CS 441: Syllabus

Syllabus for Spring 2010

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.


Milestones 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 turn in one written report and give one 20-30 minute presentation to your classmates.

There are four groups in this class. Groups 1 and 2 will present their milestone reports on Thursdays of odd-numbered weeks and groups 3 and 4 will present theirs on Thursdays of even-numbered weeks. 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 24 hours before the corresponding oral presentation.

WeeksMilestoneWritten Report
1, 2 Literature Search
  • Bibliography with each paper summarized
  • 1 page project proposal

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3, 4 Initial Code Demonstration
  • Figures demonstrating functional modeling code
  • Discussion of challenges to achieving Milestone 2
  • Plan for Milestone 3
5, 6 Results Part I
  • Figures containing initial results
  • Discussion of challenges to achieving Milestone 3
  • Plan for Milestone 4

Spring Break
7, 8 Results Part II
  • Figures containing better results with some analysis
  • Discussion of challenges to achieving Milestone 4
  • Draft of poster
9, 10 Analysis Part I
  • Analysis of results
  • Discussion of challenges to achieving Milestone 5
  • Draft of Figures and captions for final write-up
11, 12 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:

Written Milestone Reports 35%
Oral Milestone Reports 35%
Participation 15%
Final Write-up and Presentation 15%

Grading Written Milestone Reports

The grade for each report will depend on teamwork and content:

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 presentation 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. Better questions lead to higher grades. Part of your grade will depend upon written questions, passed to me at the end of each group presentation.

Grading the 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), on clarity (is it well written?), and teamwork (like the milestone reports, part of your grade will depend on your contribution to the team). 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.


Ideally, each team will have one biologist, one mathematician, and one computer scientist in it. We will come close to that ideal in this course. One obvious question is "What is the role of each team member?" For this course, each of you is responsible for writing code, carrying out numerical experiments, and analyzing results. Since this is the bulk of the work, and all of you have experience doing this, it makes sense that everyone should contribute to it. Why, then, have people with different backgrounds on each team? The answer is that there are frequently moments in which expertise is needed in one area or another. In those moments, there should be a member of the group prepared to apply their expertise. For example, the biologist will probably have a larger role in the literature search. The computer scientist will have a larger role in the initial design of the code. And the mathematician will have a larger role in ensuring the correctness of the mathematics in the write-up and in the code.

Poster Presentation

April 28-30, 2010 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 17. More details about that later.


Attendance and Participation

This course will be run like a series of research group meetings. In a research group, 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 meetings. First, you need 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. The presentation times cannot be delayed, because the schedule simply doesn't allow for it. Because there is flexibility in the content of each written milestone report (i.e. you can talk about challenges instead of results), you should not have any problem making your deadlines. 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. 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.