BIOL398-05/S17

This page is currently under construction.

Announcements

• The GRNsight home page has been fixed and is now working. — Kam D. Dahlquist 18:50, 30 April 2015 (EDT)
• The deadline for the Week 14 Assignment has been postponed to midnight Thursday, April 30 (Wednesday night/Thursday morning). The deadline for the Week 14 shared journal has been postponed to midnight Tuesday, May 5 (Monday night/Tuesday morning).
• Grades have been posted for the Journal Club Presentation, Week 4 Redux, Week 5, and Week 9 assignments on the MyLMU Connect Grade Center.

— Kam D. Dahlquist 19:00, 28 April 2015 (EDT)

Upcoming Seminars

• There are no further seminars for the remainder of the semester.

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 13		Syllabus walkthrough Pairwise interviews Basic acquaintance information Register for the OpenWetware Wiki
	Thurs Jan 15	Chemostat	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 Introduction to population growth, nutrients, and the chemostat Evolution of Homer Simpson Jan 16: last day to add or drop a class without a grade of W	Week 1 Assignment Due midnight 1/20 Class Journal Week 1
2	Tues Jan 20	Matlab tutorial Try to work through Parts 1-9 of this tutorial before coming to class. We will use this to build a chemostat model in class.	Introduction to Matlab and simulating the chemostat
	Thurs Jan 22	Matlab Tutorial Materials matlab driver for nutrient/colony model matlab DE function for nutrient/colony model matlab driver for chemostat model matlab DE function for chemostat model	Introduction to Matlab and simulating the chemostat (cont'd) Nitrogen metabolism Slides on MyLMUConnect	Week 2 Assignment Due midnight 1/27 Class Journal Week 2
3	Tues Jan 27	ter Schure et al. (1995) J. Bacteriology	Journal Club 1 Slides on MyLMUConnect Meet in Seaver 202 today
	Thurs Jan 29		Introduction to Matlab and simulating the chemostat (cont'd)	Week 3 Assignment Due midnight 2/3 Class Journal Week 3
4	Tues Feb 3	First Draft of Notes	Return of the Chemostat: steady states and multiple nutrients
	Thurs Feb 5	Chemostat_dynamics_2n.m‎‎ ‎ Two_nutrient_min_chemostat_script.m‎ Simple_fit_fn.m‎ ‎ Simple_estimation_script.m‎	Estimation in the chemostat and metabolism	Week 4 Assignment Due midnight 2/10 Class Journal Week 4
5	Tues Feb 10	Berg, Tymoczko, Stryer (2002) Biochemistry, 5th ed., Sections 8.1, 8.2, 8.3, 8.4 Chemical Kinetics Background	Introduction to Enzyme Kinetics
	Thurs Feb 12	Notes on the Chemostat and biochemical reactions	Metabolic pathway modeling project	Week 5 Assignment Due midnight 2/17 Class Journal Week 5
6	Tues Feb 17		Metabolic pathway modeling project	The Week 6 Assignment has been CANCELLED Revisions to the Week 4 Assignment Due midnight 2/26
	Thurs Feb 19		Spring Break
7	Tues Feb 24		Metabolic pathway modeling project
	Thurs Feb 26	Sainz et al. (2003) (available on MyLMUConnect		Week 7 Assignment Due midnight 3/3 Class Journal Week 7 Class Journal Due midnight 3/5
8	Mar 3		Research Presentation 1: Metabolic Pathways Lucia & Lauren, Karina & Natalie, Will & Jeffrey PowerPoint Presentation Guidelines Oral Presentation Grading Rubric
	Mar 5		Research Presentation 1: Metabolic Pathways Alyssa & Tessa, Kristen & Kara	The Week 8 Assignment has been CANCELLED
9	Tues Mar 10	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 Transcription animation Translation animation Slides on MyLMUConnect
	Thurs Mar 12	Alberts et al. (2002) Ch. 8: Microarrays, Campbell & Heyer Ch. 4 on MyLMUConnect, Brown & Botstein (1999), DeRisi et al. (1997), Microarray animation	Introduction to microarrays	Week 9 Assignment Due midnight 3/17 Class Journal Week 9
10	Tues Mar 17	Notes for Today, Anova Data, Exploratory Data	Probability and Statistics
	Thurs Mar 19		Statistics continued (microarray spreadsheet) Mar 20: Last day to withdraw or change to credit/no-credit status	Week 10 Assignment Due midnight 3/24 Class Journal Week 10
11	Tues Mar 24	Tai et al. (2007) Molecular Biology of the Cell 18: 5100-5112, Lee et al. (2002) Science 298: 799-804, Vu and Vohradsky (2007) Nucleic Acid Research 35: 279-287	Journal Club 2: Meet in Seaver 202 PowerPoint Presentation Guidelines Oral Presentation Grading Rubric
	Thurs Mar 26	Ernst & Bar-Joseph (2006) BMC Bioinformatics	Clustering	Week 11 Assignment Due midnight 4/7 NOTE different due date Class Journal Week 11
	Mar 31, Apr 2		Cesar Chavez Day/Easter Break
12	Tues Apr 7	Alberts et al. (2002) Ch. 7: An Overview of Gene Control, Ch. 7: DNA-Binding Motifs, and Regulatory Transcription Factors	Finding candidate transcription factors
	Thurs Apr 9	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 4/14 Class Journal Week 12
13	Tues Apr 14	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 16	GRNmap software zipFile on Lionshare	Gene regulatory network modeling project: estimating parameters	Week 13 Assignment Due midnight 4/21 There is no class journal assignment this week
14	Tues Apr 21		Gene regulatory network modeling project: estimating parameters
	Thurs Apr 23		Gene regulatory network modeling project: estimating parameters	Week 14 Assignment Deadline extended to midnight 4/30 Class Journal Week 14 Deadline extended to midnight 5/5
15	Tues Apr 28		Gene regulatory network modeling project	Week 15 Assignment Due midnight 5/7 NOTE different due date Class Journal Week 15
	Thurs Apr 30	If you want to regenerate graphs after the fact, use these: regenerate graphs script function needed by the script	Gene regulatory network modeling project: forward simulation
Finals	Thurs May 7		Final Research Presentation: Gene Regulatory Networks 8:00AM	Final Report due 5:00 PM, Friday, May 8

Course Information

Instructors

• Kam D. Dahlquist, Ph.D.
  • Phone: (310) 338-7697
  • E-mail: kdahlquist at lmu dot edu or e-mail Dr. Dahlquist through OpenWetWare
  • Office: Seaver 218
  • Office hours: MW 10:00 – 11:00 AM, T 3:30 – 4:30 PM, R 1:30 – 2:30 PM, and by appointment
• Ben G. Fitzpatrick, Ph.D.
  • Phone: 310-338-7892
  • E-mail: bfitzpatrick at lmu dot edu or e-mail Dr. Fitzpatrick through OpenWetWare
  • Office: UH 2753
  • Office hours: TR 11:00 AM -- 12:00 PM, W 1:30-2:30 PM, or by appointment

Prerequisites/Recommended Background

• BIOL 398-04: 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
• MATH 388-01: MATH 123 (Calculus for Life Sciences II) or MATH 132 (Calculus II); BIOL 101 (General Biology 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. Each student is allowed two "sick" days (automatically excused absences) during the semester. Further unexcused absences from class will result in a 5% deduction from the overall course grade for each absence. Every effort should be made to attend class on oral presentation days as the content of that day's class is dependent on student participation. Unexcused absences from an oral presentation will result in a grade of zero for the presentation. 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

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 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 398-04 on MyLMUConnect (the MATH and BIOL sections of the course are merged into one site under BIOL 398-04). The MyLMUConnect site may be used for materials that cannot be made public on the OpenWetWare.org wiki.

E-mail Communication

At times we 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 instructors at night or on the weekend will be answered the next school day. Please CC both instructors on all e-mail messages related to this class.

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

University Core Curriculum

This course fulfills the following requirements in the University Core Curriculum:

• Integrations: Interdisciplinary Connections
• Upper Division Oral Communication Flag

Course Work and Grading

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

Weekly electronic lab notebook/journal assignments (10 points each)     140 points 
Oral presentations (journal club and research)                          150 points 
Final Written Report                                                    100 points
Total                                                                   380 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 typically due every midnight on Tuesday PST (Monday night/Tuesday morning); consult the schedule for specific due dates for each assignment. 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. 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. 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. An unexcused absence from a research presentation will result in a grade of zero for the presentation.

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 Friday, May 8 at 5:00 PM. The Final Written Report must be completed to receive a passing grade in the 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. 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/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 hard copy of your summary of the seminar, in-class, 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, the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus, the expectation is that you will complete 6 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.

Additional resources on Academic Honesty

• Honor Code Agreement
• LMU Honor Code and Process, University Bulletin
• 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
• BIOL 368: Bioinformatics Laboratory LibGuide

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. 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 page, the course web site at http://www.openwetware.org/wiki/BIOL398-04/S15.