BIOL368/F16

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

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Contents

Announcements

  • Grades for the second research presentation have been posted on the MyLMU Connect Grade Center. Kam D. Dahlquist 14:34, 22 November 2016 (EST)

Upcoming Seminars

  • Hannon Library Faculty Pub Night: Dr. David Moffet, Department of Chemistry and Biochemistry, Untangling Amyloid: Slowing the Progression of Alzheimer's Disease and Type 2 Diabetes, Tuesday, December 6, 5:30-7:00 PM, Von der Ahe Family Suite (library level 3), reservation required
    • Note that you may obtain extra credit for attending one of Dr. Moffet's seminars only.
  • Biology Department Seminar: Ryan Ellingson, CSULA/UCLA, Friday, December 9, 3:00-4:00 PM, LSB 120, Challenging a textbook case of species selection: Does loss of dispersal make evolutionary winners, or the walking dead?

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 MyLMUConnect.

Week Date Reading Topic Assignment
1 Aug 30 Peter Denning Voices of Computing and Computing is a Natural Science, Chapter 1 of On Becoming a Biologist by John Janovy, Jr. on MyLMUConnect
  • Syllabus & Academic Honesty discussion
  • Introduction to Bioinformatics
  • Introduction to the OpenWetWare Wiki
  • Sept. 2: Last day to add or drop a class without a grade of W
Week 1 Assignment

Due midnight 9/6

Class Journal Week 1

2 Sept 6 Molecular Genetics Explorer Protocols listed on the Week 2 Assignment page, Schnell (2015) Week 2 Assignment

Due midnight 9/13

Class Journal Week 2

3 Sept 13 Markham et al. (1998); Cohen et al. (2008) review; Exploring HIV Evolution Handout (on MyLMU Connect); Bioinformatics for Dummies Chapters 1, 2, 3
  • Begin HIV Evolution Project
Week 3 Assignment

Due midnight 9/20

Class Journal Week 3

4 Sept 20
  • Journal Club 1
  • HIV Evolution Project
Week 4 Assignment

Due midnight 9/27

Class Journal Week 4

5 Sept 27
  • HIV Evolution Project
  • Guest Lecture from Glenn Johnson-Grau
Week 5 Assignment

Due midnight 10/4

Class Journal Week 5

6 Oct 4
  • HIV Evolution Project
Week 6 Assignment

Due midnight 10/11

Class Journal Week 6

7 Oct 11 Bodenreider & Stevens (2006); Aspinall (2005); Noble (2012) Week 7 Assignment

Due midnight 10/18

Class Journal Week 7

8 Oct 18 Week 8 Assignment

Due midnight 10/25

Class Journal Week 8

9 Oct 25 Andrianov & Anishchenko (2009), Kirchherr et al. (2011), Kwong et al. (1998)
  • Journal Club 2
  • HIV Structure Project
Week 9 Assignment

Due midnight 11/1

Class Journal Week 9

10 Nov 1 Week 10 Assignment

Due midnight 11/8

Class Journal Week 10

11 Nov 8
  • HIV Structure Project Progress Reports
Week 11 Assignment

Due midnight 11/15

Class Journal Week 11

12 Nov 15 Week 12 Assignment

CANCELLED

13 Nov 22 Rigden et al. (2016), DataONE: Why Data Management, DataONE: Data Sharing No Week 13 Assignment

Happy Thanksgiving!

14 Nov 29 Brown & Botstein (1999), Campbell & Heyer Chapter 4 (on MyLMUConnect)
  • Biological Databases Lightning Talks
  • DNA Microarray Project
Week 14 Assignment

Due midnight 12/6

Class Journal Week 14

15 Dec 6 * Hebly et al. (2014), Schade et al. (2004), Tai et al. (2007)
  • DNA Microarray Project
Week 15 Assignment

Due midnight 12/13

Class Journal Week 15

Finals Dec 13 Tuesday, 2:00-4:00 PM Final Exam period

Final Project Presentations

Course Information

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 1:00-3:00 PM, Tuesdays 9:30-11:30 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 112 (General Biology Laboratory II), Biology 202 (Genetics), Chemistry 220 (Organic Chemistry I)

Class Meetings & Attendance

Tuesdays 1:10 PM – 5:00 PM, Seaver 120

This is a hands-on laboratory course, thus attendance at all class meetings is required. This class meets continuously between 1:10 PM and 5:00 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. All students are governed by the LMU Student Conduct Code and the LMU Community Standards Publication.
  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, pagers, and other communication or music devices must be turned off and put away out of sight. Your own laptops and/or tablet may be used to conduct the class exercises; however, if they are being used for other purposes and become distracting to you or others, you will be asked to put them away.

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 MyLMUConnect (otherwise known as Blackboard). The MyLMUConnect site 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

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 (the more memory the better)

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, such as maintaining journals and notebooks and managing your files and code, which facilitate reproducible research.
  • To gain computer, data, and information literacy skills.
  • 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 three areas:

Individual electronic laboratory notebook/journal assignments          140 points
Shared journal assignments                                              42 points
Journal club presentations                                              80 points 
Research project presentations                                         120 points 
Information literacy (additional points added to two assignments)       43 points 
Total                                                                  425 points

Grades will be posted on the MyLMU Connect Grade Center for this course.

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 midnight on Tuesday PDT (Monday night/Tuesday morning); consult the schedule for specific due dates for each assignment.
    • Note that the OpenWetWare server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00 on the server.
  • Each weekly assignment has an individual component and a shared component. You will 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).
    • Late journal entries will be accepted up to one week later for up to half credit.
  • The instructor and/or TA will read and comment on how to improve your journal entries on your User Talk page.
  • Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
  • Generally, your journal entries will consist of:
    • Workflow and other documentation for hands-on exercises and projects
    • Answers to any specific questions posed in the exercise
    • Acknowledgments section (see Week 1 assignment for details)
    • References section (see Week 1 assignment for details)
    • Shared reflection on your learning, assigned readings, or ethics case studies.

Journal Club Presentations

Each bioinformatics project will begin with a "Journal Club" where students will present and lead discussion of research articles from the primary literature. Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations will not be accepted. An unexcused absence from a journal club presentation will result in a grade of zero for the presentation.

Research Presentations

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 give his or her presentation, late oral lab reports will not be accepted. An unexcused absence from a journal club presentation 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 non-Biology Department seminars, you must turn in a one-page summary of the seminar 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 (http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf), 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 that can range from receiving no credit for the assignment, failing the class, to expulsion. 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.

Click here for an online version of the LMU Academic Honesty Policy and Procedures.

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/dssfor additional information.

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/F16.


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