BIOL398-01/S10

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| [http://www.nature.com/nature/journal/v393/n6686/full/393648a0.html Kwong et al. (1998), [http://tinyurl.com/Stanfield1999 Stanfield et al. (1999)], [http://tinyurl.com/yjpgvpx Stanfield et al. (2003)]
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| [http://www.nature.com/nature/journal/v393/n6686/full/393648a0.html Kwong et al. (1998), [http://tinyurl.com/Stanfield1999 Stanfield et al. (1999)], [http://tinyurl.com/yjpgvpx Stanfield et al. (2003)], ''Bioinformatics for Dummies'' Ch. 11
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Revision as of 13:52, 23 February 2010

BIOL398-01: Bioinformatics Laboratory

Loyola Marymount University

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Announcements

  • Anton Weisstein (one of the authors of the Markham et al. 1998 paper) has responded to some of the class questions. His answers are recorded on the Class Journal Week 4 page.
  • Record your Windows and Mac tips & tricks in the course Help page.


Schedule

Updates to the schedule will be posted here. Readings need to be completed in preparation for class.

Week Date Reading Topic Assignment
1 Jan 19 Introduction to Bioinformatics

Slides can be found on MyLMUConnect site

Introduction to the OpenWetware Wiki

Week 1 Assignment

Due midnight 1/25

2 Jan 26 Protocols listed on Molecular Genetics Explorer page Molecular Genetics Explorer

Jan 25: last day to add or drop a class without a grade of W

Week 2 Assignment

Due midnight 2/1

Class Journal Week 2

3 Feb 2 Bioinformatics for Dummies Introduction, Chapters 1 & 2 Intro to biological databases/literature databases (slides on MyLMUConnect, LMU LibGuide)

Begin HIV Evolution Project

Week 3 Assignment

Due midnight 2/8

Class Journal Week 3

4 Feb 9 Markham et al. (1998), Cohen et al. (2008) review, Exploring HIV Evolution Handout Journal Club 1 slides are on MyLMUConnect

HIV Evolution Project

Week 4 Assignment

Due midnight 2/15

Class Journal Week 4

5 Feb 16 HIV Evolution Project

Guest lecture by Glenn Johnson-Grau on Web of Science

Week 5 Assignment

Due midnight 2/22

Class Journal Week 5

6 Feb 23 HIV Evolution Project Week 6 Assignment

Due midnight 3/1

Class Journal Week 6

7 Mar 2 Bring your Bioinformatics for Dummies book to class; Read Ch. 4, 6. HIV Evolution Project Presentations

Begin HIV Structure Project

Week 7 Assignment

Due midnight 3/8

Class Journal Week 7

8 Mar 9 Kwong et al. (1998), [http://tinyurl.com/Stanfield1999 Stanfield et al. (1999), Stanfield et al. (2003), Bioinformatics for Dummies Ch. 11 Journal Club 2

HIV Structure Project

Week 8 Assignment

Due midnight 3/15

9 Mar 16 TBA HIV Structure Project Week 9 Assignment

Week midnight 3/22

10 Mar 23 TBA HIV Structure Project Presentations

Mar 26: Last day to withdraw or change to credit/no-credit status

Week 10 Assignment

Due midnight 3/29

Mar 30 Spring Break
11 Apr 6 TBA Journal Club 3

Begin DNA Microarray Project

Week 11 Assignment

Due midnight 4/12

12 Apr 13 TBA DNA Microarray Project Week 12 Assignment

Due midnight 4/19

13 Apr 20 TBA DNA Microarray Project Week 13 Assignment

Due midnight 4/26

14 Apr 27 TBA DNA Microarray Project Final Presentations Week 14 Assignment

Due midnight 5/3

Course Information

Instructor

Prerequisites/Recommended Background

Biology 202 (Genetics), Chemistry 220 (Organic Chemistry I), Chemistry 222 (Organic Chemistry II)

Class Meetings & Attendance

Tuesdays 8:00 AM – 12:00 PM, Seaver 120

This is a hands-on laboratory course, thus attendance at all class meetings is required. 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. LMU has published H1N1 flu prevention guidelines that are applicable to this course: http://www.lmu.edu/resources/emergency/status/H1N1.htm

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. You are responsible for your own learning and for being a good class citizen.
  2. We will act with honesty and integrity at all times.
  3. We will always treat individuals with respect.
  4. Class will start promptly on time.
  5. 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.
  6. You are expected to bring the required materials to each class session.
  7. Cell phones, pagers, and other communication or music devices will be turned off.

Additionally, 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 398-01 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

Claverie, Jean-Michel & Notredame, Cedric (2006) Bioinformatics for Dummies, Wiley, ISBN-10: 0470089857.

Specific readings are given on the schedule and may be revised. Readings will also be assigned from other sources and will be posted on the course web site or put on reserve in the library.

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 understand how biological information is encoded in the genome and to apply this knowledge to a variety of biological tasks and problems
  • To become a bioinformatics tool “power user” by practicing the skills of computer literacy and learning the following about each bioinformatics technique we use:
    • what biological questions is the technique used to answer?
    • how does the technique work?
    • how do you perform the technique?
    • what are the limitations of the technique?
  • To read and critically evaluate the primary scientific literature
  • To form opinions about the ethical, legal, and social implications of bioinformatics research consistent with your values
  • 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 and ethics case study presentations/discussions	150 points
Oral lab reports 						210 points
Total								500 points

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

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 Monday PST (Sunday night/Monday morning). Note that the OpenWetware server records the time as Eastern Standard Time (EST). 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.
  • 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 and Ethical Case Study 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.

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 2008-2010, pp. 58–59, "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." An online version of the LMU honor code is available at: http://www.lmu.edu/about/services/registrar/Bulletin/Academic_Degree_Requirements_and_Policies.htm. You are required to sign the Honor Code Agreement for this course. The Davidson College Department of Biology Statement on Plagiarism has been adopted for this course. Please also follow these Guidelines for Literature Citations in a Scientific Paper.

Special Accommodations

Students with special needs who need reasonable modifications, special assistance, or accommodations in this course (such as a documented disability [physical, learning, or psychological]) should contact the Disability Services Office (Daum Hall, Room 224, x84535, http://www.lmu.edu/dss) as early in the semester as possible. All discussions will remain confidential. In addition, please schedule an appointment with the instructors 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/BIOL398-01/S10.


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