Harvard:Biophysics 242r/2011/Course Development Log

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(Thursday, 2010 December 9)
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**Tuesday, January 18, 100 pm to 230 pm: William Shih
**Tuesday, January 18, 100 pm to 230 pm: William Shih
**Wednesday, January 19, 100 pm to 230 pm: Adam Marblestone
**Wednesday, January 19, 100 pm to 230 pm: Adam Marblestone
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*Ask Vatsan to give a rehearsal computer demo on Thursday, February 17 from 100 pm to 230 pm
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*Request required and optional reading lists to be emailed to us one week in advance of lecture.
*Request required and optional reading lists to be emailed to us one week in advance of lecture.
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=Wednesday, 2010 December 8=
=Wednesday, 2010 December 8=

Revision as of 15:43, 9 December 2010

Contents

Thursday, 2010 December 9

Course Development Deadlines

  • Midterm-project spec. sheets due by Friday, January 7
  • Have practice sessions for the three software demos
    • Monday, January 17, 100 pm to 230 pm: John Sadowski
    • Tuesday, January 18, 100 pm to 230 pm: William Shih
    • Wednesday, January 19, 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.


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
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