Spring 2023Course Information for Spring 2023
Instructor: Prof. Stephanie R. Taylor (srtaylor)
Tues/Thurs, 11:00-12:15, Davis 122
Office Hours
Typical Office hours:
- Mondays 4-5pm (my office or Davis 122)
- Wednesdays 4-5pm (my office or Davis 122)
- Wednesdays 8-10pm (by appointment over Zoom)
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
- Course Google Drive (accessible only if you log in with a Colby username)
- BioClock Studio at UCSD (they have great tutorials on circadian terminology). I recommend the following videos
- Free-Running Periods
- Naming Conventions
- Phase Response Curves
- Mammalian Molecular Entrainment to Light and Networks (it has more details about the signaling pathways than we need, but it does a great job telling the overall story)
Their glossary of circadian terms is also a great reference.
- 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