  • The instructor and/or TA will read and comment on how to improve your journal entries on your User Talk page.
  • Generally, your individual journal entries will consist of:
    • Invocation of your individual template (see Week 1 assignment for more details)
    • Purpose: a statement of the scientific (not learning) purpose of the assignment.
    • Combined Methods/Results: documentation of your workflow for hands-on exercises and projects. It should include:
      • The protocol you followed in enough detail for someone else to be able to conduct the same investigation.
      • Answers to any specific questions posed in the exercise
      • Screenshots and images as appropriate
      • Data and files: links to all data and files used and generated
    • Scientific Conclusion: a summary statement of the main result of exercise/research
    • Acknowledgments section (see Week 1 assignment for more details)
    • References section (see Week 1 assignment for more details)
  • Generally, your shared journal entry (on a separate class page) will include a reflection on your learning, assigned readings, or ethics case studies.

Oral Presentations

Each bioinformatics project in the course will begin with a "Journal Club" where students will present and lead discussion of research articles from the primary literature. The final step in the scientific method is communication of the results to the scientific community. In bioinformatics, the communication takes place in the form of peer-reviewed papers, presentations and posters at conferences, and through websites. To build your scientific communication skills, you will give an oral research presentation for each of the bioinformatics projects assigned in the course. Because that day’s class content is dependent upon each student being ready to present and lead discussion, late presentations will not be accepted. An unexcused absence from a class on presentation day will result in a grade of zero for the presentation.

Extra Credit

Students may accumulate up to 2.5% of their final grade in extra credit by attending Biology Department seminars and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology Department seminars may be approved in advance for extra credit at the instructor’s discretion. To receive credit for these seminars, you must turn in a one-page hard copy of your summary of the seminar in class, within one week of the date of the seminar or they will not count as extra credit.

Work Load Expectations

In line with LMU’s Credit Hour Policy (LMU’s Credit Hour Policy), the work load expectation for this course is that for every unit of course credit, you will complete a minimum of two hours of out-of-class student work each week. This is a 1-unit course. Thus, the expectation is that you will complete 2 hours of studying outside of class per week.

University Policy on Academic Honesty

Loyola Marymount University is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences. The minimum penalty for an instance of academic dishonesty in this course, even on a 1-point assignment or extra credit assignment, is a one-letter grade penalty in the course and a zero on the assignment. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

You are required to sign the Academic Honesty Agreement for this course.

Academic Honesty Resources

Americans with Disabilities Act - Special Accommodations

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit http://www.lmu.edu/dss for additional information. In addition, please schedule an appointment with the instructor early in the semester to discuss any accommodations for this course for which you have been approved.

Health and Wellness

There are many resources for student wellness on campus. A central website for students is: http://lionwellness.lmu.edu.

Emergency Preparedness

To report an emergency or suspicious activity, contact the LMU Department of Public Safety by phone (x222 or 310-338-2894) or at the nearest emergency call box. In the event of an evacuation, follow the evacuation signage throughout the building to the designated safe refuge area where you will receive further instruction from Public Safety or a Building Captain. For more safety information and preparedness tips, visit http://www.lmu.edu/emergency.

Revision Notice

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this course web site at http://www.openwetware.org/wiki/BIOL368/S20.