BIOL368/F14

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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Contents

Announcements

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 27
  • Introduction to Bioinformatics
  • Introduction to the OpenWetWare Wiki
  • August 29: Last day to add or drop a class without a grade of W
Week 1 Assignment

Due midnight 9/3

Class Journal Week 1

2 Sept 3 Molecular Genetics Explorer Protocols listed on the Week 2 Assignment page
  • Molecular Genetics Explorer
Week 2 Assignment

Due midnight 9/10

Class Journal Week 2

3 Sept 10 Bioinformatics for Dummies Introduction, Chapters 1, 2,
  • Intro to biological databases/literature databases
  • Guest Lecture by Librarian Glenn Johnson-Grau
  • Begin HIV Evolution Project
Week 3 Assignment

Due midnight 9/17

Class Journal Week 3

4 Sept 17 Markham et al. (1998); Cohen et al. (2008) review; Exploring HIV Evolution Handout (on MyLMU Connect); Bioinformatics for Dummies Chapter 3
  • Journal Club 1
  • HIV Evolution Project
Week 4 Assignment

Due midnight 9/24

Class Journal Week 4

5 Sept 24
  • HIV Evolution Project
Week 5 Assignment

Due midnight 10/1

Class Journal Week 5

6 Oct 1 Week 6 Assignment

Due midnight 10/8

Class Journal Week 6

7 Oct 8 Week 7 Assignment

Due midnight 10/15

Class Journal Week 7

8 Oct 15 Huang et al. (2005), Stanfield et al. (1999), Merk & Subramaniam (2013), Bioinformatics for Dummies, Ch. 4, 6, 11. Bring book to class.
  • Journal Club 2
  • HIV Structure Project
Week 8 Assignment

Due midnight 10/22

Class Journal Week 8

9 Oct 22
  • HIV Structure Project
Week 9 Assignment

Due midnight 10/29

Class Journal Week 9

10 Oct 29
  • HIV Structure Project Presentations
  • Introduction to DNA Microarrays
  • Oct 31: Last day to withdraw or change to credit/no-credit status
Week 10 Assignment

Due midnight 11/5

Class Journal Week 10

11 Nov 5 Brown & Botstein (1999)

DeRisi et al. (1997)

Campbell & Heyer Chapter 4 (on MyLMUConnect)

Week 11 Assignment

Due midnight 11/12

Class Journal Week 11

12 Nov 12 Individual Journal Club papers on for DNA Microarray Project
  • DNA Microarray Project
Week 12 Assignment

Due midnight 11/18 Note different due date!

Class Journal Week 12

13 Nov 19 Dahlquist et al. (2002), Doniger et al. (2003), Salomonis et al. (2007)
  • Journal Club 3
  • DNA Microarray Project
Week 13 Assignment

Due midnight 12/3

Class Journal Week 13

14 Nov 26 Thanksgiving Break No Week 14 Assignment

Happy Thanksgiving!

15 Dec 3 DNA Microarray Project Week 15 Assignment

Due midnight 12/10

Class Journal Week 15

Finals Dec 10 Wednesday, 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: Seaver 218
  • Office hours: Tuesdays 2:00-4:00 PM, Thursdays 9:00-11:00 AM and by appointment (send me an e-mail or sign up for a time on the sheet on my office door)

Teaching Assistant

  • Stephen Louie

Prerequisites/Recommended Background

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

Class Meetings & Attendance

Wednesdays 1:00 PM – 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, 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.
  7. All students are governed by LMU Community Standards Publication.

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 that 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 (formerly known as Blackboard). The MyLMUConnect site may be used for materials that cannot be made public on the OpenWetWare.org wiki.

Required Texts

Required 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 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 be confident in "leaving your comfort zone", flourishing outside of it, and learning more about bioinformatics on your own.

Course Work & Grading

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

Electronic laboratory notebook/journal assignments          140 points
Journal club presentations                                  150 points 
Oral lab reports                                            210 points 
Total                                                       500 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 Laboratory Notebook/Journal

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 a 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 entries that the instructor will read and grade. You will use the OpenWetWare site to complete the assignments as well. The following guidelines apply:

  • Your weekly journal entry is due every midnight on Wednesday PDT (Tuesday night/Wednesday morning). Note that the OpenWetWare server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00 on the server.
  • You will earn 10 points per weekly submission. Late journal entries will be accepted up to one week later for up to half credit.
  • The instructor 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
    • Reflection on your learning

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. In addition, we may also discuss ethical case studies relating to the topics in the course. Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations and ethics case studies will not be accepted.

Oral Lab Reports

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 web sites. To build your scientific communication skills, you will give an oral lab report 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.

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. Students arriving late to the seminar will not be granted credit—so don’t be late!

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 expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” Click here for an online version of the LMU Honor Code and Process.

You are required to sign the Honor Code Agreement for this course.

Academic Honesty Resources

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.

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/F14.


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