CS 441: Syllabus

Syllabus for Spring 2016

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

  1. 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.
  2. 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.
  3. 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.
  4. 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:


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 give one 20-30 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.

WeeksMilestoneWritten Report
1, 2 Literature Search
  • Bibliography with each paper summarized (done per person)
  • Goals for each person (done per person)
  • 1 page project proposal (done as a group)
3, 4 Initial Code Demonstration
  • Figures demonstrating functional modeling code
  • Discussion of challenges to achieving Milestone 2
  • Plan for Milestone 3
5, 6, 7 Results Part I
  • Figures containing initial results
  • Discussion of challenges to achieving Milestone 3
  • Plan for Milestone 4

Spring Break
8, 9 Results Part II
  • Figures containing better results with some analysis
  • Discussion of challenges to achieving Milestone 4
  • Draft of poster
10, 11 Analysis Part I
  • Analysis of results
  • Discussion of challenges to achieving Milestone 5
  • Draft of Figures and captions for final write-up
12, 13 Analysis Part II
  • Analysis of results
  • Discussion of challenges to achieving Milestone 6
  • Draft of final write-up


The course grade will be determined as follows:

Activity Percentage Graded as individual or group
Written milestone reports 35% individual
Oral milestone reports 15% group
Participation 15% individual
Scientific poster (at CLAS) 15% group
Final write-up and presentation 20% group

Grading Written Milestone Reports

The grade for each report will depends on content. I want to know 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.

Grading Oral Milestone Presentations

The grade for the oral presentations is based largely on your ability to communicate your research to me and to your classmates. In order to receive a high grade, 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.

Grading Class Participation

The grade for class participation will depend largely on your willingness to ask questions during or after another group's presentation. Part of your grade will depend upon written questions, passed to me at the end of each group presentation.

Grading the Scientific Poster, Final Write-Up and Presentation

The final write-up and presentation will be graded based on the level of sophistication of the research (design of numerical experiments and depth of analysis) and on clarity (is it well written?). The final presentation will be graded on content and polish. This presentation should be streamlined, yet understandable.

For more information about expectations and the assignment of grades, see this document.

Poster Presentation at CLAS

April 28, 2016 is the date of the Colby Liberal Arts Symposium at which each group will present a poster.


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.


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/.