Professor and TA contact info and class meeting policy

• Instructor: Joel Grodstein, joel.grodstein@tufts.edu, https://www.eecs.tufts.edu/~joelg. Directions to my office are here,
• Class time/place: Mo/We 9:00-10:15am, Halligan 169
• Office hours: Mon/Wed 12:30-1:30 in Halligan 222, or by appt
• TA: none
• For emergencies or private matters, please e-mail or see me directly.

Calendar, syllabus and final projects

• The class calendar is here.
• The syllabus is here.
• A flashy advertisement for the class is here.
• You may choose any final project that you're interested in. Some potential choices are here.

Powerpoint slides for the lectures

• Unit 0: Day 1 course intro


• Unit 1a: How cells make voltages: steady-state bioelectricity
• Unit 1b: How neurons work so fast: quasi-steady-state bioelectricity
• Backgrounder: circuits


• Unit 2a: Neurons, sEMG and prosthetics
• Unit 2b: Your nervous system and bioelectrical medicine; getting rid of pain and pills


• Unit 3: Cardiac bioelectricity; engineering a fail-safe heart


• Unit 4a: Bio backgrounder
• Unit 4b: Weird nature and morphogenesis: how your body got its shape, and growing spare parts
• Unit 4c: Worms or cancer

Real physical labs (Skittles diffusion, surface-EMG and electrocardiogram)

• First, the all-important legal and safety overviews, as well as the ECE department's standard safety information
• Here's an overview of how to build the breadboard and hook up the electrodes to your body to read your ECG and surface-EMG. Also, 3M has published a nice website with more info, which also shows standard locations for an ECG (we won't quite use those locations, though).
• If you've not used an oscilloscope before, here's a reasonable tutorial
• Real lab 1: Skittles diffusion
• Real lab 2: surface-EMG lab; the answers will be here
• Real lab 3: taking your electrocardiogram; the answers will be here
• Turn in your lab reports on the web 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).

Simulation labs

• You can use any computer that has Python installed to do your simulation labs. It's easy enough to install it on your own PC with Thonny.
• You can find the Bitsey code here: sim.py, edebug.py, eplot.py and sim_toolbox.py. You will also need the appropriate version of main.py for each lab (see below).
• Simulation lab 1: steady-state bioelectricity, this lab's version of main.py, which is main_vlab1_SS.py. The answers will be here
• Simulation lab 2: quasi-steady-state bioelectricity; main_vlab2_QSS.py. The answers will be here
• Simulation lab 3: building a neuron; main_vlab3_neuron.py. The answers will be here
• Simulation lab 4: cardiac GJs; main_vlab4_cardiac_GJ.py. The answers will be here
• Simulation lab 5: building a worm; main_vlab5_worm.py. The answers will be here
• Turn in your lab reports on the web at the link given above in the real-labs section.

Backgrounders

• Background: electricity and circuit analysis from Khan Academy and elsewhere, and a little quiz on it.
• Background: Introduction to biology slides 4a and videos (14:09 total): intro(1-5, 5:28), the machine in a cell(5-7, 8:41)
• more optional biology videos (45:23 total) proteins(8-11, 8:03), dogma 1(12-13, 6:53), and 2(14-16, 9:31), if-then(17-20, 9:14), wrapup(21-23, 11:42)
• The syllabus lists several excellent books and articles for background reading.
• Audio file on the history of diffusion

Python and Thonny

If you're interested, here are some background slides to help you learn Python.
• variables
• loops
• arrays
• if-then
• functions
• 2D arrays
• objects
And here are some Thonny videos
• Installing packages (like numpy)
• running a program with command-line parameters
• Using "run to cursor"