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 and MIT Biological Engineering
 * Dane Wittrup
 * Michael Strano
 * Dan Anderson
 * Paula Hammond

=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
 * Tal: Feng Zhang?, George Church?: DNA-binding proteins (transcription activator like)
 * 1) 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
 * Tal: Feng Zhang?, George Church?: DNA-binding proteins (transcription activator like)
 * 1) 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
 * 1) 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