Course Information for Spring 2016
Time: TR 9:30-10:45 or TR 11:00-12:15
Place: Davis 117/122
Final Exam (oral presentations): Wed May 11th at 1:30pm
Instructor Information
Prof. Stephanie R. Taylor (srtaylor
)
Office: Davis 114
Email: s r taylor _at_ colby _dot_ edu
Office hours: M 1-3, T 2:30-4:30, F 1-3
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
- 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