BIOL388/S25
Announcements
Upcoming Seminars
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 14 |
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| Thurs
Jan 16 |
Jan 17: last day to add or drop a class without a grade of W |
Week 1 Assignment
Due 12:01am 1/25 | ||
| 2 | Tues
Jan 23 |
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| Thurs
Jan 25 |
Alberts et al. (2002) Molecular Biology of the Cell Ch. 6: From DNA to RNA and Ch. 6: From RNA to Protein | Central Model of Molecular Biology: transcription | Week 2 Assignment
Due 12:01am 1/30 | |
| 3 | Tues
Jan 28 |
Central Model of Molecular Biology: translation | ||
| Thurs
Jan 30 |
Regulation of gene expression in prokaryotes
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Week 3 Assignment
Due 12:01am 2/6 | ||
| 4 | Tues
Feb 4 |
Cell Collective basic Lac operon model | ||
| Thurs
Feb 6 |
Cell Collective basic Lac operon model | Week 4 Assignment
Due 12:01am 2/13 | ||
| 5 | Tues
Feb 11 |
Cell Collective advanced Lac operon model | ||
| Thurs
Feb 13 |
Cell Collective advanced Lac operon model | Week 5 Assignment
Due 12:01am 2/20 | ||
| 6 | Tues
Feb 18 |
"Under the hood" of the Lac operon model | ||
| Thurs
Feb 20 |
"Under the hood" of the Lac operon model | Week 6 Assignment
Due 12:01am 2/27 | ||
| 7 | Tues
Feb 25 |
"Under the hood" of the Lac operon model | ||
| Thurs
Feb 27 |
Model "show and tell" | No Week 7 Assignment | ||
| Mar 3, 5 | Spring Break | |||
| 8 | Tues
Mar 11 |
Eukaryotic gene regulation | ||
| Thurs
Mar 13 |
Alberts et al. (2002) Ch. 8: Microarrays, Campbell & Heyer Ch. 4, Brown & Botstein (1999), DeRisi et al. (1997), Microarray animation | Introduction to microarrays | Week 8 Assignment
Due 12:01am 3/20 | |
| 9 | Tues
Mar 18 |
Probability and statistics | ||
| Thurs
Mar 20 |
Probability and statistics | Week 9 Assignment
Due 12:01am 3/27 | ||
| 10 | Tues
Mar 25 |
Scientific presentations | ||
| Thurs
Mar 27 |
Journal Club presentation | Week 10 Assignment
Due 12:01am 4/3 | ||
| 11 | Tues
Apr 1 |
Microarray data analysis
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| Thurs
Apr 3 |
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Week 11 Assignment
Due 12:01am 4/10 | ||
| 12 | Tues
Apr 8 |
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| Thurs
Apr 10 |
Apr 11: Last day to withdraw or change to credit/no-credit status |
Week 12 Assignment
Due 12:01am 4/24 NOTE Different Due Date | ||
| 13 | Tues
Apr 15 |
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| Thurs
Apr 17 |
Easter Break | No Week 13 Assignment | ||
| 14 | Tues
Apr 22 |
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| Thurs
Apr 24 |
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Week 14 Assignment
Due 12:01am 5/1 | ||
| 15 | Tues
Apr 29 |
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| Thurs
May 1 |
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Week 15 Assignment
Due 1:00pm 5/9 NOTE Different Due Date | ||
| 16 | Tues
May 6 |
Final Research Presentation during class | ||
| Finals | Fri
May 9 |
Final Deliverables Due 1:00 PM |
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: FEA 289
- Office hours: Tuesdays 2:00-3:30 PM, Thursdays 3:00-4:30 PM, and by appointment. Login to Brightspace to find Calendly link to schedule an in-person or Zoom 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: Tuesdays and Thursdays 2:00-3:00 PM, and by appointment.
Prerequisites/Recommended Background
- BIOL 388: MATH 123 (Calculus for Life Sciences II) or MATH 132 (Calculus II) or MATH 204/MATH 205 (Applied Statistics); BIOL 201 (Cell Function); or consent of instructor
- MATH 388: 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 9:55 – 11:10 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.
Note that the last day to add or drop a class without a grade of W is January 17. The withdrawal or credit/no-credit status deadline is April 11.
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 Course-Related Behavior and Student Conduct Code.
- 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 and other ancillary devices must be turned off and put away out of sight. Your own laptop and/or tablet may be used to conduct the class exercises, provided that you have confirmed with the instructor that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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 388-01/MATH 388-01 on Brightspace (the MATH and BIOL sections of the course are merged into one site under "Spring 2025 Biomathematical Modeling (BIOL 388-01, MATH-388-01)"). 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 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 two major modeling projects throughout the semester.
Course Objectives and Learning Outcomes
- You understand the structure, function, and regulation of prokaryotic and eukaryotic 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
Course Work and Grading
Your work in this course will be assessed in three areas:
Individual electronic lab notebook/journal assignments (12 points each) 156 points Shared class journal assignments (3 points each) 39 points Oral presentations 155 points Final project deliverables 50 Total 400 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 this wiki that we will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferable to other applications. The following guidelines apply:
- Your weekly journal entry is typically due at 12:01 AM on Thursday PST (Wednesday night/Thursday morning); consult the schedule for specific due dates for each assignment.
- Each weekly assignment has an individual component and a shared component. You will earn 12 points per weekly submission for the individual journal entry and 3 points per submission for the shared class 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:
- Statement of purpose of the assignment/exercise
- Documentation of workflow (methods) in enough detail so that the results can be reproduced
- Results, backed up by data, images, and files, and answers to any specific questions posed in the exercise
- Scientific conclusion
- 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.
Oral Presentations
You will give three oral presentations in this course. An informal "show and tell" presentation at the end of the Lac operon project, a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature, and a research presentation on your final project. 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.
Final Project Deliverables
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 9 at 1:00 PM. The Final Written Report must be completed to receive a passing grade in the course.
Extra Credit
Students may accumulate up to 2.2% (10 points) of their final grade in extra credit by attending Biology or Mathematics Department seminars and completing the seminar sheets. Each seminar attended is worth 2 points with up to 5 seminars (10 points) 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.
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. The minimum penalty for an instance of academic dishonesty in BIOL/MATH 388, even on a 1-point assignment or extra credit assignment, is a one-letter grade penalty in the course and a zero on the assignment. 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. Note that students may not submit assignment or paper prompts to CourseHero, Chegg, online artificial intelligence tools, or any other such website; answers or papers derived from such sites are considered to be a direct violation of the Academic Honesty policy. 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.
You are required to sign the Academic Honesty Agreement for this course.
Academic Honesty Resources
- LMU Academic Honesty Policy and Procedures
- Academic Honesty Agreement (on Brightspace)
- The Davidson College Department of Biology Statement on Plagiarism
- Guidelines for Literature Citations in a Scientific Paper (on Brightspace)
- BIOL 478 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/BIOL388/S25.
