5th International Workshop

on Bio-Design Automation


The schedule of abstracts to be presented as talks and posters. Detailed instructions for presenters are below.


Clore Lecture Hall, ground floor of the Huxley Building, Imperial College, London, UK.
The poster session will be in Huxley 341/342, with poster set up open from 8:30am Friday morning.

All tea and lunch breaks will take place in Huxley 341.
Directions: Map


(Updated on July 13, 2013)

Friday, July 12th
8:00 - 9:00Registration
9:00 - 9:15Opening Remarks
9:15 - 10:15Domitilla Del Vecchio. From Context-dependence to Modularity in Biological Circuits
10:15 - 10:30Coffee Break
Talk Session 1: Engineering, Parts, and Standardization
10:30 - 10:55 (17) Michal Galdzicki, Ernst Oberortner, Mathew Pocock, Jacqueline Quinn, Mandy Wilson, Evan Appleton, Bryan Bartley, Jacob Beal, Swapnil Bhatia, Robert Cox, Raik Grunberg, Goskel Misirli, Hector Plahar, Nicholas Roehner, Larisa Soldotova, Guy-Bart Stan, Doug Densmore, Chris Myers, Herbert Sauro and Anil Wipat.
Recent Advances in the Synthetic Biology Open Language
10:55 - 11:20 (30) Jacqueline Quinn, Jacob Beal, Swapnil Bhatia, Patrick Cai, Joanna Chen, Kevin Clancy, Robert Sidney Cox, Michal Galdzicki, Nathan Hillson, Akshay Maheshwari, Chris Myers, Umesh P, Matthew Pocock, Cesar Rodriguez, Herbert Sauro, Larisa Soldatova, Guy-Bart Stan, Mandy Wilson, Drew Endy.
Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology
11:20 - 11:45 (28) Michal Galdzicki, Bryan A. Bartley, Sean C. Sleight, Evren Sirin and John Gennari.
Version Control for Synthetic Biology
11:45 - 12:10 (33) David Kong, Jonathan Babb and Todd Thorsen, Scott Wick, Jeremy Gam, Ron Weiss and Peter Carr.
Microfluidic Genetic Circuit Assembly
12:10 - 13:30Lunch
13:30 - 14:30Alfonso Jaramillo. Computational design of RNA circuits for signal processing in bacteria
Talk Session 2: Characterization and System Identification
14:30 - 14:55 (23) Claudio Angione, Jole Costanza, Giovanni Carapezza, Pietro Lio' and Giuseppe Nicosia.
Identifiability Analysis to Characterize Mitochondrial Diseases
14:55 - 15:20 (24) Boyan Yordanov, Neil Dalchau, Paul Grant, Jim Haseloff, Stephen Emmott and Andrew Phillips.
Automated Ratiometric Characterization using GEC
15:20 - 15:35 Coffee Break
15:35 - 16:35Richard Kitney. Foundational Resources in Synthetic Biology.
Industry Panel
16:35 - 17:35 Panel topic: The Entrepreneurial Spirit in BioDesign Automation: from startups to spinouts to internal innovation.
Jacob Beal - BBN
Jaqueline Quinn - Autodesk
Wolf-Ekkehard Matzke - MINRES Technologies
Debra Conway - Cybio
Malcom Wilson - Cronus Technologies on behalf of Hudson Robotics
Jim Hollenhorst - Agilent
18:30 - 20:00Dinner
Saturday, July 13th
8:30 - 9:00Registration
9:00 - 10:00Jeff Hasty. Engineered Gene Circuits: From Oscillators to Synchronized Clocks and Biopixels
10:00 - 10:15 Coffee Break
Talk Session 3: CAD Tools for Synthetic Biology
10:15 - 10:40 (19) Evan Appleton, Jenhan Tao and Douglas Densmore.
Interactive Experimentally Driven Algorithms for Optimized DNA Assembly
10:40 - 11:05 (16) Linh Huynh and Ilias Tagkopoulos.
Optimizing module matching for synthetic gene circuit design automation
11:05 - 11:30 (21) Nicholas Roehner and Chris Myers.
Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models
11:30 - 11:55 (13) Jonathan Blakes, Ofir Raz, Natalio Krasnogor and Ehud Shapiro.
A New Algorithm for Combinatorial DNA Library Assembly
11:55 - 13:30 Lunch and Poster session
Talk Session 4: Biological Circuit Design and Assembly
13:30 - 13:55 (26) Noah Davidsohn, Jacob Beal, Aaron Adler, Fusun Yaman, Yinqing Li, Zhen Xie and Ron Weiss.
Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition
13:55 - 14:20 (12) Maximilian Weitz, Jongmin Kim, Korbinian Kapsner, Erik Winfree, Elisa Franco and Friedrich Simmel.
Dynamical diversity of a programmable molecular oscillator in droplet microreactors
14:20 - 14:45 (27) Michael Guinn, Yi Li and Leonidas Bleris.
A 2-input Decoder Circuit in Human Cells
14:45 - 15:00 Coffee Break
15:00 - 16:00Howard Salis. Clone Less, Know More: Efficient Optimization of Circuits and Pathways with Next Generation Biophysical Modeling
Talk Session 5: Applications
16:00 - 16:25 (14) Wolf-Ekkehard Matzke, Michael Stumpf and Thorsten Mascher.
Towards Industrial Strength BDA - A Short Essay
16:25 - 16:50 (4) Pablo Carbonell, Pierre Parutto and Jean-Loup Faulon.
RetroPath: Automated Pipeline for Embedded Metabolic Circuits.
16:50 - 17:15 (32) Jole Costanza, Claudio Angione, Giovanni Carapezza, Pietro Lio' and Giuseppe Nicosia.
Multi-objective Optimization of Escherichia coli for Direct Production of 1,4-butanediol
Closing remarks
17:15 - 17:30 


(9) Joanna Chen, Rafael Rosengarten, Douglas Densmore, Timothy Ham, Jay Keasling and Nathan Hillson.
 j5 and DeviceEditor: DNA assembly design automation
(25) Jole Costanza, Claudio Angione, Giovanni Carapezza, Pietro Lio' and Giuseppe Nicosia.
 Pareto-based Gene and Pathway Sieve for Biofuel Production
(20) Vishwesh Kulkarni, Evgeny Kharisov, Naira Hovakimyan, Marc Riedel and Jongmin Kim.
 Load Capacity Improvements in DSD Systems Using Partially Open Feedback Control
(31) Ruei-Yang Huang, De-An Huang, Hui-Ju Katherine Chiang, Jie-Hong Roland Jiang and Francois Fages.
  Species Minimization in Computation with Biochemical Reactions
(22) Eric Kelsic, Hattie Chung, Harris Wang and Roy Kishony.
  Position-specific codon bias within an essential gene of E. coli
(1) Tuval Yehezkel.
  Development and application of automated DNA editing technology
(6) Hector Plahar, Timothy Ham, Joanna Chen and Nathan Hillson.
  JBEI-ICE: An Open Source Biological Part Registry
(15) Kevin Clancy, Kok Hien Gan, Brandon Ang, Kin Chong Sam, Yong Ming Chen, Reina Angelica, Bee Im Teo, Wolfgang Strenzl, Michael Muth, Brynne Stanton, Virgil Rhodius, Ying-Ja Chen, David Raab, Lian Seng Loh, Chris Voigt, Douglas Densmore and Todd Peterson.
  Vector NTI® Express Designer - a new bioinformatics platform for synthetic biology design
(34) Arturo Casini, Tom Ellis and Geoff Baldwin. Computationally designed DNA linkers to enhance a novel automated DNA assembly standard
(2) Gregory Linshiz, Nina Stawski, Sean Poust, Changhao Bi, Jay Keasling and Nathan Hillson.
  PR-PR: Cross-platform standard language for automation of Synthetic Biology research
(7) Sayane Shome, Pablo Cárdenas, Pedro Fernandes, Gerd Moe-Behrens and Alioune Ngom.
  SynBio App Selector: An Application Selection Engine for Synthetic Biology
(8) Pablo Cárdenas, Sayane Shome, Pedro Fernandes, Alioune Ngom and Gerd Moe-Behrens.
  SynBrick: A Crowdsourcing Game for Synthetic Biology
(29) Rishi Ganguly, Peng Liu, Swapnil Bhatia, Christopher Voigt and Douglas Densmore.
  Cello: A software workflow for modular design and compilation of genetic circuits
(18) Aaron Adler, Fusun Yaman and Jacob Beal.
 Online Tools for Characterization, Design, and Debugging.
(5) Eduardo Abeluik, Yuri Bendaña, Rodrigo Pavez, Nathan Hillson and Michael Fero.
  A NoSQL approach to a synthetic biology database.
(10) Vishwesh Kulkarni, Boyan Yordanov, Andrew Phillips and Jongmin Kim.
  Biomolecular Implementation of Linear Dynamical Systems.
(3) Ehud Magal.
  Robot QC methods.

Instructions for Oral and Poster Presentations

Oral presentations

Oral presentations will each be 20 minutes + 5 minutes of Q&A. We will be providing a projector and a laptop computer for the presentations. Please bring your slides on a USB stick at least 10 minutes before your session begins so that we can load them on our laptop computer to minimize delay between presentations.

Poster presentations

The maximum poster size that can be displayed is: