Fall 2020Syllabus for Fall 2020
Course Outline
This course is an introduction to the field of molecular systems biology, which aims to understand the mechanisms underlying complex biological processes. Key to this endeavor is the process of formulating and analyzing mathematical models. In this course, we will learn how to relate mechanistic insights gleaned from data to cartoon drawings of the system, then how to translate the cartoon drawing into mathematical expressions, next how to use optimization techniques to fit any unknown parameters, and finally how to analyze models by simulating biological experiments and assessing sensitivity to perturbation.Topics
- Formulating models using standard kinetics (what math to use)
- Motifs in biological systems (understanding common pieces of models)
- Simulation techniques (how to solve ODE's with a computer)
- Parameter-fitting through optimization (finding parameter values that minimize our error)
- Sensitivity analysis (assessing how a model reacts to changes in parameters)
Grading
The course grade will be determined as follows:
| Homework Assignments | 20% |
| Short Presentation of Figure in Journal Article | 5% |
| Projects | 55% |
| Final Project | 15% |
| Class Participation | 5% |
Work outside of class time
There are two types of work you need to do regularly outside of class: (1) homework assignments which help you learn new material (by reading or trying out some new code), and (2) projects, which give you the opportunity to study a topic in depth. On most days there will be both a project and a homework due at some point in the near future. Please plan accordingly. You will need to balance both types of work for this course. In addition, once or twice during the semester, you will be asked (in advance) to explain a figure in a journal article (from the homework) to your classmates.You may work with a partner on the projects. I will be assisting the pairing, and you will be asked to identify people you do and don't want to be paired with. We may adjust who is paired with whom, but my intention is to allow people to work together on multiple projects. Each pair turns in 1 project for grading. If you choose to work alone, that is alright, but I will be grading each project as if 2 people worked on it.
Homework Assignments
In general, homework assignments are meant to give you additional practice with coding and reading journal articles. Grading for the homework assignments will be essentially boolean. As long as you turn in a complete set of answers and demonstrate (with the quality of the answer) that you put your best effort into them, you will receive full credit. Late or incomplete homeworks will have points deducted.
A note about the readings: Instead of using a textbook for this course, we are going straight to the source, and will be reading journal articles. To help you make the most this experience, all readings will be accompanied by a set of questions. The questions are designed to help you get the most out of the paper.
Figure Presentations
Approximately twice in the semester, you will also be given the responsibility of presenting one or more figures in a journal article. Plans are evolving for how those presentations will be delivered, but the non-COVID approach is a presentation in class. I may continue to use that approach for on-campus students. I may use a Zoom meeting for those who are off-campus, or may have students record videos. It depends on whether or not there is a time that will work for all of the remote students. Grading for a figure presentation will also be essentially boolean, and I will develop a rubric and distribute it soon. What I can say here is that presenting a figure involves explaining to your classmates what was done to generate the data for the figure, how to read the figure, and what conclusions can be drawn from the results.Projects
There will be one project for each topic in covered in the course. This means there will be 5 projects during the semester, each of which gives you the opportunity to explore that topic in depth, and one final project, which includes all 5 topics. For each project, you will complete a Juypter Notework, which will include Python code, plotted results, and text summarizing and analyzing your methods and results. A set of questions will provide the framework for your code-writing and analysis. Because I want you to have the chance to engage deeply and to have some intellectual autonomy, these questions are intentionally open-ended and there will not be a detailed set of instructions.Projects are meant to be more polished and will be graded with greater attention to detail. Both partners will receive the same grade for the project, but the relative contributions and willingness to listen will affect participation grades individually. For each project, each partner will fill out a separate google form, indicating what role they played, what role their partner played, and whether or not the ground rules were followed (see details below for ground rules). The write-ups should be neat and thorough, yet succinct. Answering all of the questions adequately will earn you a B+. To earn an A- or A, you must be particularly convincing and thorough when you answer the "why?" or "how?" or "what if?" questions. This does not mean that I want you to turn in reams of paper. It means that you should include carefully chosen additional examples or evidence to back up your point. Code that runs additional examples, or which creates a figure that summarizes a lot of results are particularly helpful at boosting grades. The questions I will be asking myself when I am grading are, for example: Does this make sense? Do they make it clear why she came to their conclusions? Are they being precise? Do they include the appropriate mathematics when they are called for?
Projects are graded on a 30 point scale. Here is a rough guide to grading:
| Notebooks include requested code and figures. No extra work was done. | 25 |
| Notebooks include requested code and figures. There is a small amount of extra work to support points. | 26 |
| Notebooks include requested code and figures. There is a medium amount of extra work to support points. | 27 |
| Notebooks include requested code and figures. There is a large amount of extra work to support points. | 28 |
| Notebooks include requested code and figures. There is an even larger amount of extra work to support points. | 29 |
| Wow | 30 |
Late Policy: If a project is turned in more than 1 week late, then you can earn only 26 out of 30 points. This policy is intended to encourage you to keep moving forward and not to spend lots of time on an early project when you should be moving forward.
Working with Partners
My goal is for you to have a partner in this class so that you can discuss material with at least one other person, so that you can go deeper in the material and help unstick each other with the coding. I am going to assign partners, with your input. As a class, we will elaborate this set of ground rules for how you carry out your partnerships.- Neither of us will work on the project without the other's permission.
- The documents with which we are working are equally accessible to both partners. We will share the documents by .... (Note from SRT: You may want to use DropBox, since GoogleDocs isn't going to work well for Jupyter Notebooks.)
- For each project, we will split up the work by ....
- We will take turns taking the lead on every other project. By "taking the lead", we mean...
- We will make sure we listen to each other's ideas.
- We will fulfill our tasks, but if something goes wrong (e.g. an injury), we will tell our partner, so that alternate arrangements can be made.
Class Participation
The material in this course covers multiple disciplines and is best learned by asking questions and discussing with others. Your participation grade will depend on your post-project Google forms and on your general engagement in the course, which you can demonstrate by participating in class discussions, appearing on others tudents's lists of acknowledgements, or coming to office hours.Office Hours
Please visit me in my office and on Zoom! I will post official office hours, but am also willing to help over email and may be able to make additional Zoom meetings.Collaboration and Academic Honesty
This policy applies to anyone you work with other than your partner.Computer science, both academically and professionally, is a collaborative discipline. In any collaboration, however, all parties are expected to make their own contributions and to generously credit the contributions of others. In our class, therefore, collaboration on homework and programming assignments is encouraged, but you as an individual are responsible for understanding all the material in the assignment and doing your own work. Always strive to do your best, give generous credit to others, start early, and seek help early from both your professors and classmates.
The following rules are intended to help you get the most out of your education and to clarify the line between honest and dishonest work. We reserve the right to ask you to verbally explain the reasoning behind any answer or code that you turn in and to modify your project grade based on your answers. It is vitally important that you turn in work that is your own. We do use automated plagiarism detection software, so please be sure to abide by these, rather minimal, rules. Reports of academic dishonesty are handled by an academic review board and a finding of academic dishonesty may result in significant sanctions. For more details on Colby's Academic Integrity policies and procedures, see colby.edu/academicintegrity.
- If you have had a substantive discussion of any programming project with a classmate, then be sure to cite them in your write-up. If you are unsure of what constitutes "substantive", then ask me or err on the side of caution. As one rule of thumb, if you see more than 10 lines of someone else's code, then you should cite them. You will not be penalized for working together.
You must not copy answers or code from another student either by hand or electronically. Another way to think about it is that you should be talking English with one another, not Python.
Religious Holidays
Colby College supports the religious practices of students, faculty, and staff, but we don't always know which people will observe which holidays. Since I need to plan course activities in advance, I need to know in advance, if you need to miss a class or have a deadline adjusted in order to observe a holiday. Please notify me by e-mail at least 14 days in advance of any religious holiday that will affecty your ability to participate in this course.The Colby Affirmation
Colby College is a community dedicated to learning and committed to the growth and well-being of all its members.
As a community devoted to intellectual growth, we value academic integrity. We agree to take ownership of our academic work, to submit only work that is our own, to fully acknowledge the research and ideas of others in our work, and to abide by the instructions and regulations governing academic work established by the faculty.
As a community built on respect for ourselves, each other, and our physical environment, we recognize the diversity of people who have gathered here and that genuine inclusivity requires active, honest, and compassionate engagement with one another. We agree to respect each other, to honor community expectations, and to comply with College policies.
As a member of this community, I pledge to hold myself and others ccountable to these values.
Sexual Misconduct/Title IX Statement
Colby College prohibits and will not tolerate sexual misconduct or gender-based discrimination of any kind. Colby is legally obligated to investigate sexual misconduct (including, but not limited to sexual assault and sexual harassment).
If you wish to speak confidentially about an incident of sexual misconduct, please contact Colby Counseling Services (207-859-4490) or the Director of the Gender and Sexual Diversity Program, Emily Schusterbauer (207-859-4093).
Students should be aware that faculty members are considered responsible employees; as such, if you disclose an incident of sexual misconduct to a faculty member, they have an obligation to report it to Colby’s Title IX Coordinator. “Disclosure” may include communication in-person, via email/phone/text, or through class assignments.
To learn more about sexual misconduct or report an incident, visit www.colby.edu/sexualviolence/.