Harvard:Biophysics 242r/2011/Course Development Log

Wed, 2011 June 29

Peng:

preparation for fall teaching.

Wednesday, 2011 January 19

caDNAno tutorial notes

• Demo of 6hb only
• Spend five minutes reviewing all caDNAno buttons
• Spend five minutes summing up design guidelines
• Spend ten minutes reviewing online examples

Midterm project spec sheets

• We want to have these ready by Wednesday, 2011 February 2

Tom Schaus demo rehearsal

• Schedule for Thursday, 2011 February 10 at 215 pm

Thursday, 2010 December 9

Course Development Deadlines

• Midterm-project spec. sheets due by Friday, January 7
• Midterm projects: writeup by Peng

1. Hairpin devices: analyze thermodynamic behavior using NuPack
2. DNA circuit

• Midterm projects: writeup by William

1. Bipedal walker
2. Thermal ratchet
3. Electrophoretic ratchet

• Midterm projects: writeup by Vatsan

1. RosettaDesign/FoldIt

• Have practice sessions for the three software demos
  • Tuesday, January 18, 100 pm to 230 pm: John Sadowski
  • Wednesday, January 19, 100 pm to 230 pm: William Shih
  • Thursday, January 20, 100 pm to 230 pm: Adam Marblestone
• Ask Vatsan to give a rehearsal computer demo on Thursday, February 17 from 100 pm to 230 pm

Other details

• Ask speakers to email to us a pdf version of slides 24 hours before lecture so that students can look them over.
• Request required and optional reading lists to be emailed to us one week in advance of lecture.
• Form teams on Monday, February 7 after Dave Zhang's lecture
• No after class project meetings until Monday, February 7
• Adam put a link to this openwetware page on the Harvard course site.

Wednesday, 2010 December 8

• William would like to give the directed molecular evolution lecture, thus we don't need to invite an outside speaker for this topic
• Potential lecturers from MIT Chemical Engineering [1] and MIT Biological Engineering [2]
  • Dane Wittrup [3]
  • Michael Strano [4]
  • Dan Anderson [5]
  • Paula Hammond [6]

Thursday, 2010 December 2

To do list

• (WS) Contact Jim Collins on Monday, 2010 December 6; he had indicated verbally that he might be interested and available
• (WS) Email Neel Joshi and Feng Zhang to determine scheduling
• (WS) Email course lecture invitations to Collin Stultz, Milan Stojanovic, Mahadevan, and David Liu/Xi Chen
• Come up with deadlines for midterm project spec sheets (including exercises forcing students to use software packages)
• Come up with practice sessions for some of the lectures

Changes

• NuPack sequence design session: manual versus automated sequence selection
• January 14 deadline: Kinetics software demo practice session: either it happens on this day, or it doesn't go in the course

Saturday, 2010 November 28

Second-half semi-confirmed lecturers (we have six, we need twelve total)

• Shawn Douglas: caDNAno v2 (April 6)
• Adam Marblestone: Methods for nanodevice characterization (March 21)
• Joanna Aizenberg (one of the following: March 28, March 30, April 25, April 27)
• George Church: minimal self-replicating systems and hybrid electronic-biochemical systems (March 23)
• Neel Joshi:
• Feng Zhang: zinc finger versus Tal: DNA-binding protein design

On the invite list (we need at least two more)

• Jim Collins
• Collin Stultz
• Milan Stojanovic
• Mahadevan
• David Liu or Xi Chen: Directed molecular evolution

Thursday, 2010 November 25

To do list

• Course synopsis writeup, distribution to attract students (e.g. SysBio graduate students)
• Continue inviting more speakers for the second half of the course
• Resolve kinetics simulation lecture situation
• Work on specification sheets for midterm projects

---

• Kinetics simulation demo
  • Option 1: Dave Zhang learns new software for Yin lab and for class lecture (dual purpose)
  • Option 2: Fly in someone else (e.g. Joseph Schaeffer)
  • Option 3: Abandon plans to have this session, move Adam's characterization session into this area
• We'll include a Rosetta Protein Design project (or subproject) for one of the groups
• Semi-confirmed lecturers for second half of course
  • Shawn Douglas
  • George Church
  • Joanna Aizenberg
  • Neel Joshi
  • Adam Marblestone
• Who else should we be inviting?

• Midterm projects: writeup by Peng

1. Hairpin devices: analyze thermodynamic behavior using NuPack
2. DNA circuit

• Midterm projects: writeup by William

1. Bipedal walker
2. Thermal ratchet
3. Electrophoretic ratchet

• Midterm projects: writeup by Vatsan

1. RosettaDesign/FoldIt

• More projects

1. Rotary motors
2. DNA computers

Thursday, 2010 November 18

• Course time and place set: CLSB521 Mondays and Wednesdays 100pm to 230pm, then optional project session from 230pm to 330pm
• We need to fill 11 lecture slots after the midterm projects, and one more lecture slot before the midterm projects

• Wyss Institute candidate lecturers besides the core teaching team
  • George Church: technological trends associated with self-assembled nanodevices
  • Feng Zhang?: tal proteins
  • Neel Joshi: peptides and other polymers
  • Joanna Aizenberg: photonic structures, hair microstructures
  • Mahadevan: microtubule design or other topics
  • Radhika Nagpal and/or Justin Werfel: distributed systems and molecular programming
  • Jim Collins: riboregulators

• Other candidate lecturers
  • David Liu: Directed evolution and other applications
  • Jack Szostak: directed evolution, artificial cells
  • Milan Stojanovic
  • Irene Chen: fatty acid vesicles
  • Xi Chen: Directed evolution, unnatural nucleic acid analogues
  • Howard Berg: flagella
  • Dane Wittrup: protein design

• Protein Design candidate lecturers
  • Dave Baker group member/alum: ask George for suggestions
    • Srivatsan Raman
  • Brian Kuhlman
  • Gautam Dantas
  • Bruce Tidor

Protein engineering candidate lectureres

1. Tal: Feng Zhang?, George Church?: DNA-binding proteins (transcription activator like)
2. Neel: peptide or peptide-like structures

• Joanna Aizenberg: inorganic structure design
• Mahadevan on microtubule design
• Michael Brenner on self-assembly
• Drug delivery, nano
• Top-down nanofabrication
• Radhika: distributed systems

• Midterm projects

1. Hairpin devices
2. Molecular motors
3. Bipedal walker
4. Thermal ratchet
5. Electrophoretic ratchet
6. Rotary motors
7. DNA computers

• Suggested final projects (could be more ambitious than midterm projects, although not necessarily)

Thursday, 2010 October 28

• Scheduling constraints
  • Systems Biology seminar series one Thursday per month from 4 pm to 5 pm
  • Systems Biology faculty meetings Thursdays from 1230 pm to 200 pm
  • BCMP Chalk Talks Thursdays from 1230 pm to 130 pm
  • BCMP Faculty Meetings one Tuesday per month from 2 pm to 330 pm
  • Monday, Wednesday has less constraints
  • According to Michele, 1 to 3 pm is open for Mondays and Wednesdays; we have asked Jermaine about scheduling for CLSB521 for these days
• First option
  • Mondays and Wednesdays sometime between 1 pm and 3 pm in CLSB521
• Second option
  • Tuesdays in Warren Alpert from 1000 am to 1130 am
  • Thursdays in CLSB521 from 1000 am to 1130 am

Section for working on projects

• One hour after class (i.e. Mondays and Wednesdays 230 pm to 330 pm)
  • First section meets on the first Wednesday (after caDNAno tutorial)
  • Positive inducements: food, coffee
  • Bring in Yin and Shih lab group members as well

Community building (e.g. interface with BioMOD)

• Videotape lectures and demo sessions, post some or all online

Quality control for lectures and tutorials

• Lecture pdfs and list of references must be submitted 48 hours between lecture starts
  • Some lecturers may refuse to provide pdfs
• Dry run for tutorials

Saturday, 2010 October 23

• Proposed demo sessions

1. Thursday, January 27: Structural DNA visualization software -- NanoEngineer -- John Sadowski
2. Thursday, February 3: Origami design software --- CadNano -- Shawn Douglas
3. Thursday, February 10: Thermodynamic analysis and sequenced design software -- Nupack (and maybe other sequence design software from Winfree group) --- Adam Marblestone
4. Thursday, February 17: Kinetic simulation software --- Dave Zhang

Thursday, 2010 October 21

• Make it as participatory as possible
• Joint student presentations
• Paper discussions
• Design projects

1. DNA origami
2. Hairpin devices
3. Molecular motors
4. Bipedal walker
5. Thermal ratchet
6. Electrophoretic ratchet
7. Rotary motors
8. DNA computers

• Integration, precursor, recruiting for BioMOD competition
• Schedule for 2011

1. Week 1: Jan. 25 (general overview + listing of midterm projects + DNA nano primitives), 27 (3D visualization demo session)
2. Week 2: Jan. 31 (William: overview of origami and higher-order structure), Feb. 3 (caDNAno demo session)
3. Week 3: Feb. 8 (Dave Zhang: DNA biophysics), Feb. 10 (NuPack demo session)
4. Week 4: Feb. 15 (Peng: hairpins and circuits lecture), Feb. 17 (deterministic and stochastic reaction network simulations)
5. Week 5: Feb. 22, Feb. 24
6. Week 6: Mar. 1, Mar. 3 (midterm presentations)
7. Week 7: Mar. 8 (Biophysical Society Meeting), Mar. 10 (midterm presentations)
8. Spring Break
9. Week 8: Mar. 22 (survey of natural molecular machines), Mar. 29
10. Week 9: Apr. 5, Apr. 7
11. Week 10: Apr. 12, Apr. 14
12. Week 11: Apr. 19, Apr. 21
13. Week 12: Apr. 26, Apr. 28 (first day of reading period)
14. Week 13: May 3, May 5 (reading period, final presentations)
15. Week 14: May 10, May 12 (exam period)

• Use exam period as buffer in case we need a third presentation day

• Protein engineering

1. Tal: Feng Zhang?, George Church?: DNA-binding proteins (transcription activator like)
2. Neel: peptide or peptide-like structures

• Joanna Aizenberg: inorganic structure design
• Mahadevan on microtubule design
• Michael Brenner on self-assembly
• Drug delivery, nano
• Top-down nanofabrication
• Radhika: distributed systems
• Computer demo sessions

1. caDNAno
2. NuPack
3. Deterministic and stochastic simulations of reaction networks; how can we integrate this with projects?
4. Geometric modeling tool (nanoEngineer); computer visualization

• Class size: project for 15 to 20 students (10–12 Harvard Biophysics, plus some students from other programs, undergrads)
• Do we want to have a limit on course size? perhaps 18 to 20 limit

• What size of group?
  • Two to three students per group
  • If the course size is 12, that implies 4 to 6 groups (mean of 5 groups)
  • If the course size is 20, that implies 7 to 10 groups (mean of 8 groups)
  • No more than six groups of people: upper limit on group size of two or three people
  • Group presentations for 2 to 3 class meetings

• Course activities (25 sessions total)

1. Lectures
2. Guest lectures
3. Paper discussions
4. Project presentations
5. Project brainstorming, planning
6. Computer exercises/demos
7. Laboratory demos
8. Centered around group projects
9. Experimental realization for some groups near the end
10. Ask for sequences, diagrams, simulations

• First half of course
• Group midterm project: selected from restricted list
• Group final project: open-ended

• Proposal guidelines
• Provide aims
• Background for motivation (significance, innovation)

• BioMOD teams asked to register by March 31
• List of team members, graduate teaching fellows, faculty advisors

• Goals

1. Get people to be excited about projects
2. Get people interested to participate in BioMOD

• First day: Monday, 2011 January 24
• Biophysical Society Meeting: Sat. Mar. 5 to Wed. Mar. 9
• Spring Break: Mar. 12 to Mar. 20
• Last day: Wed., 2011 April 27
• Reading period: Thur. April 28 to Thur., May 5
• Exam period: Friday, May 6 to Sat., May 14
• Grades due May 13

• Adam in charge of course wikis