BIOL368/F20

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Fall 2020

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Announcements

Upcoming Seminars

  • iSTEM Lightning Talk: Thursday, November 19, 2020; 5:30 p.m.-6:30 p.m., Value of Jesuit Education for STEM, RSVP here.
  • Asynchronous extra credit webinars: select a seminar to watch from the iBioSeminar Series.
    • The video must be a minimum of 50 minutes long to count. Videos are broken up into parts, so you may need to watch two or more parts to reach 50 minutes.
    • You must watch/listen to the entire seminar from start to finish.
    • You must turn in via e-mail, a one-page, double-spaced summary of the seminar, including the title and URL of the seminar.
    • You may receive extra credit for a total of five seminars only, i.e., the total of synchronous and asynchronous online seminars you attended cannot exceed five.
  • All asynchronous webinar write-ups are due by the last day of classes, Friday, December 11, 5:00 PM.

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 Before Class Reading During Class Topic After Class Assignment
1 Sept 3
  • Introductions
  • Syllabus & Academic Honesty discussion
  • What is Bioinformatics?
  • How to Wiki
  • Sept. 4: Last day to add or drop a class without a grade of W
Week 1 Assignment

Class journal due 12:01 AM 9/10

Individual journal due 5:00 PM 9/11

Class Journal Week 1

Academic Honesty Agreement (submit via e-mail)

2 Sept 10 Peter Denning Voices of Computing and Computing is a Natural Science, Chapter 1 of On Becoming a Biologist by John Janovy, Jr. on Brightspace Week 2 Assignment

Due 12:01 AM 9/17

Class Journal Week 2

3 Sept 17 The SIR Model; Giordano et al. (2020) Modelling the COVID-19 epidemic and implementation of population-wide interventions in Italy; Schnell (2015) Ten Simple Rules for a Computational Biologist’s Laboratory Notebook; Epstein(2008) Why model? Week 3 Assignment

Due 12:01 AM 9/24

Class Journal Week 3

4 Sept 24 Wan, et al. (2020). Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus.
  • Graph of the Day
  • Journal Club 1
  • Begin coronavirus research project 1
  • Phylogenetic trees
Week 4 Assignment

Due 12:01 AM 10/1

Class Journal Week 4

5 Oct 1
  • Graph of the Day
  • Coronavirus Research Project 1
  • Protein Structure Viewers
Week 5 Assignment

Due 12:01 AM 10/8

Class Journal Week 5

6 Oct 8
  • Graph of the Day
  • Coronavirus Research Project 1
Week 6 Assignment

Due 12:01 AM 10/15

Class Journal Week 6

7 Oct 15 Week 7 Assignment

Due 12:01 AM 10/22

Class Journal Week 7

8 Oct 22 Bodenreider & Stevens (2006); Aspinall (2005); Noble (2012); Noble (2018) Chapter 5 of Algorithms of oppression
  • Graph of the Day
  • Biological Databases
  • Guest: Dr. Stephen Speicher
Week 8 Assignment

Due 12:01 AM 10/29

Class Journal Week 8

9 Oct 29 Rigden & Fernández (2020) "NAR Database issue", DataONE: Why Data Management, DataONE: Data Sharing
  • Graph of the Day
  • Biological Database Presentations
  • Searching the literature Part 1
Week 9 Assignment

Postponed--no work is due 12:01 AM 11/5

Class Journal Week 9

10 Nov 5
  • Graph of the Day
  • Searching the literature part 1

Nov 6: last day to withdraw or apply for credit/no credit grading

Week 10 Assignment

Due 12:00 PM 11/12

Class Shared Bibliography

11 Nov 12
  • Graph of the Day
  • Searching the literature part 2
  • Prepare for Journal Club Presentations
Week 11 Assignment

Due 12:00 PM 11/19

Class Journal Week 11

12 Nov 19 Week 12 Assignment

Due 12:01 PM 12/3

Note different due date

Class Journal Week 12

13 Nov 26 No class Thanksgiving Break
14 Dec 3
  • Graph of the Day
  • Coronavirus Research Project 2
  • Course Evaluations
Week 14 Assignment

Due 12:00 PM 12/10

Class Journal Week 14

15 Dec 10

Course Information

BIOL 368-01: Bioinformatics Laboratory, 1 credit hour

Instructor

  • Kam D. Dahlquist, Ph.D.
    • Phone: (310) 338-7697 (during remote learning, forwards to my cell phone)
    • 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 (during remote learning, Zoom)
    • Office hours: Drop-in Zoom office hours will be held Mondays & Wednesdays 12:00 - 1:00 PM (link in Brightspace). To schedule an office hour appointment, use my Calendly link (link in Brightspace).

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 1:30 – 5:30 PM, synchronous online Zoom meetings (link on Brightspace)

  • This is a hands-on laboratory course, thus attendance at all synchronous Zoom meetings is required.
  • This class meets continuously between 1:30 PM and 5:30 PM. Approximately once per hour short breaks will be taken to relieve "Zoom fatigue". You are expected to always be available during this time frame, even if we sometimes break early for asynchronous work.
  • 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.
    • Accommodations will be made for students with extenuating circumstances related to COVID-19. Please schedule an office hour appointment during the first week of class or as soon as the situation arises to discuss. If asynchronous work becomes necessary, you will be expected to complete the assignments as scheduled, and we will make arrangements to substitute for in-class work.
    • Cameras should be turned on during class sessions.
    • Class sessions will be recorded and posted on Brightspace. A Zoom link to the meetings is posted on Brightspace.

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 inclusive, respectful, and conducive to learning. Diversity in our class may be reflected by differences in race, culture, age, religion, sexual orientation, socioeconomic background, and other social identities and life experiences. An inclusive and diverse learning environment encourages and appreciates the expressions of different ideas, opinions, and beliefs as opportunities for intellectual and personal enrichment. Developing this environment requires respecting what others say, their right to say it, and the thoughtful consideration of others' communication. 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 that you are not using to conduct the coursework must be turned off and put away out of sight.
  7. All students are governed by LMU Student Conduct Code. 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.
  8. Please see the Help page for additional "netiquette" guidelines.

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 (Zoom links, personal contact information, copyrighted material, Zoom recordings) 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

Texts

There is no required text to purchase for the course; electronic materials 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.

  • 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          120 points
Shared journal assignments                                              40 points
Journal club and research project presentations                        140 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 synchronous Seaver College webinars or viewing online webinars Each webinar attended is worth 0.5% with up to 5 seminars (2.5%) total.

  • Select a seminar to watch from the iBioSeminar Series or others as announced on this wiki.
  • The video must be a minimum of 50 minutes long to count.
  • You must watch/listen to the entire seminar from start to finish.
  • You must turn in via e-mail, a one-page, double-spaced summary of the seminar, including the title and URL of the seminar.
  • All webinar write-ups are due by the last day of instruction, Friday, December 11, 4:00 PM.

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.

In addition, unauthorized access to or alteration of privileged and proprietary information will also be considered a breach of the Academic Honesty Policy, examples of which are given below:

  • Unauthorized access to and/or use of privileged University documents, files, or information and/or alteration thereof by electronic or any other means.
  • Unauthorized access to and/or use of proprietary information. For example, the unauthorized dissemination of research prior to publication.
  • Unauthorized access to and/or use of University course resources and materials. For example, distributing any course materials (syllabus, assignments, exams, etc.) without explicit permission from the instructor. Therefore, dissemination or sharing of any classroom recording (e.g., Zoom or other videos posted by the instructor) without the permission of the instructor would be considered “unauthorized use” and, therefore, prohibited.

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.

Additional Resources

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/F20.