BIOL398-03/S13
Announcements
- Please fill out the RISC post-course survey. Please use "Dahlquist" as the instructor's last name.
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)
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| Thurs
Jan 17 |
Chemostat | Introduction to population growth, nutrients, and the chemostat
Discuss the Week 1 assignment (accounts should be ready to wiki at this point)
Jan 18: last day to add or drop a class without a grade of W |
Week 1 Assignment
Due midnight 1/23 | |
| 2 | Tues
Jan 22 |
Matlab tutorial Try to work thru 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 24 |
Berg, Tymoczko, Stryer (2002) Biochemistry, 5th ed., Sections 8.1-8.4 | Enzyme kinetics/nitrogen metabolism | Week 2 Assignment
Due midnight 1/25 | |
| 3 | Tues
Jan 29 |
Enzyme kinetics/nitrogen metabolism | ||
| Thurs
Jan 31 |
ter Schure et al. (1995) J. Bacteriology | Journal Club 1
|
Week 3 Assignment
Due midnight 1/31 | |
| 4 | Tues
Feb 5 |
Return of the Chemostat: steady states and multiple nutrients | Metabolic pathway modeling project | chemo_script chemostat matlabs for in-class |
| Thurs
Feb 7 |
Continuation of steady states and multiple nutrients script for today DE function | Metabolic pathway modeling project | Week 4 Assignment BGF's thoughts on Week 4 Q's
Due midnight 2/8 | |
| 5 | Tues
Feb 12 |
chemostat de model chemostat de driver script | Metabolic pathway modeling project | |
| Thurs
Feb 14 |
terSchure data | Metabolic pathway modeling project | Week 5 Assignment
Due midnight 2/15 | |
| 6 | Tues
Feb 19 |
DE file Script to solve DE Fit criterion for terSchure data Script to do parameter estimation | Metabolic pathway modeling project | |
| Thurs
Feb 21 |
Metabolic pathway modeling project | Week 6 Assignment
Due midnight 2/22 | ||
| 7 | Tues
Feb 26 |
Research Presentation 1: Metabolic Pathways
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| Thurs
Feb 28 |
Research Presentation 1: Metabolic Pathways
|
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 | |
| Thurs
Mar 14 |
Alberts et al. (2002) Ch. 8: Microarrays, Campbell & Heyer Ch. 4 on MyLMUConnect, DeRisi et al. (1997), Microarray animation | Introduction to microarrays (continued) | Week 8 Assignment
Due midnight 3/15 | |
| 9 | Tues
Mar 19 |
Introduction to Probability and Statistics | ||
| Thurs
Mar 21 |
Probability and statistics continued
Mar 22: Last day to withdraw or change to credit/no-credit status |
Week 9 Assignment
Due midnight 4/3 Note: new NEW due date | ||
| 10 | Tues
Mar 26 |
Statistics continued (microarray spreadsheet) | ||
| Thurs
Mar 28 |
Easter break | No Week 10 Assigmment | ||
| 11 | Tues
Apr 2 |
Ernst & Bar-Joseph (2006) BMC Bioinformatics | Clustering
Begin Week 12 Assignment |
|
| Thurs
Apr 4 |
Tai et al. (2007) Molecular Biology of the Cell 18: 5100-5112. | Journal Club 2 | Week 11 Assignment
Due midnight 4/4 | |
| 12 | Tues
Apr 9 |
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 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 | |
| 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 |
Gene regulatory network modeling project: estimating parameters | Week 13 Assignment
Due midnight 4/19 | ||
| 14 | Tues
Apr 23 |
Gene regulatory network modeling project: estimating parameters | ||
| Thurs
Apr 25 |
corrected estimation function | Gene regulatory network modeling project | Week 14 Assignment
Due midnight 4/26 | |
| 15 | Tues
Apr 30 |
estimation_driver.m general_parameter_estimation_function.m general_least_squares_error.m mm_network_dynamics.m sigmoidal_network_dynamics.m full_schade_data_05.xls | Gene regulatory network modeling project: forward simulation | |
| Thurs
May 2 |
Gene regulatory network modeling project: forward simulation | |||
| Finals | Thurs
May 9 |
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: W 1:00 - 2:00PM, TR 11:00AM - 12:00PM
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 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 his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
- You are responsible for your own learning and for being a good class citizen.
- We will act with honesty and integrity at all times.
- We will always treat individuals with respect.
- Class will start promptly on time.
- You are expected to come to class having done the assigned reading and preparatory work.
- 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 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 398-03 on MyLMUConnect. 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) 120 points Journal club presentations (20 points each) 40 points Research presentations (20 points each) 40 points Final Written Report 80 points Total 280 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 Friday PST (Thursday night/Friday 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.
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 Friday, May 10 at 5:00 PM.
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 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, “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
- 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.
