Course Grade

The course grade consists of the following components and percentages:

Homework: 20%

Modeling game: 30%

Course project: 50%

Homework

There will be 2 homeworks, each worth 10 points. The homeworks are intended to provide experience with constructing and evaluating models. The homeworks will use the Antimony python library to model biological systems and python matplotlib to plot results.

  • Homework 1: Due Oct 24 - gene regulation

  • Homework 2: Reconstruct the model in the Koholoenko paper cited in the references page.

Modeling Game

Students will participate in the modeling game and produce a model that conforms well with the data provided.

Course Project

The project will be to define and partially develop a tool that aids in building biomedical models. There will be a presentation, a paper, and code in a github repository. The presentation and paper should be structured as:

  1. Introduction. Describe the problem addressed.
  2. Related work.
  3. Technical approach. Describe how you wll address the problem described in the introduction. You should include relevant technical details such as algorithms, data flows, and software designs.
  4. Preliminary implementation. Provide python codes that implement one or more key elements of the technical solution.
  5. Disucssion and Future Work. Discuss the trade-offs and challenges of the approach that you propose. Describe the next steps to build a realistic tool.

The grading rubric will emphasize innovation in the problem addressed, feasibility of the technical approach, and the benefits that could be provided by the tool. The write-up is due by midnight of the last day of class, 12/7.