Course Information for Fall 2012

Time: TR 9:30 - 10:45
Place: Roberts 225
Final Exam: Wednesday, December 12th, 1:30 pm

Instructor Information

Prof. Stephanie R. Taylor (srtaylor)
Office: Roberts 224D
Email: s r taylor _at_ colby _dot_ edu
Office hours: M 1:30-3:30, T 2-5, R 1:30-3:30
By appointment (email me), and whenever my door is open

Course Description

An introduction to systems biology - the process of biological discovery through the development and analysis of mathematical models. Topics include developing and using computational methods to build, simulate, and analyze models. Students will be given weekly exercises to reinforce concepts discussed in class, the textbook, and journal articles.

Useful Links

Numerical software
- A Matlab tutorial at Clarkson University
- Scilab, an open-source alternative to Matlab
- Scipy, a Python library for numerical computing and its documentation, if you choose to travel this treacherous path
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