CS 441: Syllabus

Syllabus for Spring 2013

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.


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 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

May 1-3, 2013 is the date of Colby's undergraduate research symposium. Each group will present a poster at this symposium. There may also be another poster-presentation opportunity the weekend of April 20. More details about that later.


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

It is vitally important that you turn in work that is your own (note that this does not mean all code must be your own - it means that you must not take credit for someone else's work). In addition to the ethical implications of dishonesty, you undermine your ability to learn when you cheat. Please read Colby's Academic Integrity and Honesty Statement.