Harvard:Biophysics 242r/2011/Course Development Log: Difference between revisions
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=Thursday, 2010 November 25= | |||
*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 | |||
* | |||
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=Thursday, 2010 November 18= | =Thursday, 2010 November 18= | ||
*Course time and place set: CLSB521 Mondays and Wednesdays 100pm to 230pm, then optional project session from 230pm to 330pm | *Course time and place set: CLSB521 Mondays and Wednesdays 100pm to 230pm, then optional project session from 230pm to 330pm |
Revision as of 13:05, 24 November 2010
Thursday, 2010 November 25
- 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
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
- Dave Baker group member/alum: ask George for suggestions
Protein engineering candidate lectureres
- Tal: Feng Zhang?, George Church?: DNA-binding proteins (transcription activator like)
- 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
- Hairpin devices
- Molecular motors
- Bipedal walker
- Thermal ratchet
- Electrophoretic ratchet
- Rotary motors
- 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
- Thursday, January 27: Structural DNA visualization software -- NanoEngineer -- John Sadowski
- Thursday, February 3: Origami design software --- CadNano -- Shawn Douglas
- Thursday, February 10: Thermodynamic analysis and sequenced design software -- Nupack (and maybe other sequence design software from Winfree group) --- Adam Marblestone
- 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
- DNA origami
- Hairpin devices
- Molecular motors
- Bipedal walker
- Thermal ratchet
- Electrophoretic ratchet
- Rotary motors
- DNA computers
- Integration, precursor, recruiting for BioMOD competition
- Schedule for 2011
- Week 1: Jan. 25 (general overview + listing of midterm projects + DNA nano primitives), 27 (3D visualization demo session)
- Week 2: Jan. 31 (William: overview of origami and higher-order structure), Feb. 3 (caDNAno demo session)
- Week 3: Feb. 8 (Dave Zhang: DNA biophysics), Feb. 10 (NuPack demo session)
- Week 4: Feb. 15 (Peng: hairpins and circuits lecture), Feb. 17 (deterministic and stochastic reaction network simulations)
- Week 5: Feb. 22, Feb. 24
- Week 6: Mar. 1, Mar. 3 (midterm presentations)
- Week 7: Mar. 8 (Biophysical Society Meeting), Mar. 10 (midterm presentations)
- Spring Break
- Week 8: Mar. 22 (survey of natural molecular machines), Mar. 29
- Week 9: Apr. 5, Apr. 7
- Week 10: Apr. 12, Apr. 14
- Week 11: Apr. 19, Apr. 21
- Week 12: Apr. 26, Apr. 28 (first day of reading period)
- Week 13: May 3, May 5 (reading period, final presentations)
- 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)
- 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
- caDNAno
- NuPack
- Deterministic and stochastic simulations of reaction networks; how can we integrate this with projects?
- 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)
- Lectures
- Guest lectures
- Paper discussions
- Project presentations
- Project brainstorming, planning
- Computer exercises/demos
- Laboratory demos
- Centered around group projects
- Experimental realization for some groups near the end
- 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
- Get people to be excited about projects
- 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