CS 441: Systems Biology II

Course Information for Spring 2021

Instructor: Prof. Stephanie R. Taylor (srtaylor)

Section A: TR 9:30-10:45, Davis 102 and online
Section B: TR, 11:00-12:15, Davis 117 and online

Office Hours

Typical Office hours on Zoom (link sent on email):

• Mondays 3-5pm,
• Wednesdays 3-4pm and 8-10pm
• Thursdays 1:30-2:30pm

I often need to change my office hours to accommodate meetings. I post an image of my calendar at the beginning of each week on my home page.

By appointment (email me), and whenever my door is open

Course Description

In this course, you will apply principles learned in Systems Biology I to a particular biological system. You will be working in an interdisciplinary team to complete a semester-long project. This will involve reading journal articles, designing and running numerical experiments, and analyzing results. Throughout the semester, you will be presenting challenges and results. The course will culminate in both a poster presentation and a comprehensive journal-article styled report and oral presentation.

Useful Links

• Folder of Project Ideas (accessible to Colby community only)
• Numerical software
  • See Software page for instructions for installing the software you need for this course.
  • Numpy documentation
  • Scipy documentation
  • Matplotlib documentation
  • Jupyter Notebook documentation
• Journals and indexing services
  • Google Scholar - a good search engine for published articles
  • PubMed - a searchable database of bio-medical articles. Most of the articles we are interested in are listed here.
  • systems biology @ nature.com Nature's Systems Biology website, which links to important systems biology papers
  • Molecular Systems Biology - Nature's open access journal on molecular systems biology (this contains some great articles)
  • PLoS Computational Biology - a top-notch journal for computational biology
• Biology-related resources
  • The Medical Biochemistry Page - a page containing accessible descriptions of various aspects of medical biochemstry.
  • NCBI's Bookshelf's searchable version of Molecular Biology of the Cell 4/e - on-line version of a classic textbook (note that this is not the most recent edition)
• Systems biology standards and model repository
  • SBML.org - website for the Systems Biology Markup Language
  • SBGN.org - website for the Systems Biology Graphical Notation
  • BioModels.net - a database of mathematical models of biological systems