Spring 2021Syllabus for Spring 2023
This semester will be characterized by a group project, which will produce enough research to write a journal-style article. You will be working in groups and, every other week, will have the opportunity to share your progress with the rest of the class. There will be several milestones along the way.
Learning Goals
- Literature search: Students can search the published literature to find articles relevant to their research topic. They should be able to identify the most important articles.
- Expertise on one project: Students will demonstrate an understanding of one biological system and the relevant mathematical models. They will demonstrate proficiency in at least one technique of model creation or analysis.
- Generating and analyzing results: Students can ask relevant questions about their system and its model. They can write appropriate code to produce and analyze results.
- Communication and teamwork: Students can perform their research within a team. Further, they can discuss their research with their classmates and present their results in both oral and written formats.
Class Meetings
Class time will be used for three purposes:- For each team to work together on their project.
- For each team to consult with Stephanie about their project.
- For each team to update the rest of the class as they progress in their research projects. At each milestone (see below for details), each group will give an oral presentation with slides. Everyone in the class will be expected to ask questions and everyone in the group will be expected to answer questions.
- Fourth (rare) purpose: For Stephanie to impart knowledge and instructions to you.
Milestones
There are six milestones, and they are designed to provide support for you as you carry out your research. First, they break the project into manageable chunks. Second, they provide a mechanism for me to supply feedback. Third, they provide incentive for you to work together as a group. For each milestone, your group will give a 15-20 minute presentation to your classmates.Below is an overview of the milestones and of the content expected for the corresponding written reports. The oral presentations should contain roughly the same content. Written reports are due on the same day as the corresponding oral presentation. For Milestones 2 and on, it is fine to turn in the slides as your written report (except that the poster and paper drafts need to be turned in separately).
| Weeks | Milestone | Written Report |
|---|---|---|
| 1, 2 | Literature Search |
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| 3, 4 | Initial Code Demonstration |
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| 5, 6, 7 | Results Part I |
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| 8, 9 | Results Part II |
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| 10, 11 | Analysis Part I |
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| 12, 13, 14 | Analysis Part II |
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Final Presentations
The final exam periods are are Saturday May 15th at 9am (for Section A) and Monday May 17 at 9am). My plan is for each group to give their final presentation during one of these times.Grading
The course grade depends on these course activities:| Activity | Percentage | Graded as individual or group |
| Written milestone reports | 35% | group |
| Oral milestone reports | 15% | group |
| Participation | 15% | individual |
| Scientific poster (at CLAS) | 15% | group |
| Final paper and presentation | 20% | group |
I provide verbal and written feedback during the semester, and we collaboratively determine your grade at the end of the semester. How do you aim for an A? Aim for Excellence:
What makes a Excellent Written Milestone Report?
It should be clear what you did and what your plan is. If you ran into problems and didn't make much obvious progress, then tell me about it. An excellent report indicates to me that you spent significant time (8-10 hours outside of class per week) and thought (you may have tried many approaches, but they weren't merely scattershot) into your project.What makes a Excellent Oral Milestone Presentation?
An excellent presentation is easy for your audience (classmates who are working on different projects and your professor) to follow. The contributions of each team member must be well-integrated into a coherent presentation. This does not mean the visuals must be polished -- you should spend more time thinking about how to talk to each other and to your classmates than about making pretty slides. Also, it is perfectly acceptable to spend most of your presentation talking about failures.What makes for Excellent Class Participation?
An excellent participant is a good audience member. An excellent participant ask questions during or after another group's presentation. After each presentation, you will be asked to submit a written question or a short statement about what you learned.What makes a Excellent Scientific Poster?
An excellent scientific poster tells the story of your project graphically (with text to support it) and is understandable to a peer outside of the course. (I will give more details when it is time to draft the poster.)What makes a Excellent Final Paper?
An excellent final paper is a succinct description of your project's background, results, and analyses. (I will give more details when it is time to draft the paper.)For more information about expectations and how they relate to letter grades, see this document.
Poster Presentation at CLAS
Pre-COVID, students in CS441 presented a posters at the Colby Liberal Arts Symposium (CLAS). We had to take a break for awhile, but, this year, CLAS is back. Instead of classes, we will have CLAS on Thursday, April 27, 2023. CS441 will participate in a poster session that day..Policies
Attendance and Participation
This course will be run like a research group. Classes will emulate either time in the lab (i.e. you get to work with your group members) or group meetings. In a research group meeting, members take turns talking about the status of their research and ask for feedback from fellow researchers. It is therefore important that you attend all classes. On lab days, you want to be there to work with your group. On meeting days you want to be there to keep up-to-date with everyone's progress. Second, you should be providing feedback. Third, 15% of your grade depends on participation.Deadlines
The deadlines are designed to ensure that you are prepared to talk about your research with your fellow students. There is a small amount of wiggle room in the schedule, so it may be possible to change a presentation date. Talk to me AHEAD OF TIME if you are likely to have difficulty.Academic Honesty & Consequences for Academic Dishonesty
Honesty, integrity, and personal responsibility are cornerstones of a Colby education and provide the foundation for scholarly inquiry, intellectual discourse, and an open and welcoming campus community. These values are articulated in the Colby Affirmation and are central to this course. Students are expected to demonstrate academic honesty in all aspects of this course.
Academic dishonesty includes, but is not limited to: plagiarism (including quoting sources without quotation marks around the borrowed words and a citation); presenting another's work as one's own; buying or attempting to buy papers or projects for a course; fabricating information or citations; knowingly assisting others in acts of academic dishonesty; violating clearly stated rules for taking an exam or completing homework; misrepresentations to faculty within the context of a course; and submitting the same work, including an essay that you wrote, in more than one course without the permission of instructors.
Academic dishonesty is a serious offense against the college. Sanctions for academic dishonesty are assigned by an academic review board and may include failure on the assignment, failure in the course, or suspension or expulsion from the College. For more on recognizing and avoiding plagiarism, see the library guide: avoiding plagiarism.
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 http://www.colby.edu/sexualviolence/.