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BIOL398-05: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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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 10		Syllabus walkthrough Student introductions Academic Honesty discussion Register for the OpenWetware Wiki
	Thurs Jan 12		Discuss the Week 1 assignment Quick wiki overview User wiki page setup Introduction to the readings Cell model activity Jan 13: 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 17		Introduction to Matlab and models of population growth
	Thurs Jan 19		Growth models	Week 2 Assignment Due midnight 1/24 Class Journal Week 2
3	Tues Jan 24		Growth models
	Thurs Jan 26		Metabolic pathways and central nitrogen metabolism in yeast	Week 3 Assignment Due midnight 1/31 Class Journal Week 3
4	Tues Jan 31	ter Schure et al. (1995) J. Bacteriology	Journal Club 1
	Thurs Feb 2		Metabolism	Week 4 Assignment Due midnight 2/7 Class Journal Week 4
5	Tues Feb 7	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 9		Metabolic pathway modeling project	Week 5 Assignment Due midnight 2/14 Class Journal Week 5
6	Tues Feb 14		Metabolic pathway modeling project
	Thurs Feb 16		Metabolic pathway modeling project	Week 6 Assignment Due midnight 2/21 Class Journal Week 6
7	Tues Feb 21		Metabolic pathway modeling project
	Thurs Feb 23		Metabolic pathway modeling project	Week 7 Assignment Due midnight 2/28 Class Journal Week 7
8	Tues Feb 28		Metabolic pathway modeling project
	Thurs Mar 2		Research Presentation 1: Metabolic Pathways PowerPoint Presentation Guidelines Oral Presentation Grading Rubric	No Week 8 Assignment
	Mar 7, 9		Spring Break
9	Tues Mar 14	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
	Thurs Mar 16	Alberts et al. (2002) Ch. 8: Microarrays, Campbell & Heyer Ch. 4, Brown & Botstein (1999), DeRisi et al. (1997), Microarray animation	Introduction to microarrays	Week 9 Assignment Due midnight 3/21 Class Journal Week 9
10	Tues Mar 21		Probability and Statistics
	Thurs Mar 23		Statistics continued (microarray spreadsheet) Mar 17: Last day to withdraw or change to credit/no-credit status	Week 10 Assignment Due midnight 3/28 Class Journal Week 10
11	Tues Mar 28	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 PowerPoint Presentation Guidelines Oral Presentation Grading Rubric
	Thurs Mar 30	Ernst & Bar-Joseph (2006) BMC Bioinformatics	Clustering	Week 11 Assignment Due midnight 4/4 Class Journal Week 11
12	Tues Apr 4	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 6	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 4/11 Class Journal Week 12
13	Tues Apr 11		Gene regulatory network modeling project: estimating parameters
	Thurs Apr 13		Easter Break	No Week 13 Assignment
14	Tues Apr 18		Gene regulatory network modeling project: estimating parameters
	Thurs Apr 20		Gene regulatory network modeling project: estimating parameters	Week 14 Assignment Due midnight 4/25 Class Journal Week 14
15	Tues Apr 25		Gene regulatory network modeling project
	Thurs Apr 27		Gene regulatory network modeling project: forward simulation	Week 15 Assignment Due midnight 5/4 NOTE different due date Class Journal Week 15
Finals	Thurs May 4		Final Research Presentation 8:00 AM	Final Report due 5:00 PM, Friday, May 5

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: LSB 289
- Office hours: T 12:30 - 2:30 PM, R 11:00 AM - 1:00 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: TBA, or by appointment

Prerequisites/Recommended Background

BIOL 398-05: 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 9:40 – 10:55 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:

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.
You are responsible for your own learning and for being a good class citizen.
Class will start promptly on time.
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.
You are expected to bring the required materials to each class session.
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 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 398-05/MATH 388-01 on Brightspace (the MATH and BIOL sections of the course are merged into one site under "Biomathematical Modeling" 77775.201710). The Brightspace site may be used for materials that cannot be made public on the OpenWetWare.org wiki, such as certain readings and grades.

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 Brightspace 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:

Individual electronic lab notebook/journal assignments (10 points each)     130 points 
Shared journal assignments (3 points each)                                   40 points
Oral presentations (journal club and research)                              150 points 
Final Written Report                                                        100 points
Total                                                                    420 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/Journal Assignments

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.
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 the whole class, 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 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
- 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.

What to do if there is a OpenWetWare outage

We recommend that when doing your journal assignments, "save early, save often". That is, work in short increments, saving your work in small pieces. This will help you avoid losing your work if there is an issue with the internet.
We also recommend that you begin your assignments well ahead of the deadline so that you have enough time to complete them on the wiki.
While we do not anticipate any problems, in the event of an OpenWetWare outage near a deadline, please do the following:
- send an e-mail to both instructors notifying us of the outage, attaching a screenshot documenting the problem;
- complete the unfinished portion of the assignment as a Word document and e-mail it to both instructors. Even though you are saving it as a Word document, write it in wiki syntax so that it can be saved back to the wiki when it becomes available again.

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 5 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 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/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/BIOL398-05/S17.