2011 MPP Workshop Retreat

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Friday Harbor in the San Juan Islands, Washington State.

Welcome to the web page for the 2011 Molecular Programming Project Workshop, to be held on June 16-18, 2011 at Friday Harbor Laboratories in Washington State. The workshop, held yearly, brings together researchers (a) studying the principles of programming with chemistry and biochemistry; and (b) building novel molecular systems that implement useful computations. The workshop is sponsored by the National Science Foundation, through the Molecular Programming Project, an NSF funded Expeditions grant. The first two workshops were in Oxnard, CA in 2009 and 2010 and hosted by Caltech. This year it is UW's turn to host, so we chose the coolest place we could think of around here: Friday Harbor.

Friday Harbor is a beautiful location on an island in the Puget Sound. From the SeaTac airport it is a drive and then a ferry ride. The adventurous can take a sea plane from SeaTac instead (but if there is fog, you can be delayed). The Friday Harbor campus, which is run by the University of Washington, is perhaps a bit spartan. There are cottages that would each likely be shared by several attendees. The stunning beauty makes up for the monastic accommodations, however. Scientists have been coming to Friday Harbor for decades and have done groundbreaking work in the labs. Osamu Shimomura discovered GFP while working there over many summers. Weather can be a bit unpredictable: come prepared for rain or sun, warm or cool.

The organizers of the workshop are Eric Klavins and Sarah McDonald. If you have any questions or concerns, let us know at molecularprogramming2011@gmail.com. See you in June!

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Thursday, June 16

All Day People are arriving at SEATAC around noon. Travel to FHL takes a while, so plan ahead! Make sure you check out the Ferry Schedule.

4:00 pm Arrival at Friday Harbor Laboratories Check-in at the Commons
6:00 pm Dinner Dining Hall

7:30 pm Introductory Remarks
Eric Klavins, University of Washington
8:00 pm Nano-scale dynamic LEGOs: digital logic computation and neural network computation with DNA strand displacement cascades.
Lulu Qian, California Institute of Technology
8:30 pm Optimizing Nucleic Acid Hybridization Specificity
David Zhang, Harvard University

Friday, June 17

8:00 am Breakfast Dining Hall

9:00 am Stacking bonds: programming molecular recognition using the geometry of DNA nanostructures
Paul Rothemund, California Institute of Technology
9:30 am Keynote: Solving Hard Puzzle and Design Problems with Game-based Symbiosis of Humans and Computers
Zoran Popovic, University of Washington

10:30 am Break Commons

11:00 am Abstractions for DNA circuit design
Andrew Phillips, Microsoft Research
11:30 am Self-regulating paper network seeks adventure with synthetic biology
Barry Lutz, University of Washington
12:00 pm A cell-free expression toolbox: application to synthetic gene circuits and artificial cell
Vincent Noireaux, University of Minnesota

12:30 pm Lunch Dining Hall

2:00 pm Keynote: Controlled transport and reactions using DNA
Andrew Turberfield, University of Oxford
3:00 pm Visualizing Stochastic Simulations of Nucleic Acid Folding
Joseph Schaeffer, California Institute of Technology

3:30 pm Break Commons

4:00 pm Programmable in situ amplification for multiplexed imaging of mRNA expression
Niles Pierce, California Institute of Technology
4:30 pm Elucidation and Control of Hybridization Chain Reactions
Victor Beck, California Institute of Technology
5:00 pm Logical Verification of DNA-Based Chemical Reaction Network Implementations
Seung Woo Shin, California Institute of Technology

6:30 pm Dinner Dining Hall

8:30 pm Poster Session Dining Hall

Saturday, June 18

8:00 am Breakfast Dining Hall

9:00 am gro: A specification language for multi-celled behaviors
Eric Klavins, University of Washington
9:30 am A Mechanism for Chemical Sequence Replication Built from Designed, Modular Components
Rebecca Schulman, University of California Berkeley
10:00 am A logic-gated nanorobot for targeted transport of molecular payloads
Shawn Douglas, Harvard University

10:30 am Break Commons

11:00 am The Kinetics of Toehold-Mediated Four-Way Branch Migration
Nadine Dabby, California Institute of Technology
11:30 am On the Statistical Thermodynamics of Reversible Communicating Processes
Vincent Danos, University of Edinburgh
12:00 pm Programming Nucleic Acids Self-Assembly
Peng Yin, Harvard University
12:30 pm Concluding Remarks
MPP Leadership

1:00 pm Lunch Dining Hall

2:30 pm Hiking, small groups, organized Friday and Saturday based on interest.
Note, if you stick around Saturday and/or Sunday, you will need to find a place to stay.

Driving Directions


There is parking at various places on campus, but the best place to park is behind the Commons. It's always a good idea to carpool, but there is a lot of parking available behind the Commons. Friday Harbor Laboratories does not issue parking permits - all spaces are first come; first served.


  • You will be staying on the Friday Harbor campus. A reservation will be made for you before your arrival.
  • Friday Harbor Laboratories Contact Information:
    • Email: fhladmin@u.washington.edu
    • Phone: 206-543-1484
    • Address: Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250 USA, Map
  • When you arrive, identify yourself as an MPP 2011 Workshop attendee and you will be given your room assignment. You will be sharing a room with another attendee. Meals will be provided in the Friday Harbor Laboratories Dining Hall throughout the workshop.

Friday Harbor Laboratories Handouts

Alternative Hotels