Professor and TA contact info

• Instructor: Joel Grodstein, joel.grodstein@tufts.edu, https://www.eecs.tufts.edu/~joelg
• Office Hours: Tue, Th 3:15-4:15 (i.e., an hour before class), or by appointment in Halligan extension room 11 (except I may be in the recitation on Tuesdays). Directions are here.
• TA: Cassandra Donatelli, Cassandra.Donatelli@tufts.edu. Office hours Wed 9-10am in SEC, and Tue 10-11am at 200 Boston Ave (with an hour's advance notice)
• For emergencies or private matters, please e-mail or see me directly.

Calendar, recitation, syllabus, etc

• The tentative survey is here.
• The class calendar is here.
• In addition to the two class meetings per week, there are two optional recitation sessions, for help with the programming homeworks. They are Tuesday 3:15-4:15 (i.e., right before our Tuesday class) and Wednesday 10:30-11:30. They are in Halligan room 122 (a.k.a. the Windows PC lab).
• The syllabus is here.
• A flashy advertisement for the class is here.

Homework logistics

• You can use any Windows PC in Halligan room 122 to do your homework. You can also use any other computer that has Python installed; it's easy enough to install it on your own PC. Most Macs already have Python installed, but it's typically only Python v2 and you'll need Python v3 for this course.
• Turn in your homework on the web with at this link. It will ask you for you Halligan username and password; these are just your usual Halligan ones that you use for the Windows PC lab (not your Tufts UTLN).
• Some of the homeworks require you to start with a Python file(s) that we supply. If so, you can find them at Q:/194MSO/2018s/public_html/HW/code. You can also find them linked from the assignment on this web page.

Homeworks

• HW #0 (Introduction to Idle). The homework description is here.
• HW #1 (lx-mx tables and population growth). The homework description is here. The extra-credit solution is here.
• HW #2 (population growth with arrays). The homework description is here.
• HW #3 (stochastic tortoises). The homework description is here. The extra-credit solution is here.
• HW #4 (kinetic proofreading). The homework description is here. Here are the files kinetic_proofreading.py, sim_infrastructure.py and sim_library.py The extra-credit solution is here.
• HW #5 (soft robotics). The homework description is here. Here are the files manducaEv.py, manducaFitness.py and manducaGraph.py
• HW #6 (chemotaxis). The homework description is here. Here are the files chemo_high.py and chemo_high_classes_swarm.py
• HW #7 (bioelectricity). The homework description is here.

Quiz solutions

• Quiz #1 solutions
• Quiz #2 solutions
• Quiz #3 solutions

Lecture slides

• Course intro
• Population modeling
• differential equations
• kinetic proofreading
• soft robotics and genetic algorithms
• bacterial chemotaxis
• bioelectricity

Python slides

• variables
• loops
• arrays
• if-then
• functions
• 2D arrays
• objects

Background reading

• Bioelectricity background reading: a planaria primer, a paper on chemically morphing a planaria into a related but different species, and one on complex regeneration in moose and fiddler crabs.
• The best introduction to bioelectricity I've found is "Biological Physics: Energy, Information, Life" by Philip Nelson. It's the textbook for PHYS 25, and so the bookstore may have some copies left. Tisch has two copies, but they're both out at the moment. You can borrow my copy for a few days as well. My own notes on the book's material are here and here.