Monday, July 27

8:00 - 9:00 : Keynote Address (Room 124)

Opening Remarks
  Douglas Densmore, Marc Riedel, and Soha Hassoun

Keynote Address
  Drew Endy


9:00 - 10:30 : Session 1 - Models and Algorithms (Chair: Jaijeet
Roychowdhury, Room 124)

Synthesizing Sequential Register-Based Computation with Biochemistry
  Adam Shea, Brian Fett, Marc Riedel, and Keshab Parhi

DOMINANT-EDGE PATHWAY: A Weighted Graph Algorithm for Identifying
Dominant Metabolic Pathways
  Ehasn Ullah, Kyongbum Lee, and Soha Hassoun

Simplified Biochemical Models using Factor Graphs
  Chris Winstead and Chris Myers

Computer-Aided Synthetic Biology: How Multiscale Models can Rationalize
the Design of Synthetic Gene Networks
  Vassilis Sotiropoulos, Jonathan Tomshine, Katherine Volzing,
  Poonam Srivastava, and Yiannis Kaznessis


10:50 - 11:30 : Session 2: Experimental Biology (Chair: Ron Weiss,
Room 124)

Automated Design of Synthetic Ribosome Binding Sites to Control
Protein Production
  Howard Salis, Ethan Mirsky, and Christopher Voigt

Programmed Control of Cellular Function: An in-cell Disease Prevention
Device
  Sangram Bagh, Mahuya Mandal, and David McMillen


11:30 - 12:00 : Morning Poster Session (Rm 125)

An Adaptive Data Structure for Biological System Design
  Douglas Densmore, Bing Xia, Josh Kittleson, Timothy Ham, and J.
  Christopher Anderson

Applying Circuit Topological Analysis Techniques to Networks in
Systems Biology
  Sherief Reda

A Rigorous Approach to the Design of Oligonucleotides for PCR-based
Gene Synthesis
  P.J.  Steiner

Bridging Synthetic Biology Models and Experiments using PoBoL
  Michal Galdzicki, Deepak Chandran, Herbert Sauro, Daniel Cook,
  and John Gennari

Contamination Aware Droplet Routing for Digital Microfluidic Biochips
  Tsung-Wei Huang and Tsung-Yi Ho

Designing Single-Duplex DNA Nanostructures by Abstraction
  Shogo Hamada and Satoshi Murata

From Electronic to Biological Design Automation: Building the Bridge
  Giuseppe Nicosia


12:00 - 1:30 : Lunch


1:30 - 2:15 : Keynote Address (Room 124)

Keynote Address
  Ron Weiss


2:15 - 3:40 : Session 3 - Tools and Parts (Chair: Herbert Sauro,
Room 124)

Design Tools for Synthetic Virology
  Dimitris Papamichail and Steven Skiena

A Framework for Modeling Modular DNA Parts: Towards the Predictable
Design of Synthetic Systems
  Ty Thomson

Synthetic Biology: A New Application Area for Design Automation
Research
  Chris Myers, Nathan Barker, Kevin Jones, Hiroyuki Kuwahara, Curtis
  Madsen, Nam-Phuong Nguyen, and Chris Winstead

GenoCAD
  Matthew William Lux, Yizhi Cai, and Jean Peccoud

Bridging Synthetic Biology Design and Experiments using PoBoL
  Deepak Chandran, Michal Galdzicki, and Alec Nielsen


3:50 - 4:30 : Session 4 - Languages and Standardization (Chair:
Yiannis Kaznessis, Room 124)

Towards a High-Level Programming Language for Standardizing and
Automating Biology Protocols
  Vaishnavi Ananthanarayanan and William Thies

BioBrick Open Language: A Keystone for Efficient Development and
Communication of Standard Biological Parts
  Ceasar Rodriguez, Doug Densmore, and Drew Endy


4:30 - 5:00 : Afternoon Poster Session (Rm 125)

Genetic Edge Detection
  Jeff Tabor

JBEI Registry: Towards a Distributed Web of Registries
  Timothy Ham, Zinovii Dmytriv, Paul Adams, and Jay Keasling

Overcoming Abstraction Barriers in Synthetic Biology Systems
  Austin Che

PoBoL in the Lab: Structured Organization of Biological Samples for
Laboratory Management and Automation
  Alec Nielsen, Deepak Chandran, Michal Galdzicki, Sean Sleight,
  Herbert Sauro, Daniel Cook, and John Gennari

TinkerCell: a CAD application for Synthetic Biology
  Deepak Chandran, Frank Bergmann, and Herbert M.  Sauro

Toward Automatic Design of DNA Logic Gates and Devices
  Ibuki Kawamata, Fumiaki Tanaka, and Masami Hagiya

Workflow Design for Synthetic Biology Using Clotho and Kepler
  Douglas Densmore, Thien Nguyen, and J.  Christopher Anderson


5:00 - 5:50 : Panel Session (Moderator: Douglas Densmore, Rm 124)

Panel Discussion
  Lou Scheffer (HHMI and Cadence), Kevin Clancy (Invitrogen), Claes
  Gustafsson (DNA 2.0), and Ron Weiss (MIT)