BIOL398-03/S13

Announcements

• NOTE: This page is still under construction.

Schedule

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

Week	Date	Reading	Topic	Assignment
1	Tues Jan 15		Syllabus walkthrough Pairwise interviews (report back after each sub-bullet) Basic acquaintance information Like a cell/not like a cell Register for the OpenWetware Wiki RISC Assessment Pre-course survey
	Thurs Jan 17	Berg, Tymoczko, Stryer (2002) Biochemistry, 5th ed., Sections 8.1-8.4	Introduction to nitrogen metabolism Discuss the Week 1 assignment (accounts should be ready to wiki at this point) Quick wiki overview User wiki page setup Introduction to the readings Slides are posted on MyLMUConnect Jan 18: last day to add or drop a class without a grade of W	Week 1 Assignment Due midnight 1/17 Class Journal Week 1
2	Tues Jan 22		Introduction to enzyme kinetics (biochemistry/math) Slides are posted on MyLMUConnect
	Thurs Jan 24	Chem Kinetics Background Matlab tutorial	Enzyme kinetics/nitrogen metabolism	Week 2 Assignment Due midnight 1/24 Class Journal Week 2
3	Tues Jan 29	ter Schure et al. (1995) J. Bacteriology	Journal Club 1 Slides are posted on MyLMUConnect
	Thurs Jan 31		Metabolic pathway modeling project	Week 3 Assignment Due midnight 1/31 Class Journal Week 3
4	Tues Feb 5		Metabolic pathway modeling project
	Thurs Feb 7	Chemostat	Metabolic pathway modeling project	Week 4 Assignment Due midnight 2/7 Class Journal Week 4
5	Tues Feb 12		Metabolic pathway modeling project
	Thurs Feb 14		Metabolic pathway modeling project	Week 5 Assignment Due midnight 2/14 Class Journal Week 5
6	Tues Feb 19	Lander (2010) BMC Biology	Metabolic pathway modeling project
	Thurs Feb 21	ter Schure et al. (1995) Microbiology	Metabolic pathway modeling project Slides are posted on MyLMUConnect	Week 6 Assignment Due midnight 2/22 Note NEW due date Class Journal Week 6
7	Tues Feb 26		Metabolic Pathway Modeling Project
	Thurs Feb 28		Research Presentation 1: Metabolic Pathways PowerPoint Presentation Guidelines Guide to Critiquing Talks	NO Week 7 Assignment Have a Happy Spring Break!
	Mar 5, 7		Spring Break
8	Tues Mar 12	Alberts et al. (2002) Molecular Biology of the Cell Ch. 6: From DNA to RNA and Ch. 6: From RNA to Protein	Introduction to the Central Dogma of Molecular Biology and Gene Expression Slides on MyLMUConnect Transcription animation
	Thurs Mar 14	Alberts et al. (2002) Ch. 8: Microarrays, Campbell & Heyer Ch. 4 on MyLMUConnect, DeRisi et al. (1997), Microarray animation	Central Dogma (continued) Introduction to DNA microarrays Slides on MyLMUConnect Translation animation	Week 8 Assignment Due midnight 3/17 Class Journal Week 8
9	Tues Mar 19		Microarrays ("low level analysis") Slides on MyLMUConnect
	Thurs Mar 21		Introduction to probability and statistics Mar 18: Last day to withdraw or change to credit/no-credit status	Week 9 Assignment Due midnight 3/24 Class Journal Week 9
10	Tues Mar 26		Statistics continued (T test)
	Thurs Mar 28 Easter break	Schade et al. (2004) Molecular Biology of the Cell 15: 5492–5502.	Journal Club 2	No Week 10 Assignment
11	Tues Apr 2	Alberts et al. (2002) Ch. 7: An Overview of Gene Control, Ch. 7: DNA-Binding Motifs, and Ch. 7: How Genetic Switches Work	Review of Week 8 Assignment Regulatory Transcription Factors Start Week 11 Assignment in class
	Thurs Apr 4		Cesar Chavez Day, no class	Week 11 Assignment Due midnight 4/5 Class Journal Week 11
12	Tues Apr 9	Ernst & Bar-Joseph (2006) BMC Bioinformatics	Clustering Finding candidate transcription factors
	Thurs Apr 11	Oltvai & Barabasi (2002) Science, Lee et al. (2002) Science, Harbison et al. (2004) Nature, and MacIsaac et al. (2006) BMC Bioinformatics	Gene regulatory networks	Week 12 Assignment Due midnight 4/12 Class Journal Week 12
13	Tues Apr 16	Sontag et al (2004) Bioinformatics, Kim et al. (2007) Comp Bio Chem, and Vu and Vohradsky (2007) Nucleic Acid Res	Gene regulatory network modeling project: estimating parameters
	Thurs Apr 18	TBA	Gene regulatory network modeling project: estimating parameters	Week 13 Assignment Due midnight 4/19 Class Journal: Week 13
14	Tues Apr 23	TBA	Gene regulatory network modeling project: estimating parameters
	Thurs Apr 25			Week 14 Assignment Due midnight 4/26 Class Journal Week 14
15	Tues Apr 30	TBA	Gene regulatory network modeling project: forward simulation
	Thurs May 2	TBA	Gene regulatory network modeling project: forward simulation
Finals			Final Research Presentation: Gene Regulatory Networks 8:00AM	Final Report due 5:00 PM, Friday, May 10

Course Information

Instructors

• Kam D. Dahlquist, Ph.D.
  • Phone: (310) 338-7697
  • Email Dr. Dahlquist through OpenWetWare
  • Office: Seaver 218
  • Office hours: MW 12:00 - 2:00PM and by appointment
• Ben G. Fitzpatrick, Ph.D.
  • Phone: 310-338-7892
  • Email Dr. Fitzpatrick through OpenWetWare
  • Office: UH 2726
  • Office hours: MW 2:00 - 3:00PM, TR 1:30 - 2:30PM

Prerequisites/Recommended Background

MATH 123 (Calculus for Life Sciences II) or MATH 132 (Calculus II); BIOL 201 (Cell Function); CHEM 220 (Organic Chemistry I), or consent of instructor

Class Meetings and Attendance

TR 9:25 – 10:40 AM, Seaver 120

This is a hands-on, participatory 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 instructors 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 mathematician 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 instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

Classroom Conduct

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. Refer to LMU’s Community Standards for the Student Conduct Code, Section IV. D, or to the Lion’s 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 their behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:

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.
6. You are expected to bring the required materials to each class session.
7. Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

Course Web Site

This is the course web site and wiki, hosted by OpenWetWare.org. You will need to register with OpenWetware.org to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to 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 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 Materials

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 the OpenWetware wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.

Materials (must be brought to each class meeting)

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

Course Description

Introduction to mathematical and statistical concepts closely related to research problems in biology. Biological topics include the structure, function, and regulation of the three major types of cellular pathways: metabolic, signaling, and gene regulatory pathways. Mathematical topics include statistical analysis of biological measurements, dynamic modeling of biological systems, and fitting models to observed data. Students will critically evaluate the primary literature and carry out three major modeling projects throughout the semester.

Course Objectives and Learning Outcomes

• You understand the structure, function, and regulation of the three major types of cellular pathways: metabolic, signaling, and gene regulatory pathways
• You understand and apply quantitative tools for studying cellular pathways, including the construction and analysis of dynamic models, the comparison of models to observed data, and the refinement and validation of models
• You show discipline and proficiency in day-to-day scientific and mathematical best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
• You recognize and care about how the biological, mathematical, and statistical issues presented in this course relate to and affect society, our daily lives, and ourselves
• You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and mathematics on your own
• You learn how to communicate and work effectively with colleagues from different disciplines

Course Work and Grading

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

Weekly electronic lab notebook/journal assignments (10 points each)     110 points
Journal club presentations (20 points each)                              40 points
Research presentations (20 points each)                                  40 points
Final Written Report                                                     80 points
Total                                                                   270 points

Final course grading scale:

94.0-100.0%		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. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills 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 instructors 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 instructors 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 Presentations

Each modeling 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.

Research Presentations

The final step in the scientific method is communication of the results to the scientific community. This 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 a research presentation (oral lab report) for each of the modeling 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 research presentations will not be accepted.

Final Written Report

In addition to the research presentation, the culmination of your third modeling project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions will be posted on the OpenWetware site. The Final Written Report cannot be accepted any later than Thursday, May 5 at 10:00AM (the conclusion of the scheduled final exam time for this course).

Extra Credit

Students may accumulate up to 2.5% of their final grade in extra credit by attending Biology or Mathematics 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/Mathematics Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these 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 2010-2011, pp. 59–61, “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 Undergraduate Bulletin.

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

Additional resources on Academic Honesty

• The Davidson College Department of Biology Statement on Plagiarism
• Guidelines for Literature Citations in a Scientific Paper
• LRC presentation on plagiarism (PowerPoint presentation)
• Notes on plagiarism from an electrical engineering & computer science perspective

Americans with Disabilities Act

Students with special needs as addressed by the Americans with Disabilities Act who need reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services Office. Any student who currently has a documented disability (physical, learning, or psychological) needing academic accommodations should contact the Disability Services Office (Daum Hall Room 224, 310-338-4535) as early in the semester as possible. All discussions will remain confidential. Please visit http://www.lmu.edu/dss for additional information.

Course Assessment

We ask that students in this class participate in the Research on the Integrated Science Curriculum (RISC) Survey administered by Dr. David Lopatto at Grinnell College, which will allow the instructors to evaluate the effectiveness of this course. Students are asked to complete the student pre-course and post-course surveys.

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 page, the course web site at http://www.openwetware.org/wiki/BIOL398-03/S13.