BE 107, Spring 2015

BE 107: Exploring Biological Principles Through Bio-Inspired Design
Instructors Michael Dickinson (BBE), flyman@caltech.edu Richard Murray (CDS/BE), murray@cds.caltech.edu Chris Kempes (CMS/GPS), ckempes@gmail.com Floris van Breugel (BE), floris@caltech.edu Lectures: TuTh, 10:30-12, location TBD Office hours: by appointment	Teaching Assistants David Flicker (ME) Melissa Tanner (ME) Lab session: Wed, 1-4 or 7-10 pm (determine later), location TBD Open lab hours: Mon, 1-4 pm, location TBD

Course Description

Students will formulate and implement an engineering project desired to explore a biological principle or property that is exhibited in nature. Students will work in small teams in which they build a hardware platform that is motivated by a biological example in which a given approach or architecture is used to implement a given behavior. Alternatively, the team will construct new experimental instruments in order to test for the presence of an engineering principle in a biological system. Example topics include bio-inspired control of motion (from bacteria to insects), processing of sensory information (molecules to neurons), and robustness/fault-tolerance. Each project will involve proposing a specific mechanism to be explored, designing an engineering system that can be used to demonstrate and evaluate the mechanism, and building a computer-controlled, electro-mechanical system in the lab that implements or characterizes the proposed mechanism, behavior or architecture.

Lecture Schedule

Date

Topic

Reading

Homework

Week 1

• Tue lecture (31 Mar): Motivation (bio and engineering; 60m) + class logistics (30m) - Michael and Richard
  • Michael: 15 min class motivation and then 30 min on cool biology
  • Richard: 30 min on cool engineering, then 15 min on class logistics
• Wed lab session #1, 7-10 pm: Introductory Tracking Experiment
• Thu lecture (2 Apr): Programming concepts - Richard
  • Wiki's, subversion, plotting data using python (will use later)
• HW/lab description out on Tue, due following Tue
• Lab hours on Mon, 1-4 pm

Week 2 (RMM out of town on Wed-Fri)

• Tue lecture (7 Apr): Mechanical design and fabrication - Floris (or Joel B?)
• Wed lab session #2, 7-10 pm: CAD, Fabrication, Arena
• Thu lecture (9 Apr): Biomechanics - Michael (or Chris)
• HW/lab description out on Tue, due following Tue
• Lab hours on Mon, 1-4 pm

Week 3 (RMM out of town on Mon-Thu)

• Tue lecture (14 Apr): Electrical design, sensing and actuation - David (or Joel B?)
• Wed lab session, 7-10 pm: Sensors/Actuators (Braitenberg bug)
• Thu lecture (16 Apr): Animal sensors/actuators - Michael
• HW/lab description out on Tue, due following Tue
• Lab hours on Mon, 1-4 pm

Week 4 (MHD out of town all week, RMM might be out of town on Thu)

• Tue lecture (21 Apr): Control systems - Richard
• Wed lab session, 7-10 pm: Controls and Arduino
• Thu lecture (23 Apr): Feedback principles in biology - Floris, with input from Michael
• HW/lab description out on Tue, due following Tue
• Lab hours on Mon, 1-4 pm

Week 5

• Tue lecture (28 Apr): Image processing - Pietro (with backup)? (or Floris)
• Wed lab session, 7-10 pm: Vision/ROS
• Thu lecture (30 Apr): Animal vision systems - Michael
• HW/lab description out on Tue, due following Tue
• Lab hours on Mon, 1-4 pm

Week 6

• Tue lecture (5 May): estimation - Richard
  • Include things that might mirror what nature does (eg, DGC)
  • Kalman filtering; use in avoiding higher order derivatives
• Wed lab session, 7-10 pm: Tracking
• Thu lecture (7 May): Experiment design - Michael (or Chris)

• HW/lab description out on Tue, due following Tue
• Lab hours on Mon, 1-4 pm

Week 7

• Tue lecture (12 May): Robotics/autonomy - Richard
• Lab hours on Wed, 7-10 pm (projects)
• Thu lecture (14 May): Animal behavior - Michael
• Lab hours on Mon, 1-4 pm (projects)

Week 8

• Tue lecture (19 May): Evolution - Chris
• Lab hours on Wed, 7-10 pm (projects)
• Thu lecture (21 May): Systems design - Richard + Floris?
  • This could be swapped with animal navigation lecture
• Lab hours on Mon, 1-4 pm (projects)

Week 9

• Tue lecture (26 May): TBD
  • Hold for topics to be decided later. Could do lab presentations?
  • Could also be a talk on bioinspired control algorithms - Floris
• Lab hours on Wed, 7-10 pm (projects)
• Thu lecture (28 May): TBD
• Lab hours on Mon, 1-4 pm (projects)

Grading

The final grade will be based on homework and a final exam:

• Lab reports (40%) - There will be 6 one-week labs, with a lab writeup (wiki page, with data) due no later than Tuesday at 10:30 am (start of class). Late writeups will not be accepted without prior permission from the instructors.
• Final project (40%) - The last three weeks of the course will be used to implement a project the demonstrates the principles and tools that are covered in the course. Students will work in groups of 2-3, with a single grade assigned to the group.
• Class/lab participation (20%) - Students will be assigned by the lecturers and TAs based on their participation in class discussions and lab sessions.

Collaboration Policy

Collaboration on lab work is encouraged. All lab writeups that are handed should reflect your understanding of the lab work and results at the time of writing.

Final projects collaborative.