Program
The schedule of abstracts to be presented as talks and posters. Detailed instructions for presenters are below.
Location
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
Agenda
(Updated on July 13, 2013)
| Friday, July 12th | |
|---|---|
| 8:00 - 9:00 | Registration |
| 9:00 - 9:15 | Opening Remarks |
| Keynote | |
| 9:15 - 10:15 | Domitilla Del Vecchio. From Context-dependence to Modularity in Biological Circuits |
| 10:15 - 10:30 | Coffee 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 - 13:30 | Lunch |
| Keynote | |
| 13:30 - 14:30 | Alfonso 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 |
| Keynote | |
| 15:35 - 16:35 | Richard 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 - 20:00 | Dinner |
| Saturday, July 13th | |
| 8:30 - 9:00 | Registration |
| Keynote | |
| 9:00 - 10:00 | Jeff 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 |
| Keynote | |
| 15:00 - 16:00 | Howard 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 | |
Posters
| (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:
- A0: 1189 x 841 mm or
- 46.8 x 33.1 in
- Orientation: Portrait